NBIC Events

RSG BioCafe: "How to get a Nature cover?"

Thu, 01 Jan 1970 01:00:00 +0100

Illustrations in scientific publications tremendously help in clarifying complex biological systems. Think about nature covers, textbooks and 3D visualizations.
RogierTrompertis an artist specialized in Scientific Illustration.Tromperthas worked for several scientist, pharmaceutical companies and publishers combining his artistic skills with (3D) MRI and CT imaging techniques to make the perfect illustration. In this BioCafé there will also be a Tips ’n Tricks session by a professional publisher on how to pimp your thesis. Registration for this event is required, so please send an e-mail to: rsg-netherlands@iscbsc.org with your name, institute and whether you want come and eat dinner after the BioCafe.

BE Live IT 2009 conference

Mon, 12 Oct 2009 17:10:00 +0200

The BE Live IT conference 2009 is a unique pan-European conference in order to exchange valuable experiences and gain innovative ideas and views on how best to use the bioinformatics tools in your day-to-day R&D activities.

The two previous editions brought together from all over Europe numerous high level researchers, managers and bioinformaticians from the pharma, red, green, white biotechs, agro/agri-food, chemical and cosmetics industries. Registration: The attendance registration fee is set at Euro 350. Early birds registration will guarantee a free 3 star hotel room during the event . The Early birds registration period will end on 15 September 2009. Information: For further information (attendance, sponsorship, exhibition booths, etc.) and on-line registration do visit the conference website www.beliveit.org.

Life Sciences Momentum 2009 - Empowering the future

Tue, 20 Oct 2009 23:20:00 +0200

Life Sciences Momentum 2009 will offer insight into the latest developments in science and technology, the state of affairs within Dutch academia and industry, and the emerging opportunities for society and business. Life Sciences Momentum 2009 will focus on four key topics: discover opportunities, build on strength, encourage continuity and share responsibility. This year's Momentum promises to be the best year yet, as the event will cover the entire Life Sciences field. NGI expects a record number of guests from industry, science, government, healthcare, civil society organisations, education, finance, politics and media. Why Momentum 2009? The first and foremost purpose of the annual Momentum events is to offer a platform on which the Netherlands' Life Sciences sector has the chance to take stock of the current situation, look at best practices, and make plans to move forward. All the Netherlands' major players will be there to address these and any other topics. Through workshops, speeches, interactive sessions and the networking Plaza, you can find out just what's going on, and get advice on how to move forward in this exciting and highly promising field of science. Life Sciences Momentum 2009 is organized by the Netherlands Genomics Initiative. More information and registration via www.momentum2009.org

Schrodinger seminar: The application of Recent Advances in Biomolecular Modeling to Drug Discovery Problems

Wed, 21 Oct 2009 14:39:00 +0200

The seminar is jointly organized by Dr. Martine Prevost, Structure and Function of Membrane Biology Laboratory at the Université Libre de Bruxelles, and Schrödinger Inc. and it will take place at the Université de Bruxelles. The seminar is suitable for attendees with varying backgrounds, from those with little experience in the use of computational techniques wanting to learn more about their potential impact on drug discovery, to practicing computational chemists wanting to learn more about the use of recent advances in the Schrödinger suite and take advantage of the introductory training and direct contact with Schrödinger scientists. The seminar is divided into two sessions:

A morning session with presentation of case studies highlighting the use of key techniques such as loop refinement, protein flexibility in ligand docking via Induced Fit Docking, detection of multiple binding modes in ligand-based design, QM/MM methods and the exposure of the XP scoring function to identify key protein/ligand interactions for lead optimization.
The afternoon session will provide an opportunity for introductory demo on the use of Schrödinger software and for direct interaction with Schrödinger application scientists.

Registration
Participation is free of charge, but seats are limited. Please register by contacting: Katia Dekimeche
Senior Account Manager, Academia and Government
Schrödinger
katia.dekimeche@schrodinger.de

RSG BioCafe 'Visualize your science!'

Fri, 23 Oct 2009 17:54:00 +0200

The last two years the Regional Student Group has been organizing BioCafe's. These events are a nice opportunity to hear more from other research fields, to improve your "soft skills" like presenting your work, and to get in touch with other PhD students in the Netherlands. The topic of the next BioCafe is: Visualize your science! For the first time the RSG invited an international speaker: Nils Gehlenborg from the EBI will discuss his work on visualizing large microarray datasets. The second speaker is Michel Westenberg from Eindhoven University of Technology, and will reveal to us the visualization of biological networks. This Biocafé will be concluded with a visualization Quickfire during which each participant will have the opportunity to show his/her favorite/coolest/best image. You will have 30 seconds to explain why, what and how you made the image. Registration for this event is required, so please send an e-mail to rsg-netherlands@iscbsc.org with your name, institute and whether you want come and eat dinner after the BioCafe. If you want to show your work, you can also send in 1 ppt-slide containing the image and your name. Where: Poort van Kleef, (second floor of Café Carré), Mariaplaats 7, Utrecht

International EMBnet-RIBio Conference 2009

Mon, 26 Oct 2009 15:38:00 +0100

The main topic of the conference will be: High Throughput Technologies, the Interface of Bioinformatics and Systems Biology and Open Software for Bioinformatics and Systems Biology.

The International EMBnet-RIBio Conference 2009 will be jointly organized by the European Molecular Biology network (EMBnet) and the Red Iberoamericana de Bioinformática (RIBio). This will be the first time the EMBnet's Annual General Meeting will take place outside of Europe, bringing together bioinformaticians from all over the world, together with the Iberoamerican Annual General Meeting, and representatives of other major Bioinformatics societies in the World. The conference is open to submissions. Besides the main topic submissions will be accepted in all areas of bioinformatics (such as genomics, proteomics, transcriptomics, metagenomics, data and text-mining, ontologies, education and e-learning tools available in Bioinformatics). There is funding available for ISCB affiliated students to attend the meeting provided they submit an abstract to the conference. More information can be found in the abstract guidlines on the website mentioned below.

Workshop Basic data analysis on gene expression arrays (BAGE)

Mon, 26 Oct 2009 15:03:00 +0100

Upcoming 26-27 October the Research School Molecular Medicine organizes again the Workshop on Basic data analysis on gene expression arrays at the Erasmus MC. This 2-Day Workshop will cover the basic understanding of the workflow, required for the analysis of gene expression arrays (Illumina and Affymetrix). The second day will be mainly about advanced Ingenuity Pathway Analysis. It is primarily organized for PhD students and postdocs of the Erasmus Postgraduate School Molecular Medicine, Nihes and MGC. But other participants are also welcome but need to pay a fee. For more information and registration, please go to: www.molmed.nl.

Tutorial on Computational Systems Biology

Mon, 02 Nov 2009 15:02:00 +0100

This tutorial is organised in conjunction with Formal Methods 2009. This one-day tutorial provides an introduction to computational systems biology, starting with a crash course on molecular biology for computer scientist and continuing with discrete, continuous and stochastic modeling techniques, as well as formal methods-based approaches. A demonstration is included on Copasi (Complex Pathway Simulator), a useful tool for modeling and simulating sysbio projects. The well known heat shock response, that the lecturers and their research groups have been working on already for some years, will serve as a running example connecting the various topics. Lecturers: Ion Petre and Ralph-Johan Back, Abo Akademi University, Finland Registration deadline: October 16, 2009

Second International Workshop on Computational Models for Cell Processes

Tue, 03 Nov 2009 15:20:00 +0100

This workshop is organised in conjunction with Formal Methods 2009. Computational systems biology is an exciting new application area for applied mathematics and computer science. This workshop of the 16th International Symposium on Formal Methods fosters an excellent platform gathering researchers in formal methods and related fields that are interested in the wealth of opportunities and challenges in systems biology. Invited speakers:

Jasmin Fisher (Microsoft Research Cambridge)
Hidde de Jong (INRIA Grenoble - Rhone-Alpes)
Grzegorz Rozenberg (University of Leiden)

Registration deadline: October 19, 2009

Dynamics of Patterns Day

Wed, 04 Nov 2009 14:23:00 +0100

The DoP Days offer a Dutch discussion forum for current issues in nonlinear dynamics and pattern formation. The CWI will plan 2 to 3 half-day seminars per year for an audience of physicists, mathematicians and other interested disciplines. The sixth Dynamics of Patterns Day (DoP Day) will be held in combination with the inaugural lecture of KNAW visiting professor Willi Jäger on Nov 4, 2009, in the Trippenhuis (KNAW-building) in walking distance from Amsterdam Centraal Station, for directions see http://www.knaw.nl/contact/contact_eng.html.

Next Generation Sequencing Congress

Mon, 16 Nov 2009 15:56:00 +0100

This 2-day conference provides an overview of the current options of next-generation sequencing platforms, technologies, applications and the newest computational tools for the analysis of next-generation sequencing data. The congress is held in conjunction with qPCR Congress, and is organised by Oxford Global Conferences.

Next-generation sequencing technologies are revolutionizing biology by allowing for genome-wide transcription factor binding-site profiling, transcriptome sequencing, and more recently, whole-genome resequencing. These technologies will provide a genome-wide sequence readout as an endpoint to applications ranging from chromatin immunoprecipitation, mutation mapping and polymorphism discovery to noncoding RNA discovery. The event will attract over 120 senior-level decision makers working in bioinformatics & data management, next generation sequencing, discovery, RNA profiling, molecular genomics, and clinical & diagnostics development from the UK, Europe and US. This prestigious event provides a forum for practitioners and researchers to learn more about key solutions being provided to their industry, network with their peers, and address key industry concerns through a series of cutting edge conference presentations in a professional yet relaxed environment. Over two days, the two events will attract over 120 senior-level decision makers working in discovery, gene expression, molecular biology, clinical development and data management from the Europe's leading pharmaceutical and biotech companies, academic and research institutions. In keeping with Oxford Global's highly successful life sciences series, an expert panel of 45 speakers will present a full conference programme covering the following topics: NGS in High Throughput Sequencing Platforms, Applying NGS to Genomic and Genetic Research and Data Analysis/Strategies/Management. There will be a series of partnering sessions, where it will be possible to meet with a select number of vendor companies. There are also a number of social, networking activities at which it will be possible to forge new and strengthen existing relationships with other delegates.

FGCN Launch Symposium

Thu, 19 Nov 2009 00:00:00 +0100

Forensic genomics is a new area of genetic research with clear expectations for forensic applications. It focuses on the use of genomic data to reveal information that can finally be extracted from DNA of biological crime scene samples to help criminal justice professionals to identify victims and suspects. The Netherlands enjoys a top global position in this exciting new field of providing genomic use for societal benefit. The Forensic Genomics Consortium Netherlands (FGCN) is organizing a launch symposium on 19 November 2009 at the Netherlands Forensic Institute (NFI) in The Hague. The program will offer presentations by international speakers on different uses of genomics in various fields of forensic sciences. You will also witness a perspective outlook at future possibilities of solving crimes with the help of research obtained by FGCN. Finally, there will be a (optional) tour about the science and high-quality forensic services at the NFI. For more information about the consortium and a full description of the program, please visit the website at www.forensicgenomics.nl. The way crime is solved is about to change. This is your chance to be there when it does.

SWAT4LS Semantic Web Applications and Tools for Life Sciences

Fri, 20 Nov 2009 16:59:00 +0100

This workshop will provide a venue to present and discuss benefits and limits of the adoption of technologies and tools provided by the Semantic Web in biomedical informatics and computational biology. It will bring together researchers, both developers and users, from the various fields of Biology, Bioinformatics and Computer Science, to discuss goals, current limits and some real use cases for Semantic Web technologies in Life Sciences.

The adoption of semantic enabled applications and collaborative social environments is ever more common in the Life Sciences. The Semantic Web provides a set of technologies and standards that are key to support semantic markup, ontology development, distributed information resources and collaborative social environments. Altogether the adoption of the Semantic Web in the Life Sciences had potential impact on the future of publishing, biological research and medicine. The programme for the 2009 edition of SWAT4LS in in definition. The workshop will range over one full day (from 9.00am to 6.30pm), and will be followed by a social dinner. The scientific programme will include:

invited lectures
oral communications on applications, tools and use cases, selected from submissions
poster/demo session
a panel discussion on perspectives of the Semantic Web in life sciences

The keynote speakers of the 2009 edition of SWAT4LS will be:

Barend Mons, Erasmus Medical Center, Rotterdam and Leiden University Medical Center
Michael Schroeder, Biotechnology Center TU Dresden
Alan Ruttenberg, Science Commons

For more information and registration visit the website: http://swat4ls.org/2009/

Open Source in Biology: exception or alternative to intellectual property?

Fri, 20 Nov 2009 00:00:00 +0100

Introduction
Intellectual property rights have been introduced and strengthened in the last decades, including those on source code and genetic code. An important difference between informatics and biology is, however, that shortly after the introduction of intellectual property rights, an alternative became available in informatics. The open source movement has demonstrated since the early eighties that innovation in informatics is possible on the basis of the sharing and the improvement of the source code of software programs and operating systems. A comparable development occurs in biology as a consequence of the tensions between intellectual property and changing conceptions in research about genes, genomes, proteomes, cells and so forth. Increasingly this involves digital information that needs to be shared and modelled in distributed networks. It is in this context that open source appears as an alternative to intellectual property: it is among several exceptions to intellectual property that become necessary when genetic information and genetic modification are involved. The aim of this seminar is to open for discussion about a different kind of interpretation of open source in biology. Could open source in biology also be about a more desirable alternative? – could it be a counterbalance to the further increase in private control and public regulation of genetic resources that are the crucial for sustainable agriculture and biodiversity conservation? The speakers are:

Prof dr. Guido Ruivenkamp (Athena Institute, Vrije Universiteit & CTC, Wageningen University)
Prof dr. Jack Kloppenburg (Department of community and environmental sociology, University of Wisconsin-Madison)
Dr. Jan Velterop (Concept Web Alliance, Netherlands Bioinformatics Centre)
Prof dr. ir. Steve Hughes (Egenis, University of Exeter)
Dr. Jane Calvert (Innogin, University of Edinburgh)

Programme and more information about registration can be found in the pdf-file below.

Workshop NDNS+: Statistics and the Life Sciences

Mon, 23 Nov 2009 10:32:00 +0100

The NDNS+ cluster organizes approximately twice per year workshops. The next next workshop in this series is: Statistics and the Life Sciences: High-dimensional inference and complex data. High-dimensionality has become a permanent feature of many data structures in the life sciences. From genetics to environmental sciences, from medical sciences to biology, data is rushing towards the statistician who needs to keep a cool head. This workshop presents the coolest heads in the field. The organizers are Ernst Wit, Edwin van den Heuvel, and Siem Heisterkamp.

"On science and professional practice: Where education and knowledge meet"

Thu, 10 Dec 2009 08:59:00 +0100

In the Netherlands, Universities of Applied Sciences (UAS, in Dutch 'HBO') play an important role in translating new scientific knowledge to its application in professional practice. The meeting "On science and professional practice: Where education and knowledge meet" brings together representatives of UAS and of 37 Dutch 'BSIK' research programmes, including the NBIC BioRange programme, to exchange information on how these programmes can contribute to education and applied research at UAS and vice versa, how research programmes can benefit from UAS' knowledge on the professional practice. The meeting is hosted by SenterNovem (part of the Ministry of Economic Affairs) and the 'HBO Raad', the Dutch organisation of UAS. On behalf of BioRange, Celia van Gelder, project leader education at NBIC, is part of the organising committee and she will present an update and results of the NBIC's activities in collaborating with Dutch UAS on, among others, setting up a network of teachers and organising teacher training sessions. In addition, there will be a BioRange booth at the conference exhibition. Please note that the official language during the meeting will be Dutch. More information about the event including the full programme and information about registration is available here.

RSG BioCafé at the evening before BBC

Sun, 13 Dec 2009 00:00:00 +0100

13 Dec 2009 -

Benelux Bioinformatics Conference 2009

Mon, 14 Dec 2009 17:06:00 +0100

The Benelux Bioinformatics Conference is a two-day international conference on bioinformatics. Computational methods and mathematical models are playing an ever increasing role in large-scale "omics" molecular biology, leading to the emergence of bioinformatics as a scientific discipline within Systems Biology, with major applications in health and green biotechnology. The Benelux Bioinformatics Conference is the primary community event for bioinformatics researchers in the Netherlands, Belgium, and Luxemburg with excellent networking opportunities. The conference is aimed at both academic and industry researchers. Both days will feature:

Extended keynote presentations on recent breakthroughs in bioinformatics and Systems Biology
Short presentations contributed by the participants and detailing recent advances
Extensive poster sessions for informal discussions and networking

Participants are invited to submit their poster abstracts by October 19, 2009. The short contributions will be selected from the poster abstracts by the scientific committee.

CFP Statistical Methods for Post-Genomic Data Workshop

Mon, 21 Dec 2009 12:58:00 +0100

The 2010 edition of Statistical Methods for Post-Genomic Data workshop, SMPGD’10, will be held the 14th and 15th of January in Luminy, Marseille.

This edition will welcome three invited speakers, three invited sessions and one contributed session. Among others, the following topics will be discussed:

Epigenetics (ChIP)
Networks Analysis
Comparative Genomics
Feature Selection and Statistical Learning

IBIVU Symposium: Comparing building blocks of life

Mon, 11 Jan 2010 15:50:00 +0100

On the occasion of Walter Pirovano defending his thesis "Comparing building blocks of life - Sequence alignment and evaluation of predicted structural and functional features" (BioRange/NBIC), the IBIVU will organise a symposium on Friday 15 January 2010 at the Vrije Universiteit - W&N building room C121.

Advances in Genomics 2010

Thu, 28 Jan 2010 00:00:00 +0100

Advances in Genomics 2010 is a 2 day symposium centered around 2 core technologies in the field of genomics: real-time quantitative PCR and massively parallel sequencing (both second and third generation, together labeled as next generation). The meeting takes place on January 28-29, 2010, in Ghent (Belgium), a vibrant city known for its science and culture. Please check out the program for most up to date information on the impressive list of confirmed speakers. Important dates
Abstract submission : September 1 – November 30, 2009
Registration deadline : December 24, 2009

WikiPathways Curation Jamboree

Tue, 09 Feb 2010 11:23:00 +0100

WikiPathways (www.wikipathways.org) is an open, collaborative platform for the curation of biological pathways, created to facilitate the contribution and maintenance of pathway information by the biology community. WikiPathways currently contains hundreds of pathways for 18 species. Have you heard about WikiPathways and wanted to contribute, but didn't know where to start? Here's your chance! On February 11th-12th, a curation event is organized to improve the quality of the pathways. The main focus of this event is to make the pathways more informative by adding descriptions and literature references. Curation events are open to all registered WikiPathways users, no prior experience necessary!

How to participate

Check out the Guidelines page to get a sense of the curation tasks involved: http://www.wikipathways.org/index.php/Curation_Jamboree_2010
Register at WikiPathways and start curating! Be sure to add your name to the list of participating curators here: http://www.wikipathways.org/index.php/Curation_Events

Support
WikiPathways admins and curators will be available in an online chat channel to answer questions immediately. (See http://www.wikipathways.org/index.php/Curation_Jamboree_2010 for details). You can also post questions to the WikiPathways mailing list: wikipathways-discuss@googlegroups.com If you have comments about a specific pathway and would like to start a discussion about it, you can do that on the Discussion page of the pathway in question. You can access the Discussion page via the Discussion tab at the top of the pathway page. Can't make it this time?
If you can't participate this time around, stay tuned on the wikipathways-announce mailing list for future events, or check the Curation Events page at WikiPathways
(http://www.wikipathways.org/index.php/Curation_Events) or the Community Interest section of WikiPathways main page.

WikiPathways was developed in one of the NBIC BioRange projects: see more.

BIO MDA meeting

Wed, 13 Jan 2010 10:19:00 +0100

The next BIO MDA meeting is scheduled on Thursday 18th of February 2010 at Wilhelmina Kinderziekenhuis, Utrecht and it will start at 13:30. Two presentations will be given:

13:30 – 14:30: Marcel Reinders – Inference of biological networks
14:30 – 15:00: coffee break
15:00 – 16:00: Daniel Vis – Hormones, dynamics and networks

Important: Please contact Margriet Hendriks wether you are planning to attend the meeting, e-mail: m.hendriks-9@umcutrecht.nl For more information, take a look at the website mentioned below.

NBIC thematic meeting: Protein Structures Bioinformatics

Mon, 01 Mar 2010 15:20:00 +0100

The Centre for Molecular and Biomolecular Informatics (CMBI) is co-organising this meeting on March 1^st in Nijmegen. This NBIC thematic meeting aims to bring together all scientists working in the field of protein structure bioinformatics. Location
UMC St Radboud
NCMLS Building, Colloquium Room
8th Floor, Route 289
Geert Grooteplein Zuid 26-28
6525 GA Nijmegen
The Netherlands Registration
The registration has been closed. Programme
10:00 Reception / registration / coffee
10:25    Welcome by G. Nicolaes, University of Maastricht

10:30    Dr. Elmar Krieger, Yasara; Graz, Austria
         “Homology modelling with YASARA”
10:45    Discussion

11:30    Dr. Jürgen Haas, Swiss Institute of Bioinformatics (SIB)/Biozentrum;
Basel, Switzerland
         “Preparing structures for bioinformatics, i.e. GROMACS”
12:15    Discussion

12:30    Lunch
13:30    Prof. dr. Bert de Groot, Max Planck Institute for Biophysical Chemistry;
   University of Goettingen, Germany
         “Using GROMACS in the modelling world”
14:15    Discussion

14:30    Dr. Sander Nabuurs, CMBI; UMC St Radboud Nijmegen
         “Homology models and dynamics for drug design”
15:15    Discussion

15:30    Closing remarks by Ad van Gorp, Lead Pharma

15:35    Tea
16:00    Discussion about the organisation of protein structure bioinformatics in
the Netherlands (and its neighbours)
17:00    Drinks

DNA-labs on the road conference

Fri, 12 Mar 2010 09:30:00 +0100

The DNA-labs on the road is a great hit among high schools, teachers and students. Hundreds of teachers and thousands of students can tell about the success of this educational project. But the DNA-labs continues in developing educational material and giving insights in modern genomics research. Enough reasons for telling everyone about our progress: The 'DNA-labdag' is a national conference on genomics for high school teachers and technical assistants. With keynote speakers: forensic geneticist Prof. Dr. Peter de Knijff (genetics and human evolution) and Prof. Dr. Jan Hoeijmakers (DNA and ageing). And workshops on genomics and didactics. Several workshops include bioinformatics and the NBIC-project 'bioinformatics@school'. Read more about the 'DNA-labdag' on www.dnalabdag.nl (Dutch).

Course: Next generation sequencing (NGS) data analysis

Wed, 17 Mar 2010 09:56:00 +0100

Onderzoeksschool Medisch Genetisch Centrum Zuid-West Nederland is organising the 3rd edition of the 'Next generation sequencing (NGS) data analysis' course at the Leiden University Medical Center. This course aims at PhD students, postdocs, and senior researchers who are interested in, planning, or already working with next-generation sequencing. Researchers from both the genomics and bioinformatics fields are welcome. Currently available technologies as well as hardware and software solutions will be presented and discussed. The focus of the course will be on the data and ways to analyse the data. Course organizers are: Matthew Hestand, Judith Boer and Johan den Dunnen (LUMC) NBIC is sponsoring this course. You can register via the MGC website: http://www.medgencentre.nl

International Symposium on Integrative Bioinformatics (IB2010)

Fri, 15 Jan 2010 09:19:00 +0100

This sixth annual meeting will be held in Cambridge, United Kingdom, on March 22-24, 2010. Biological data are scattered across thousands of biological databases and hundreds of scientific journals. Current high throughput genomics technologies generate large quantities of high dimensional data. Microarray, NMR, mass spectrometry, protein chips, gel electrophoresis data, Yeast-Two-Hybrid, QTL mapping, gene silencing, and knockout experiments are all examples of technologies that capture thousands of data points, often in single experiments. The challenge for Integrative Bioinformatics is to capture, model, integrate, and analyse these data in a consistent way to provide new and deeper insights into complex biological systems. This sixth meeting on Integrative Bioinformatics will be of interest to Bioinformaticians, Computer Scientists and others working in, or interested in finding out more about, the developing area of integrative bioinformatics. There will be opportunities to present and discuss methods, theoretical approaches, and their practical applications. IB2010 is organized by Rothamsted Research, The University of Cambridge and the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben. For more information, visit the website.

NBIC Conference 2010

Mon, 29 Mar 2010 10:22:00 +0200

Announcement of the fifth edition of the Netherlands Bioinformatics Centre Conference: Date: 29 & 30 March 2010
Venue: Congrescentrum De Werelt, Lunteren Programme
This year the conference will consist of 2 separate days: a closed BioRange Project Meeting on March 29 aimed at the NBIC programmes and researchers and an open 2nd NBIC Conference day on March 30.

Additional information can be found here

Inserm workshop: Interactomics: at the crossroads of biology and bioinformatics

Mon, 21 Dec 2009 11:16:00 +0100

Phase I • Critical assessment
March 30- April 1, 2010 • Saint-Raphaël • France

Aims:
Proteins rarely act alone: they often interact with other macromolecules in order to accomplish their functions. Protein-protein interactions are therefore critical to most biological processes. Systematic approaches for identifying them have been developped over the years, such as yeast two-hybrid or affinity purification-mass spectrometry. These methods have enabled the mapping of complex interaction networks in various model organisms, which are profoundly modifying our understanding of cellular mechanisms by providing us with an integrated view of biological processes. However, due to their complexity, such networks can be intimidating and difficult to take advantage of by hypothesis-driven experimental biologists. The main difficulties are typically methodological and technical (for example knowledge and application of bioinformatics tools), but also and more fundamentally they stem from the changes in reasoning required by the systems biology approach. Protein-protein interaction networks being a very rich but neglected source of information, the workshop will present the main strengths and challenges in producing and using this data. Indeed, a better understanding of the processes, questions and solutions proposed by labs that produce and analyze interactomics data should facilitate its general use. The topics addressed will include:

identifying protein-protein interactions: high-throughput methods, validation of results, quality assessment;
protein-protein interaction databases: contents, standards, direct submissions;
topological and functional analysis of protein-protein interaction networks: methods and tools;
application to biological questions: candidate genes, signaling, host-pathogen interactions, development, evolution.

Audience:
Researchers, physicians, post-docs, technicians, engineers and students interested in the interactome approach and the analysis of existing protein-protein interaction data, in order to benefit to their own research projects.

Phase II • Technical workshop
May 2010 • Marseille

Program:
Participants will learn to use existing tools for extracting functional information from publicly available molecular interaction data. The course is aimed at two subgroups of participants, depending on their computer skills. The goal is to enable the participants to study their own results in the light of previously known biomolecular interactions. 15 participants will be selected among the phase I participants.

7th International Symposium on Networks in Bioinformatics (ISNB 2010)

Thu, 10 Sep 2009 11:29:00 +0200

The 7th International Symposium on Networks in Bioinformatics (ISNB 2010) is scheduled on 22 and 23 April 2010 and is likely to continue its success from previous years in bringing different disciplines together to discuss ongoing research in bioinformatics and biology of networks. The focus of 7th International Symposium on Networks in Bioinformatics will be on biological networks such as metabolic networks, signal transduction pathways and genetic regulatory networks. This year the aim is to include topics like modeling of cells, tissues, gene regulation and biomineralisation. The organisation also wants to invite researchers working on gene networks in plants (e.g. Arabidopsis), model organisms such as Drosophila and organisms with a relatively simple and basal body plan such as sponges and scleractinian corals. Understanding of these networks is crucial for understanding molecular and cellular processes in the organism or system under study. This field is subject of lively research and both experimental and computational approaches are used to elucidate the biological networks. The bioinformatics of biological networks involves a broad range of research and approaches. Research includes the identification of regulatory elements in DNA, developmental biology, genome context analysis, modelling and simulation of pathways, reconstruction of pathways from experimental data, visualization of pathways, and the representation of pathways in database, graphs and mark-up languages. The program of ISNB2010 is now available on the conference website mentioned below. Keynote speakers are:

Dr. Steffen Klamt (Structural and Functional Analysis of Cellular Networks, Max Planck Institute for Dynamics of Complex Technical Systems, Germany)
Tomer Shlomi (Computer Science Department, Technion - Israel Institute of Technology, Israel)
Dr. Tali Raveh-Sadka (Segal lab of Computational Biology, Weizmann Institute of Science, Israel)
Dr. Katy Wolfsencroft (School of Computer Science, University of Manchester, UK)
Prof. dr. Yaochu Jin (Honda Research Institute, Germany)
Dr Yulia Kraus (Dept. of Evolutionary Biology, Moscow State University, Russia; Dept. of Molecular Evolution and Development, University of Vienna, Austria)
Dr. Frederic Marin (Biogeosciences University of Dijon, France)
Dr. Anthony Bertucci (Centre Scientifique de Monaco, Avenue Saint Martin, Monaco)

Organizers:
Bioinformatics Laboratory, Academic Medical Center (AMC), Amsterdam
Section Computational Science, University of Amsterdam
Regulatory Networks Group, CWI, Amsterdam

14th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2010)

Sun, 25 Apr 2010 17:13:00 +0200

RECOMB 2010 is the fourteenth in a series of well-established scientific conferences bridging the areas of computational, mathematical, and biological sciences. The conference features keynote talks by preeminent scientists in the life sciences, together with presentations of refereed research papers in computational biology. The conference series aims at attracting research contributions in all areas of computational molecular biology, including: molecular sequence analysis; recognition of genes and regulatory elements; molecular evolution; protein structure; structural genomics; analysis of gene expression; biological networks; sequencing and genotyping technologies; drug design; probabilistic and combinatorial algorithms; systems biology; computational proteomics; structural and funcional genomics; information systems for computational biology and imaging. The origins of the conference are in the mathematical and computational side of the field, and there remains a certain focus on computational advances. However, the effective applications of computational techniques to achieve biological innovation remains a central aspect of the conference.

Catalytic mechanisms by biological systems: at the interface between chemistry and biology

Fri, 26 Feb 2010 13:59:00 +0100

Recent developments of in vitro, in vivo and in silico research on biocatalytic reaction mechanisms are continuously advancing our insight of the chemistry and biochemistry of catalytic mechanisms by biological systems. The structural and dynamical properties of the proteins are of key importance in this respect. At this conference advanced methodological approaches will be covered, ranging from high resolution kinetic protein crystallography, neutron crystallography, NMR, and mass spectroscopy to single molecule spectroscopy and enzymology. The importance of stability, regulatory, substrate-binding and kinetic properties of enzymes in the context of cellular processes will be highlighted. New emerging technologies important for biocatalysis research for example using transition state analogues and directed evolution methods allow for more insight into the biocatalytic mechanisms. Also bioinformatics and biocomputational approaches are very important in this respect. The conference is aimed at bringing together experts working at the interface of this multidisciplinary research field to facilitate stimulating discussions on this fascinating topic, which is also of key importance for the development of biotech related applications. The multidisciplinary program will provide an ideal framework for getting to know the experts as well as the latest developments in this research field. There will be approximately 25 invited speakers. Participants are encouraged to bring posters, which will be on display during the whole length of the meeting in the lecture hall. Selected poster topics can be included for a general talk. The number of participants is limited to 120.

Workshop BioTM-2010

Wed, 13 Jan 2010 09:47:00 +0100

Text mining has become indispensible in many biological and biomedical sciences. Having to keep up with an increasing number of publications, text mining techniques enable retrieval and analysis of large amounts of documents in a fully automated fashion. They allow for extraction of facts described in the literature that have not yet been recorded in databases, thus providing a necessary tool to obtain a complete overview of all available knowledge.

Recently, the application of text mining and natural language processing techniques to the biological and medical sciences has recieved increasing interest. In addition to many new workshops and conferences arising in this domain, recently also a number of community-wide tasks were conducted to benchmark text mining techniques on specific challenges (e.g. BioCreative, BioNLP Shared Task, ...).

By discussing the latest developments and potentially new applications in text mining amongst scientists in both academia and industry, this workshop aims to provide a broad view on text mining tools in biology and biomedicine. The workshop aims at a broad public, including researchers with an interest in text mining but with little or no experience in this domain. To this end, the workshop will start with an extensive tutorial on text mining in the bio-sciences, providing sufficient background knowledge for novices.

Next, a number of keynote talks will be given by leading scientists, presenting the latest advances in the field. Furthermore, participants are highly encouraged to submit an abstract describing their own work. They will be given the opportunity to present this work in 5min flash presentations, as well as to present a poster during the coffee and lunch breaks.

Finally, there will be a round-table discussion about the broader applicability of text-mining tools in the biological sciences, trying to bridge the gap between theoretical algorithms and experimental work. For more information: visit the website mentioned below.

Patent workshop IOP Genomics

Mon, 08 Feb 2010 10:54:00 +0100

The Netherlands Genomics Initiative, NL Patent Office and the Programme Office IOP Genomics kindly invite you to participate in the Patent Workshop 2010.This workshop will discuss basic patent facts, as well as look at knowledge protection from a genomics/Life Science point of view. If you are a PhD student, postdoc or projectleader from either academia or a company,
wanting to know more about patents, this is the workshop for you! The workshop takes place on 11 May 2010 at the Patent Office in Rijswijk and is free of charge. For more information or registration, please contact:
Ms. Anjali Raghoenath
anjali.raghoenath@agentschapnl.nl
phone 088-6025496

CCGrid-Health 2010

Mon, 17 May 2010 16:50:00 +0200

Grids are becoming increasingly popular for HealthCare applications including medical imaging, bioinformatics and drug discovery. Although extensive research effort is being carried out in the area of grids and distributed systems, current HealthGrid developers often rely on ad-hoc developments, sometimes ignoring elaborated solutions that may help solving their issues in a more elegant way. At the same time, many research works remain hardly applicable to HealthGrid applications due to unrealistic assumptions. HealthCare applications currently offer complete use-cases for data and computing grids involving not only performance concerns but also data management, security, reliability and user-friendliness. This workshop aims at reserving room for discussion about the challenges for the construction and deployment of grids in Healthcare within CCGrid, offering a contact opportunity between HealthGrid application developers and contributing to reduce the gap between the research and production grid communities. The workshop has the goals of obtaining an overview of ongoing efforts in health-related grid applications; obtaining an overview of challenges (technologies, achievements, gaps, roadblocks); and identifying common requirements to lead to future developments in collaboration between Health and Computing Sciences. The workshop will be collocated with CCGrid 2010, the 10th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing to take place in May 17-20, 2010, Melbourne, Victoria, Australia. The presented papers will appear in the CCGrid'2010 proceedings. Important dates:

Papers due: 18 December 2009
Notification of acceptance: 11 January 2010
Camera-ready: 5 February 2010
Workshop: 17-20 May 2009

Additional information, including Program Committee:
http://www.science.uva.nl/~silvia/CCGrid-Health/

Summer School on Nonlinear Dynamics in Biological Networks

Wed, 13 Jan 2010 10:09:00 +0100

Between May 17th and 28th 2010, the Centre for Applied Mathematics in Bioscience and Medicine (CAMBAM) in collaboration with the Mathematical Biosciences Institute (MBI), will host a joint summer school under the theme "Nonlinear Dynamics in Biological Networks". Summer School 2010 aims to prepare students to satisfy the increasing demand in academia, government, and industry for people with cross-disciplinary training who, with various degrees of competence, can speak the languages of the mathematical, physical and biological sciences.

Students and postdoctoral fellows who register for the session, which lasts for a duration of 2 weeks, will have the opportunity to benefit from the instruction of international experts in the field of mathematical modeling, nonlinear dynamics and biological networks. They will also have the opportunity to apply their knowledge and skills through the various lab activities that have been scheduled, and also through the presentation of students' projects which by all measures, will be the highlight of CAMBAM-MBI Summer School 2010 activities. DEADLINE DATE FOR SUBMISSION OF APPLICATIONS IS MARCH 1, 2010
There is no tuition fee and the Summer School organizers have committed to cover accommodation costs for participants who opt to stay in the McGill Residence for the two weeks. However, students are expected to cover the full cost of their travel to and from Montreal as well as their upkeep during the two weeks. In addition, persons who have been selected to participate in the Summer School will be expected to pay a registration fee. After receipt of notification of participation from the Summer School organizers, students will have up to March 15th, 2010 to pay the $150 registration fee. Thereafter and up to April 15th, students will have to pay $200. For more information you can contact: Michael C. Mackey, Ph.D. FRSC
Joseph Morley Drake Professor of Physiology Department of Physiology Centre for Applied Mathematics in Bioscience & Medicine
(CAMBAM)
McGill University
3655 Promenade Sir William Osler, Room 1124 Montreal, Quebec H3G 1Y6 CANADA
email: michael.mackey@mcgill.ca

26th Annual Symposium on Chemometrics

Thu, 01 Apr 2010 14:47:00 +0200

This year's edition of the Annual Symposium on Chemometrics will be centered on two themes, namely Visualisation and the use of Prior Knowledge. The Annual Symposium on Chemometrics aims at presenting the current state of the art in chemometric research in the Netherlands. It is meant as a platform for the different research groups to present their recent work. This year the symposium will be split in a morning session around methods allowing the integration of prior knowledge in models and an afternoon session around visualisation. Several speakers from various disciplines will illustrate this, drawing upon their hands-on experience. Additionally the day will be closed with a lively discussion around the use and abuse of statistics in athletic sports. Participants are invited to share their work during the poster session that will take place during the lunch break. For more information about registration and poster submission, please visit the website mentioned below.

Workshop Statistical challenges of NGS in plants

Fri, 19 Feb 2010 09:54:00 +0100

Next Generation Sequencing (NGS) technologies will soon enable us to sequence plant genomes for less than 1000 euros. This will accelerate plant genomics and biological research. However, the dramatic expansion in both the availability of sequence data and the range of sequencing-based applications requires new statistical and bioinformatics techniques & approaches to unlock the sequence-treasury. The aim of this workshop is to build a community of researchers that are facing the design and analysis of experiments involving high-throughput sequence data. This community provides a low-entry platform for the presentation and discussion of problems, best-practice, solutions, ideas and future directions to empower its members.

The workshop will have only oral presentations by invitation. In addition, contributed papers will be highly appreciated via poster presentations. Marco Bink of the Plant Research International is chair of the workshop. This workshop is organised within EU Cost Action TD0801 "Statistical challenges on the 1000€ genome sequences in plants". The main objective of the Action is to use and/or develop, through coordinated international efforts, efficient statistical and bioinformatics tools and strategies in order to produce, assemble, analyze, and integrate high-throughput genomic sequence data, aiming at a better understanding of biological systems in plants.

ICCS 2010: "Celebrating 10 years of Advancing Computational Thinking"

Mon, 31 May 2010 00:00:00 +0200

In 2010 ICCS celebrates its 10th anniversary in Amsterdam. For this great event five world leading keynote speakers will give their vision on Computational Science now and in the future. The International Conference on Computational Science 2010 (ICCS 2010) aims to bring together researchers and scientists from mathematics and computer science as basic computing disciplines, researchers from various application areas who are pioneering advanced application of computational methods to sciences such as physics, chemistry, life sciences, and engineering, arts and humanitarian fields, along with software developers and vendors, to discuss problems and solutions in the area, to identify new issues, and to shape future directions for research, as well as to help industrial users apply various advanced computational techniques. The theme for ICCS 2010 in Amsterdam is "Advancing Computational Thinking", to mark several decades of progress in computational science theory and practice, leading to greatly improved applications in science. The conference will focuse on recent developments in methods and modelling of complex systems for diverse areas of science, scalable scientific algorithms, advanced software tools, computational grids, advanced numerical methods, and novel application areas where the above novel models, algorithms and tools can be efficiently applied such as physical systems, computational and systems biology, environmental systems, finance, and others. Besides excellent keynote speakers, out of the submitted papers to main track and workshops, some 30% high-quality papers will be selected for presentation at the conference and publication in the proceedings, published by Elsevier in their new Procedia Computer Science series. For paper submission and more information about the conference please visit the conference website: http://www.iccs-meeting.org/

EMBRACE Workshop for Web Service Providers in Bioinformatics: Syntax, Semantics and Publishing

Fri, 23 Apr 2010 22:42:00 +0200

The workshop will introduce comprehensive guidelines for design, semantic annotation and publishing of SOAP-based Web Services in the area of life sciences. The participants should be familiar with the basic concepts of Web Services, and should preferably already have produced or have been involved in the production of one or more such services.

The emerging EMBRACE Guidelines for Web Service providers will be discussed in detail. The following issues of key importance to Web Service interoperability, easiness of use and visibility to the community will then be covered in depth: use of externally defined data types (example: BioXSD), semantic annotation (example: EDAM) and publishing (example: BioCatalogue).

All the points above will be illustrated with hands-on exercises. They will be performed on the participants' own Web Services. Thus, each participant should have remote access to his/her own Web Service generation workbench. Windows laptops with SSH and X11 will be provided on request.

The workshop will be held at the Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, building 208, in Lyngby, Denmark, very close to Copenhagen. It will both start and end at mid-day (Jun 2 and 4, respectively) leaving ample time to reach most European destinations on the same day.

To apply for the workshop, please sign up through the on-line application form below.

8th [BC]2 Basel Computational Biology Conference

Wed, 28 Apr 2010 10:57:00 +0200

The 8th Basel Computational Biology Conference 2010 "Regulation and Control in Biological Systems" on June 24 & 25, 2010 will take place at the Conference Center Basel, Switzerland.

Invited speakers include:

Marvin Cassman (San Francisco, CA, USA)
Dalia Cohen (Rosetta Genomics, Rehovot, Israel & Philadelphia, PA, USA)
Keith O. Elliston (Genstruct Inc., Cambridge, MA, USA)
Ernst Hafen (Institute of Molecular Systems Biology, ETH Zürich)
Vassily Hatzimanikatis (EPF Lausanne & SIB)
Dagmar Iber (D-BSSE, ETH Zürich & SIB)
Douglas A. Lauffenburger (MIT, Cambridge, MA, USA)
Ivan Montoliu (Nestlé Research Center Lausanne)
Erik van Nimwegen (Biozentrum University of Basel & SIB)
Corrado Priami (Microsoft Research - University of Trento Centre for Computational and Systems Biology, Italy)
Uwe Sauer (Institute of Molecular Systems Biology, ETH Zürich)
Ehud Shapiro (Weizmann Institute of Science, Rehovot, Israel)
Jörg Stelling (ETH Zürich & SIB)
Mihaela Zavolan (Biozentrum University of Basel & SIB)
Philip Zimmermann (ETH Zürich)
Winners of the SIB young bioinformatician awards 2010

The annual Basel Computational Biology Conference brings together scientists from academic research and companies interested in the field of computational biology. The main goal of the conference is to provide a platform for informal communication and fruitful discussion between speakers and participants. [BC]² is a conference of the Swiss Institute of Bioinformatics.

3rd Benelux Next-generation sequencing Users Meeting

Tue, 18 May 2010 15:55:00 +0200

This users meeting aims to bring together scientists from the Netherlands, Belgium and Luxembourg that are working with or are planning to start working with any of the next-generation sequencing platforms, to exchange experiences, identify complementary interests and common problems and to enhance interaction between individuals at all levels. The primary focus of this meeting is on user experiences and networking, rather than scientific breakthroughs. The symposium is free for anyone interested, although registration is required. Deadline for abstract submission and registration is June 14, 2010 For more information, a preliminary programme and registration form, please visit the website.

6th ISCB Student Council Symposium

Tue, 26 Jan 2010 11:54:00 +0100

The 6th ISCB Student Council Symposium will take place in Boston on July 9, just before ISMB 2010. The ISCB Student Council Symposium is a forum for students and young researchers in the fields of Computational Biology and Bioinformatics. Participants will have the opportunity to present their work to an international audience, build a network within the community and develop important soft skills in an environment that fosters exchange of ideas and knowledge. Meet your colleagues and chat about your science! Keynote speakers:

Dr. D. Altshuler, Broad Institute
Dr. G. Bader, University of Toronto
Dr. L. Hunter, University of Colorado

The agenda includes student presentations, poster session with presentation and poster awards and more surprises to come. Check out all updated information on the website: http://symposium.iscbsc.org There will be travel fellowships available to attend the symposium.

ISMB 2010: the 18th Annual International Conference on Intelligent Systems for Molecular Biology

Tue, 26 Jan 2010 11:15:00 +0100

ISMB 2010 will be held in Boston, Massachusettes, USA, July 11 - July 13, 2010. The conference will feature an exciting scientific program including scientific tracks, posters, demonstrations, and featuring ten internationally renowned keynote presenters. Key dates:

Call for Workshop Track submissions closes Friday, February 12, 2010
Call for Highlights Track submissions closes Friday, February 26, 2010
Call for Late Breaking Research Track submissions closes Friday, March 12, 2010
Call for Posters submissions closes Friday, March 19, 2010
Call for Technology Track submissions closes Friday, April 23, 2010
Call for Art and Science Exhibition submissions closes Friday, April 23, 2010

Details available here: http://www.iscb.org/ismb2010

BIOCOMP'10: International Conference on Bioinformatics and Computational Biology

Tue, 09 Feb 2010 16:53:00 +0100

BIOCOMP is an important track of WORLDCOMP which is the largest annual gathering of researchers in computer science, computer engineering and applied computing. 2,000 or more attendees are anticipated from over 85 countries participating at the Congress.

The motivation behind WORLDCOMP is to assemble a spectrum of affiliated research conferences into a coordinated research meeting held in a common place at a common time. The main goal is to provide a forum for exchange of ideas in a number of research areas that interact. Both inward research (core areas of computer science & engineering) and outward research (multi-disciplinary, inter-disciplinary, and applications such as those in computational biology, bioinformatics and impact on drug design) will be covered during the joint conferences. BIOCOMP/WORLDCOMP provides a unique platform for a diverse community of constituents composed of scholars, researchers, developers, educators, and practitioners. The Congress makes concerted effort to reach out to participants affiliated with diverse entities (such as: universities, institutions, corporations, government agencies, and research centers/labs) from all over the world. The congress also attempts to connect participants from institutions that have "teaching" as their main mission with those who are affiliated with institutions that have "research" as their main mission. The congress uses a quota system to achieve its institution and geography diversity objectives. BIOCOMP 2010 will be composed of research presentations, keynote lectures, invited presentations, tutorials, panel discussions, and poster presentations.

Important dates:

March 1, 2010: Submission of papers (about 5 to 7 pages)
March 25, 2010:Notification of acceptance
April 22, 2010:Final papers + Copyright + Registration
July 12-15, 2010: The 2010 International Conference on Bioinformatics and Computational Biology (BIOCOMP'10)

The 2010 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-10)

Fri, 19 Feb 2010 10:39:00 +0100

BCBGC is an important annual event in the areas of bioinformatics, computational biology, genomics and chemoinformatics and focuses on all areas related to the conference. The conference will be held at the same time and location where several other major international conferences will be taking place. The conference will be held as part of 2010 multi-conference (MULTICONF-10). MULTICONF-10 will be held during July 12-14, 2010 in Orlando, Florida, USA. The primary goal of MULTICONF is to promote research and developmental activities in computer science, information technology, control engineering, and related fields. More details about the other conferences organised can be found here: http://www.promoteresearch.org/

Open Science Summit 2010

Mon, 07 Jun 2010 08:51:00 +0200

Should be of interest to CWA supporters: This summer (July 29-31, Berkeley, California), scientists, hackers, students, patients, and activists will convene to discuss the future of our science/technology paradigm at the Open Science Summit 2010. Topics include: Synthetic Biology, Gene Patents, Open Data, Open Access, Microfinance for Science, DIY science, DIY Biology, Alternative Funding for Science, Open Source Drugs, Patent Pools, Open Health/Medicine, Patient Advocacy for Innovation

NBIC/SIB Summer School: Quantitative imaging and modelling of biological processes

Mon, 28 Jun 2010 16:27:00 +0200

Imaging is a hot topic in Systems Biology! PhD students in bioinformatics, computational biology and systems biology: "Take your chance and participate in this Summer School, spiced with tutorials and exercises."

The Summer School focuses on "Quantitative imaging and modelling of biological processes". The topics that will be included: fundamentals of biomedical image processing and image annotation, image-based modelling and simulation, imaging of specific cellular compartments, cell motility, morphogenetic processes and small animals. For more information see the attached flyer, visit the website, or contact Celia van Gelder at NBIC Education (celia.van.gelder@nbic.nl). Please note that course participation is free of charge for NBIC and NBIC-matching PhDs, while other PhDs pay a small course fee. Furthermore, central (low-cost) accomodation in Amsterdam, has been arranged by NBIC for the participants.

Colloquium - Hybrid Computing for High-Throughput Bioinformatics

Mon, 16 Aug 2010 13:34:00 +0200

Colloquium subject
Discussed will be how Convey’s revolutionary hybrid-core computing architecture, the HC-1^TM, delivers dramatically increased throughput for genomics and proteomics applications, reducing time-to-completion in some projects from months to days. Convey is working with customers and partners, including instrument manufacturers, on many facets of bioinformatics, ranging from primary analysis to reference based and de novo assembly to downstream research. Furthermore, increased performance can provide fundamental improvements in research quality by allowing previously impractical approaches. The HC-1 integrates advanced architecture and compiler technology with off-the-shelf x86 and FPGA processors, helping life sciences customers accelerate application performance while reducing energy, floor space, and management costs. The highly integrated Convey approach provides users familiar C, C++ and FORTRAN development environments without the complexity of non-standard dialects or programming models. Location
Delft: Tuesday Augustus 24, 16.00-17.00; EWI Faculty, HB9.130
Nijmegen: Tuesday Augustus 24, 11.00-14.00; NCMLS Nijmegen George Vacek
George Vacek joined Convey Computer Corporation as the global head of the Life Sciences business in November 2009. Prior to joining Convey, he held responsibility for the success of Scientific Research solutions in Hewlett Packard's High-Performance Computing Division for three and a half years. Before that he was in charge of business development for three years at OpenEye Scientific Software. He has held business and technical roles in the computational life sciences, yielding 30 research publications and contributions to several quantum chemistry programs, including Schrödinger's Jaguar. He earned his Ph.D. in Chemistry from the place University of Georgia in 1995. He also holds an M.B.A. from Portland State University and Bachelor's degrees in Physics and Mathematics from the University of Wisconsin.

Capita Selecta in Complex Disease Analysis (CSCDA2010)

Fri, 26 Feb 2010 13:45:00 +0100

The first edition of the Capita Selecta in Complex Disease Analysis focuses on epistasis and integration of -omics data sets in the post-genomic era. This mini-conference will exist of two parts:

tutorial sessions in the afternoon of day 1 (25 August 2010)
keynote speaker sessions, with discussion afternoons, on days 2-3 (26-27 August 2010)

The targeted audience has a background in life sciences, biomedical sciences, statistics, bioinformatics, statistical genetics or medicine. The abstract submission deadline is 12 April 2010.

ESF Next Generation Sequencing Meeting

Mon, 14 Jun 2010 15:37:00 +0200

Next generation sequencing technologies enable de novo and re-sequencing of DNA, transcriptome sequencing, tag-based sequencing, and metagenomics sequencing. Recent results show applications emerging in evolution, environmental, forensics and archeology. While the second-generation technologies are being further improved, third-generation sequencing is already becoming available and utilized by pioneer researchers. The meeting aims at bringing together experts in the field to present their technological and scientific advances. Invited speakers and talks selected from abstracts will feature in sessions on evolution, transcription, personalized genomes, diagnostics, bioinformatics, and new sequencing technologies. The meeting starts with hands-on computer practicals including 1000 Genome Browser and a pipeline from reads to report files. Young researchers are invited to join a special program. Keynote speakers:
Chris Tyler-Smith, Mike Wilson, Eske Willerslev, Matthias Harbers, Barbara Wold, Edwin Cuppen, Sacha van Hijum, Joris Veltman, Debbie Nickerson, Ewan Birney, Guy Cochrane, Ivo Gut, Ruiqiang Li, Jeantine Lunshof and Evan Eichler. The registration deadline of August 24 is fast approaching!
For more information, registration and abstract submission, please visit the website mentioned below.

2nd International Workshop on Biological Knowledge Discovery and Data Mining (BIOKDD'10)

Mon, 30 Aug 2010 13:47:00 +0200

With the development of Molecular Biology during the last decades, we are witnessing an exponential growth of both the volume and the complexity of biological data. For example, the Human Genome Project provided the sequence of the 3 billion DNA bases that constitute the human genome. And, consequently, we are provided too with the sequences of about 100,000 proteins. Therefore, we are entering the post-genomic era: after having focused so many efforts on the accumulation of data, we have now to focus as much effort, and even more, on the analysis of these data. Analyzing this huge volume of data is a challenging task because, not only, of its complexity and its multiple and numerous correlated factors, but also, because of the continuous evolution of our understanding of the biological mechanisms. Classical approaches of biological data analysis are no longer efficient and produce only a very limited amount of information, compared to the numerous and complex biological mechanisms under study. From here comes the necessity to use computer tools and develop new in silico high performance approaches to support us in the analysis of biological data and, hence, to help us in our understanding of the correlations that exist between, on one hand, structures and functional patterns of biological sequences and, on the other hand, genetic and biochemical mechanisms. Knowledge Discovery and Data Mining (KDD) are a response to these new trends. Topics of BIOKDD'10 workshop include, but not limited to:

Data Preprocessing: Data Storage, Representation and Management, Data Cleaning, Feature Extraction, Feature Selection.
Data Mining: Biological Data Clustering/Biclustering, Biological Data Classification, Biological Data Regression, Association Rule Learning from Biological Data, Parallel/Cloud/Grid Computing for Biological Data Mining, Text Mining and Application to Biological Sequences, Web Mining and Application to Biological Data, Analysis of Biological Networks.
Data Postprocessing: Knowledge Filtering, Knowledge Representation and Visualization, Knowledge Combination and Integration, Error Rates and Numerical Indicators.

GMOD Europe 2010

Wed, 18 Aug 2010 11:22:00 +0200

Event information
The four days of GMOD events will be held 13-16 September 2010, at the University of Cambridge. GMOD Europe 2010 includes: 1) GMOD Community Meeting, Monday & Tuesday: Project updates, developer and user presentations and best practices, project direction.
2) GMOD Satellite Meetings, Wednesday: Special interest groups where GMOD community members meet to discuss specific topics of interest.
3) InterMine Workshop, Wednesday: A one day workshop on installing, configuring and using the InterMine biological data warehouse system.
4) BioMart Workshop, Thursday: A one day workshop on using the BioMart biological data warehouse system, including accessing data through APIs. Registration
Registration is now open for these events. There is a £50 registration fee for the GMOD Meeting to cover catered lunches and other expenses. Registration for all other events is free, but required, as space is limited. These events are open to all: GMOD users, developers, prospective users, biologists, and computer scientists. See http://gmod.org/wiki/January_2010_GMOD_Meeting for an idea of what goes on at GMOD meetings. About GMOD
GMOD is a collection of interoperable open source software components for managing, visualizing and annotating biological data. GMOD incorporates many widely used tools, including GBrowse and JBrowse for genome browsing, InterMine and BioMart for data mining, Galaxy and Ergatis for workflow, Chado for data management, GBrowse_syn and CMap for comparative genomics, plus many other tools (Apollo, MAKER, Pathway Tools, Textpresso, ...). GMOD is also an active community of researchers and developers addressing common challenges in exploiting their data. If you are struggling to fully exploit your data then please consider attending GMOD Europe 2010.

7th annual RNAi & miRNA Europe

Tue, 14 Sep 2010 10:58:00 +0200

The annual RNAi & miRNA Europe is Europe's largest conference and exhibition dedicated to RNA interference. The conference will be co-located with Advances in qPCR, Epigenetics Europe and Genomics Automation Europe. Registered delegates will have access to all four meetings.

Agenda Topics:

Target Discovery and Validation
Transfection
siRNA Therapeutics
in vivo RNAi
Bioinformatics of small RNAs
siRNA library screens
microRNAs in: Disease Biology, Stem Cell Biology, Diagnostics, Virology, Biogenesis, Development

Python workshop in Karpacz

Thu, 16 Sep 2010 00:00:00 +0200

A 3-day Python workshop is organized by the Polish and German RSGs in Karpacz (located in the Carpathian Mountains in Western Poland). For more information on the contents of the course, please visit: http://pythonfriends.blogspot.com/

Mutations in proteins: structure, function, dynamics and disease

Mon, 26 Jul 2010 22:42:00 +0200

The Netherlands Society on Biomolecular Modelling (NSBM) is happy to announce its second one-day conference on protein structure and modelling related topics. Location
UMC St Radboud
NCMLS Building, Colloquium Room
8th Floor, Route 289
Geert Grooteplein Zuid 26-28
6525 GA Nijmegen
The Netherlands Programme
10:00 Reception / registration / coffee 10:20    Welcome by G. Nicolaes, University of Maastricht, presentation of NSBM 10:25    G. Vriend opening of the morning session 10:30    Mahesh Kulharia, Cardiovascular research Institute Maastricht, Maastricht
University
         “In silico simulation of the membrane binding process of coagulation factor
VIII: prediction of the phenotype in haemophilia A patients, and ramifications
for anticoagulant drug design” 11:30    Frederic Rousseau, VIB Switch Laboratory, Vrije Universiteit, Brussels,
Belgium.
         “The evolutionary relationship between protein structure and aggregation and
its consequences for disease” 12:30    Lunch and Poster sessions 14:30    Selected abstract by PhD student 14:50    Selected abstract by PhD student 15:10 Hanka Venselaar, CMBI, UMC St. Radboud
"Predicting the phenotypic effect of disease causing mutations" 16:10 Tea 16:30 Henk-Jan Joosten, Wageningen University & Research Centre.
"Predicting mutations that cause a desired phenotypic effect" 17:10    Closing remarks, poster prize award 17:20    Drinks Registration and abstract submission details To register for the meeting, please fill out the registration form. The capacity at the conference venue to put up posters is limited. If too many abstracts are handed in, priority will be given to PhD students and master students who want to present a poster that deals with the conference topic. Poster abstracts should be 1-page A4 in PDF format, not exceeding 5 Mb in size. Poster abstracts should be sent before September 6 to Gerry Nicolaes, g.nicolaes@bioch.unimaas.nl (tel +31(0)43 3881688). Two master or PhD student poster presenters will be invited to discuss their poster in a 15 minute seminar. A poster prize will be awarded to the best poster presented at the conference. Please indicate with the submitted poster abstract if you are a master student or PhD student, and wether you are interested in presenting a short seminar. The abstracts will be published on the NBIC website.

(PRIB-10) 5th IAPR International Conference on Pattern Recognition in Bioinformatics

Thu, 25 Feb 2010 17:05:00 +0100

The Pattern Recognition in Bioinformatics conference aims to bring together top researchers, practitioners and students from around the world to discuss the applications of pattern recognition methods in the field of bioinformatics to tackle problems in the life sciences. Prospective authors are invited to submit papers in the research areas of interest to the conference. These include:

Bio-sequence analysis
Gene and protein expression analysis
Protein structure and interaction prediction
Motifs and signal detection
Metabolic modelling and analysis
Systems and synthetic biology
Pathway and network analysis
Immuno- and chemo-informatics
Evolution and phylogeny
Biological databases, integration and visualisation
Bio-imaging

Pattern recognition techniques of interest include, but not limited to:

Static, syntactic and structural pattern recognition
Data mining, Data based modelling
Neural networks, Fuzzy systems
Evolutionary computation and swarm intelligence
Hidden Markov models, Graphical models

Like the previous editions, accepted papers will be published in the Springer series of Lecture Notes in Bioinformatics (LNBI). Enhanced versions of selected special session papers will be included in a special issue of Neurocomputing Journal (Elsevier). Important dates:
Paper Submission: ~~5 June 2010~~ 1 August 2010
Special Sessions Proposal: 2 March 2010
Tutorials Proposal: 2 April 2010
Author Notification: 2 June 2009
Camera Ready Papers: 2 July 2009
Early Bird Registration: 15 July 2009 NBIC is sponsoring this conference.

“BBMRI – Biobanking for Science”

Tue, 25 May 2010 19:04:00 +0200

On September 23-25, 2010, the BBMRI consortium will organise the "BBMRI – Biobanking for Science" conference focusing on scientific excellence in the various aspects of biobanking at the Novotel Amsterdam City, Amsterdam, NL.

Scientific seminar by George M. Church

Tue, 27 Jul 2010 14:25:00 +0200

On September 23, George M. Church (Professor at Harvard University, Boston) will be speaking about "How Personal Genomics and Synthetic Biology will influence healthcare". This scientific seminar is organised by Science4you in Rotterdam. On September 24 George Church will be awarded with the International Steven Hoogendijk Award in the 'Burgerzaal' of the City hall of Rotterdam. You can register for these events by sending an e-mail to m.miedema@erasmusmc.nl. Please mention the date of the event you will be visiting in the e-mail. More information can be found in de flyer attached.

ECCB10 - European Conference on Computational Biology

Mon, 01 Feb 2010 10:50:00 +0100

ECCB10 is the key European computational biology event in 2010 uniting scientists working in a broad range of disciplines, including bioinformatics, computational biology, biology, medicine, and systems biology. As part of the ECCB conference series, it will be organized this year jointly by the Belgian and Dutch bioinformatics communities. Leading bioinformatics researchers, computational biologists, and bio-IT professionals from Europe and around the world gather annually at the European Conference on Computational Biology (ECCB) for four days of presentations, poster sessions, workshops, software demonstrations, and most impotantly - networking. ECCB is the leading European meeting and a primary international conference at which people report on and discuss advances in this rapidly-expanding field. Ghent is one of Europe's most exciting medieval towns, a glorious eclectic city with spectacular buildings and a vivid cultural experience (National Geographic Traveler ranked it 3rd best historic place to visit internationally in 2008). Ghent is directly accessible by train from Brussels airport. The conference venue is highly convenient and located in a beautiful park within the city center. Invited Speakers:

Peer Bork (EMBL-Heidelberg)
Elaine Mardis (Washington University)
Michael Sternberg (Imperial College London)
Hans Westerhoff (University of Manchester, Free University of Amsterdam)
Yves Van der Peer (University of Ghent)

Key dates:

Paper submission deadline - April 9, 2010
Industry and demo track submission deadline - July 2, 2010
Poster submission deadline - June 20, 2010
Early registration deadline - August 20, 2010

For more information visit the conference website:http://www.eccb2010.org/ NBIC is Gold sponsor of the ECCB10 and will be present with an exhibition booth at the conference.

First European Student Council Symposium (ESCS1)

Sun, 26 Sep 2010 00:00:00 +0200

Event description
We are presenting here the first European Student Council Symposium in association with ECCB 2010. It will be organized as a full parallel track during the first day of the conference, which is filled with parallel workshop and tutorial tracks. The meeting is planned for Sunday September 26, 2010. The full day programme runs from 9 am to 5 pm. At 5:30 pm the first plenary lecture of the main ECCB10 conference starts. We expect an attendance of 40 to 75 students for ESCS1, with approx. 20 to 30 submitted abstracts. Preliminary programme
09:00‐09:30 ICE BREAKER: presentations
09:30‐10:30 KEYNOTE: Yves Van de Peer, VIB and University of Ghent, Belgium
10:30‐11:00 Coffee break
11:00‐12:30 STUDENTS: presentations based on abstract submission
12:30‐13:30 Lunch
13:30‐15:00 SOFT SKILLS WORKSHOP by Gijs Meeusen
15:00‐15:30    Coffee break
15:30‐17:00    SOFT SKILLS WORKSHOP continues
17:00-17:25    POSTERS: test your new presentation skills! Registration
You can register to the student symposium even if you do not attend ECCB. It only costs 100 euros, but will be 150 euros after the early registration deadline - Aug 20, 2010 (http://escs.iscbsc.org/registration) Poster submission
The Student Symposium accepts late poster submissions till August 16, with notification on August 18. We actively encourage you to submit work you are presenting at ECCB to the Student Symposium as well. (http://escs.iscbsc.org/abstract-submission)

Organization
This event is organized in conjunction with the European Conference on Computational
Biology (ECCB). Even though this project is filed by RSG‐Europe, the organization of this project is jointly done by all European RSGs. Initial planning for this event involved people from RSG‐Netherlands, RSG-France, RSG-Germany and RSG-Europe.

VPH 2010

Thu, 01 Apr 2010 15:39:00 +0200

The first of a series of international VPH Conferences (VPH2010) will be organised by the Virtual Physiological Human Network of Excellence - VPH NoE in Brussels on 30th September to 1st October, 2010. This first meeting will be held in Brussels, Belgium, and is supported by the European Commission ICT for Health / DG Information Society and Media.

The Virtual Physiological Human Network of Excellence is an umbrella project representing the Virtual Physiological Human Initiative set up by the European Commission with a budget of ~ 350 million Euros for the Framework 7 Program. The conference series is designed to be a key resource for the VPH NoE to produce a ‘VPH Vision and Strategy Document’ to inform the next European Commission calls for the VPH field for FP7, FP8 and for European large infrastructural actions. The meeting on 30th September – 1st October will be dedicated to the VPH Initiative, bringing together key representatives from VPH groups, Industry and Clinics. The first meeting is designed to be a relatively small meeting up to a maximum of 200 participants with high profile key speakers and will contain the very best of VPH research. Parallel sessions will be held on both days with proposed topics in five main themes: Organ Systems, Modelling Scales, Research Methodology, Application Domains and Data Access and Information Assurance. More information about the meeting can be found on the website mentioned below.

WTNC 2010

Thu, 01 Apr 2010 16:13:00 +0200

Natural Computing is a research area concerned with computing taking place in nature and with human-designed computing inspired by nature. It is a fast growing, genuinely interdisciplinary field involving, among others computer science, biology, and mathematics. The aim of the International Workshop and Tutorials on Natural Computing (WTNC 2010) is to provide a high-level scientific forum for the researchers in various areas of Natural Computing as well as to provide a cooperation forum for the Natural Computing and on Graph Transformations research communities. This is the 4th event in this series of meetings, with previous editions held in Barcelona, Spain (with ICGT 2002), Rome, Italy (with ICGT 2004), and Leicester, UK (with ICGT 2008). The WTNC 2010 is a satellite event to the International Conference on Graph Transformations (ICGT 2010). For more information about the workshop and about registration and abstract submission, please visit the website mentioned below.

4th International Workshop and Tutorials on Natural Computing (WTNC 2010)

Fri, 28 May 2010 12:58:00 +0200

Natural Computing is a research area concerned with computing taking place in nature and with human-designed computing inspired by nature. It is a fast growing, genuinely interdisciplinary field involving, among others computer science, biology, and mathematics. The aim of the International Workshop and Tutorials on Natural Computing WTNC 2010 is to provide a high-level scientific forum for the researchers in various areas of Natural Computing as well as to provide a cooperation forum for the Natural Computing and on Graph Transformations research communities. This is the 4th event in this series of meetings, with previous editions held in Barcelona, Spain (with ICGT 2002), Rome, Italy (with ICGT 2004), and Leicester, UK (with ICGT 2008). Invited speakers:

Reiko Heckel (University of Leicester, UK)
Erik de Vink (Eindhoven University of Technology, the Netherlands)
Sander Bohte (CWI, the Netherlands)

Important dates:

Submission: May 31, 2010
Notification: June 30, 2010
Final version: August 20, 2010
Workshop: October 2, 2010

The WTNC 2010 is organized in conjunction with the 5th International Conference on Graph Transformations.

Workshop Modeling Angiogenesis: Joining Cells, Maths and Computers

Fri, 16 Jul 2010 11:15:00 +0200

The outgrowth of new blood vessels from pre-existing vessels, called angiogenesis, is a crucial step in myriad physiological and pathological mechanisms. Unfortunately, the complicated causes and effects of angiogenesis make it very difficult to control. Computational models and simulations help unravel both the basic mechanisms of angiogenesis and can help identify the steps in the mechanisms most amenable to intervention.

A wide range of mathematical and computational models is currently available. Despite the biological insights these mathematical models have produced, modeling rarely finds application in experimental angiogenesis research yet. Why is that?

This workshop organized by the Lorentz Center will host both experimental researchers and computational models working in vascular biology, endothelial cell biology, angiogenesis, and pharmaceutics. The aim of the workshop is to:

identify the requirements for computational models to make a true impact in basic angiogenesis research, tissue engineering and drug innovation,
inventarize pre-existing and missing components of such a model, and
discuss how we can couple such components.

For more information and registration visit the website mentioned below.

The 11th International Conference on Systems Biology (ICSB 2010)

Sun, 10 Oct 2010 00:00:00 +0200

Systems biology crosses the borders and gathers the strength of traditionally separated disciplines such as biology medicine, mathematics, computer science, engineering, physics and chemistry. The ultimate goal of systems biology is to provide knowledge, tools, and systems that have a major impact on biomedical research, the diagnosis and treatment of human disease, and the development of new biotechnological and bioengineering applications. The International Conference on Systems Biology is the premiere annual meeting for anyone interested in pursuing this goal. The Scientific Programme has been designed to bring together a broad spectrum of professionals involved in disciplines such as biology medicine, mathematics, computer science, engineering, physics and chemistry. More information about the conference can be found on the conference website: http://www.icsb2010.org.uk/

NBIC BioRange Project Meeting 2010

Mon, 19 Jul 2010 16:03:00 +0200

On 11 October 2010 NBIC organises the second NBIC BioRange Project Meeting. This is a closed meeting for researchers that participate in the NBIC projects. This meeting aims at bringing together all the BioRange participants to exchange information on the current NBIC research projects. The meeting is obligatory for all researchers who participate in a BioRange project and who have a research position funded by NBIC. For more information and registration, please visit the website below.

Biocuration2010

Wed, 18 Aug 2010 11:30:00 +0200

About Biocuration2010
Biocuration2010 is the Conference of the International Society for Biocuration (ISB) and the 4th International Biocuration Conference. It is held in Tokyo, Japan, from October 11-14, 2010. This conference will provide a forum for curators and developers of biological databases to discuss their work, promote collaborations, and foster a sense of community in this active and growing area of research. Topics will include:

Text Mining
Literature Curation
Ontologies
Genome Sequence Annotation
Comparative Genomics
Functional Genomics
Crop/Plant Genome Curation
Community Curation
Data Standardization and Integration
Curation Tools/Workflows
Data Visualization
Journal/Database Interactions and Collaborations
Next Generation Sequence Annotation
Next Generation Curation

Programme
The meeting program will include:

plenary speakers:
Dr. Minoru Kanehisa (Kyoto Univ., Japan)
Dr. Paul Thomas (Univ. of Southern California, USA)
Dr. Barend Mons (Netherlands Bioinformatics Centre)
sessions:
[S1] Large Scale, Automated, Predictive Annotations
[S2] Outreach to User Communities & Community Annotation
[S3] Biocuration in Metabolomics and Systems Biology
[S4] Asian Models of Biocuration-Related Activities
[S5] Data Integration Platforms and Data Sharing
[S6] Future Directions and Challenges for Biocuration
workshops:
[W1] Curation of Protein Structure and Chemicals
[W2] Curation Interface and Software
[W3] Crop/Plant Genome Curation
[W4] New Approaches Towards Database Integration

The full meeting program can be found here: http://hinv.jp/biocuration2010/program.html
The meeting schedule can be found here: http://hinv.jp/biocuration2010/meeting_schedule.html Registration
Follow this link to register: http://hinv.jp/biocuration2010/registration.html
For questions or technical difficulties with the registration, please contact the secretariat at Biocuration2010@ics-inc.co.jp Abstract submission
The abstract submission deadline is now extended to August 31, 2010. For more information see http://hinv.jp/biocuration2010/abstract.html. Important dates
Event date: October 11-14, 2010
Abstract submission ends: August 31, 2010
Notification of acceptance: will be done by September 3, 2010
Early bird registration ends: September 6, 2010 Location
Tokyo International Exchange Center, Tokyo, Japan. Organizing Committee
http://hinv.jp/biocuration2010/committee.html

The Fourth International Workshop on Machine Learning in Systems Biology (MLSB 2010)

Mon, 21 Jun 2010 09:16:00 +0200

Objective The aim of this workshop is to contribute to the cross-fertilization between the research in machine learning methods and their applications to systems biology (i.e., complex biological and medical questions) by bringing together method developers and experimentalists. Encourage are submissions bringing forward methods for discovering complex structures (e.g. interaction networks, molecule structures) and methods supporting genome-wide data analysis. Motivation
Molecular biology and all the biomedical sciences are undergoing a true revolution as a result of the emergence and growing impact of a series of new disciplines/tools sharing the "-omics" suffix in their name. These include in particular genomics, transcriptomics, proteomics and metabolomics, devoted respectively to the examination of the entire systems of genes, transcripts, proteins and metabolites present in a given cell or tissue type.

The availability of these new, highly effective tools for biological exploration is dramatically changing the way one performs research in at least two respects. First, the amount of available experimental data is not a limiting factor any more; on the contrary, there is a plethora of it. Given the research question, the challenge has shifted towards identifying the relevant pieces of information and making sense out of it (a "data mining" issue). Second, rather than focus on components in isolation, we can now try to understand how biological systems behave as a result of the integration and interaction between the individual components that one can now monitor simultaneously (so called "systems biology").

Taking advantage of this wealth of "genomic" information has become a conditio sine qua non for whoever ambitions to remain competitive in molecular biology and in the biomedical sciences in general. Machine learning naturally appears as one of the main drivers of progress in this context, where most of the targets of interest deal with complex structured objects: sequences, 2D and 3D structures or interaction networks. At the same time bioinformatics and systems biology have already induced significant new developments of general interest in machine learning, for example in the context of learning with structured data, graph inference, semi-supervised learning, system identification, and novel combinations of optimization and learning algorithms.

Molecular biology and all the biomedical sciences are undergoing a true revolution as a result of the emergence and growing impact of a series of new disciplines/tools sharing the “-omics” suffix in their name. These include in particular genomics, transcriptomics, proteomics and metabolomics, devoted respectively to the examination of the entire systems of genes, transcripts, proteins and metabolites present in a given cell or tissue type. This workshop is organized as "core - event" of Pattern Analysis, Statistical Modelling and Computational Learning - Network of Excellence2 (PASCAL 2, http://www.pascal-network.org/). It will be part of the workshop program of ICSB 2010, The 11th International Conference on Systems Biology (11-14 OCT 2010, http://www.icsb2010.org.uk/). For more information, registration and abstract submission, please visit the website mentioned below.

7th CMSB Symposium

Wed, 06 Oct 2010 10:39:00 +0200

On Friday October 15, the Centre for Medical Systems Biology (CMSB) organises its 7th Annual Symposium, which will be held in the auditorium of NCB Naturalis (Darwinweg, Leiden). The symposium is free of charge. Also this year there is a varied programme applying to the CMSB theme "Improving diagnosis, treatment and prevention of common and rare diseases". In the morning, CMSB researchers will present their findings covering the five main CMSB research programme diseases: Alzheimer’s disease, Arthritis, Depression, Metabolic Syndrome and Migraine, and the two platforms Immunology and DIAL (Data Integration, Analysis and Logistics). In the afternoon, there is a learning/teaching/educational session ‘Biophenotyping’ with presentations that will give insight into state of the art techniques and methods in cellular phenotyping, proteomics, metabolomics and imaging. Keynote lecturer will be Aarno Palotie (Head of Medical Sequencing, Wellcome Trust Sanger Institute, UK). After his presentation "Migraine and other complex disorders" he will join the discussion session lead by Martijn Breuning on Genomics and Society, in which a panel of experts will debate with the audience on the medical and social impact of complex genetics. Besides Aarno Palotie, this panel consists of, among others, Gertjan van Ommen, Toine Pieters and Lidewij Henneman. Programme: see pdf-file in attachment
Registration: Registration is free of charge; please register at www.boerhaavenet.nl
Information: Petra van Overveld, p.overveld@lumc.nl / 071 5269551

2nd NCSB Symposium (NCSB 2010)

Tue, 26 Jan 2010 14:07:00 +0100

The next annual NCSB symposium is scheduled for Thursday and Friday 2010 October 21-22. Please reserve these two days in your agenda. Venue and programme will be announced in due course via the NCSB website.

LuciLinx Symposium

Fri, 29 Oct 2010 00:00:00 +0200

On Friday 5th November 2010 LuciLinx (the Luxembourg Bioinformatics Network) is organising their 3rd annual symposium in the Auditorium of Centre Hospitalier de Luxembourg, in Luxembourg. Theme of the Symposium is “Methods and applications in Bioinformatics: From ideas to results”. Keynote speakers are:

Andreas Keller, Febit AG Germany
Holger Stenzhorn,Uniklinikum Saarland Germany
Mario Albrecht, Max Planck Institute for Informatics Saarbrücken, Germany
Marie-Dominique Devignes & Dave Ritchie, Laboratoire Lorrain de Recherche en Informatique et ses Applications (Nancy), France

The mission of the LuciLinx network is to promote communication between bioinformaticians and biologists in Luxembourg and to increase the national and international visibility of bioinformatics research and applications in Luxembourg. More information about the symposium programme can be found on: www.lucilinx.lu Free registration by email only. Please send your name, title, institution and area of work to symposium@lucilinx.lu Due to limited seats, registration is mandatory and seats will attributed on a “first come, first serve” basis.

2nd Next Generation Sequencing Congress

Fri, 16 Jul 2010 11:35:00 +0200

Oxford Global Conferences present both the 2nd Annual Next Generation Sequencing (NGS)Congress, and the Analytical Genomics Congress which are to be held on the 15th & 16th November 2010 at the Radisson Edwardian, Heathrow in London. The congresses are to be held in conjunction with the 2nd Annual qPCR Congress.

Over the 2 days, the conferences will provides an overview of the current options of next-generation sequencing platforms, technologies, applications and the newest computational tools for the analysis of next-generation sequencing data and analytical genomics. An expert panel of 45 speakers will present a day full conference programme covering the following key topics including:

Next Generation Sequencing:

Next Generation Sequencing Technologies
Next Generation Sequencing Applications & Data Management

Analytical Genomics:

Genome Sequencing and Analysis
Next Generation Sequencing Systems and Techniques
Genomics Automation

For more information and registration please visit the websites mentioned below.

Topical Day on Bioinformatics: “From Base to Byte and back”

Fri, 01 Oct 2010 11:55:00 +0200

The MCB group of the Belgian Nuclear Research Centre SCK/CEN is organizing their Topical Day on Bioinformatics: “From Base to Byte and back” taking place at SCK-CEN in Mol on Friday 19 November 2010. Topical Days aim to bring new concepts and trends to the broad public and to foster new collaborations. “How can we mold the vast amount of diverse biological data in an accessible, interpretable way”, “Which tools do we need and what can we learn”, “How to visualize and dissect biological systems”, and “Can we redirect or even create Life”. These and other questions will be addressed by 9 internationally renowned speakers working and teaching at the foreground of Bioinformatics, Systems Biology, and Synthetic Biology. Register before 16 Oktober 2010 and enjoy a reduced registration fee. Further information on http://www.sckcen.be/nl/Evenementen/TD_BIOINFO/

CWA Conference November 2010

Tue, 25 May 2010 20:24:00 +0200

The first CWA annual conference will be held on the 22nd and 23rd of November 2010.

Conference "Connecting Biobanks"

Thu, 27 May 2010 14:10:00 +0200

Large-scale cooperation between biobanks has been successful on a global scale in the past two years. Collaboration between biobanks is essential for the future of biomedical science. For biobanks to be interoperable their content should be meaningfully linked. Biomedical and bioinformatics research groups in the Netherlands are joining forces with international partners to reach this goal. Plans and prototypic are the topics of the conference 'Connecting Biobanks'. The preliminary conference program includes:

Keynote presentations by renowned international speakers: Dr. David Cox (Pfizer), Josh Sommer (Chordoma Foundation), Prof. dr. Gert-Jan van Ommen (BBMRI-NL), Prof. dr. Kurt Zatloukal (BBRMI-EU), Prof. dr. Carole Goble (University of Manchester), Dr. Barend Mons (NBIC/CWA), Prof. dr. Paul Burton (University of Leicester)
Dedicated workshops addressing specific topics, such as data interoperability
BBMRI-NL’s official kick-off
A poster market, presenting BBMRI-NL projects aimed at enrichment and harmonization
Formal inauguration of the Global Concept Web Alliance and launch project
Presentation and demonstration of CWA partners’ developed technology and applications
Ample opportunity to interact with colleagues

The conference launches the Dutch BBRMI and is a joint effort of BBMRI-NL, CWA and NBIC. For registration and latest developments go to: www.bbmri.nl/conference2010 Conference venue: Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam.
Date: 22 November 2010 (from 9.30 till 16.00, followed by drinks). Organizing Committee

Prof. dr. Gert-Jan van Ommen, Leiden University Medical Centre
Prof. dr. Dorret Boomsma, VU University Amsterdam
Dr. Margreet Brandsma, BBRMI-NL
Prof. dr. Wouter Jukema, Leiden University Medical Centre
Dr. Olaf Klungel, University of Utrecht
Dr. Ruben Kok, NBIC
Dr. Barend Mons, Erasmus Medical Centre
Prof. dr. Dink Legemate, String of Pearls Initiative
Prof. dr. Cisca Wijmenga, University medical Centre Groningen

BBMRI-NL is the Dutch national biobanking initiative, linking over 140 existing Dutch biobanks. Within the 'hub and spoke' structure of the European Biobanking and Biomolecular Resources Research Infrastructure, BBMRI-NL is the Dutch national 'hub'. www.bbmri.nl CWA The Concept Web Alliance is a global collaborative community addressing the increasing problems associated with information overload and the interoperability of data. CWA aims to be an ‘organization of collaborating organizations’. NBIC The Netherlands Bioinformatics Centre is a collaborative institute of the bioinformatics groups in the Netherlands. Together, these groups perform cutting-edge research, develop novel tools and support platforms, create an e-science infrastructure and educate the next generations of bioinformaticians. NBIC is one of the initiators and founding sponsors of CWA.

Life Sciences Momentum 2010 - Global Connections

Tue, 07 Sep 2010 15:09:00 +0200

Life Sciences Momentum is the event of choice for discovering the latest developments in Dutch life sciences, the best place to meet colleagues and for forging new business. And this year promises to be a particularly special event, as it's the tenth anniversary of this top-level conference! Fundamentally, Momentum is about knowledge. Knowledge of the latest developments in science and technology. Of the state of affairs within relevant Dutch academia. Of emerging opportunities in business. and knowledge of the right people. Knowledge and networking in a single event. This year the focus will be on on a specific area of business - international business - and how to develop and capitalise on existing Global Connections. Registration is free of charge. The event is organised by the Netherlands Genomics Initiative. NBIC will be present at this meeting, as one of the technology centres of the Netherlands Genomics Initiative. For more information, visit the website mentioned below.

RSG-Netherlands site visit to Agendia for all PhD students

Thu, 18 Nov 2010 16:23:00 +0100

The Regional Student Group Netherlands presents its first company visit to an innovative genomics cancer diagnostics company: Agendia. Agendia uses its knowledge and expertise in the application of clinically useful gene expression profiling to facilitate breast cancer diagnosis. Agendia developed a FDA approved MammaPrint breast cancer test that is used to determine a patient’s risk of metastases. The company visit will consist of an introductory talk giving insight into the company and especially into the role of Bioinformatics at Agendia. Afterwards we will have a first hand look during a site visit, followed by a drink. Please send an email to rsg-netherlands@iscbsc.org to register.

RSG-Netherlands site visit to Agendia for all PhD students

Thu, 18 Nov 2010 16:23:00 +0100

Joint NETTAB 2010 and BBCC 2010 workshop

Wed, 13 Oct 2010 15:11:00 +0200

The joint NETTAB and BBCC 2010 workshop on "Biological Wikis"promises to be a great meeting for all researchers involved in the exploitation of wikis in biology. Come and discuss your ideas and doubts with such scientists as Alex Bateman, Alexander Pico, Andrew Su, Dan Bolser, Robert Hoffmann,Thomas Kelder, Mike Cariaso, Adam Godzik, Luca Toldo and many other who, we hope, will join the workshop. It's a great chance to follow smart tutorials and lectures on WikiPathways, WikiGenes, PDBWiki, Gene Wiki, TOPSAN, and a proficient use of Wikipedia and Semantic Wiki. See a list of keynote speakers and tutorials at http://www.nettab.org/2010/progr.html Registration is open at http://www.nettab.org/2010/rform.html The early registration deadline is set to October 29, 2010. A reduction of 20 euro applies to all fees for members of ISCB andother societies and networks.More reductions are foreseen for PhD students. Further information is availble at http://www.nettab.org/2010/

CWI-NISB Life Sciences seminar Dick de Ridder

Thu, 21 Oct 2010 00:00:00 +0200

The Life Sciences group at CWI organizes a weekly seminar in cooperation with the Netherlands Institute of Systems Biology (NISB). The seminar takes place in room L016 or L017 at CWI (new wing). The seminar is devoted to any aspects at the interface of mathematics or computer science and the life sciences. The seminar on December 3 will be presented by Dick de Ridder of the Delft University of Technology, more information can be found on: www.cwi.nl/en/node/2443

IEEE eScience Workshop on High-Performance Computing in the Life Sciences

Mon, 16 Aug 2010 13:00:00 +0200

The sixth IEEE e–Science conference, sponsored by the IEEE Computer Society´s Technical Committee for Scalable Computing (TCSC), will be held in Brisbane, Australia from 7th – 10th December 2010. The workshop: 'High-Performance Computing in the Life Sciences' will be held on December 7 and will be presented by: Prof Matthew Smith, Leibniz University of Hannover (smith@dsec.uni-hannover.de). Today, there are a variety of parallel and distributed high-performance computing platforms including multi-core architectures, GPGPUs/GPUs, clusters, grids, and clouds that, together with new programming paradigms such as MapReduce and Many Task Computing, offer a wide range of possibilities for solving compute- and data-intensive problems in an efficient manner. The purpose of this workshop is to provide the opportunity for participants to discuss and share the latest research in parallel and distributed high performance computing systems applied to problems in the Life Sciences, i.e. all fields of science that involve the scientific study of living organisms, such as biology, biochemistry, biophysics, botany, ecology, food science, medicine, medical imaging, neuroscience, pharmacology, physiology, systems biology, and zoology. Organizers:
Matthew Smith: Leibniz University of Hannover, Germany
Bernd Freisleben: University of Marburg, Germany
Thomas Friese: Siemens Healthcare, Erlangen, Germany

Important Dates:
Papers Submission Due: 15th of September 2010
Author Notifications: 7th of October 2010
Final manuscripts: 14th of October 2010
Presentation: 7th of December 2010

More information

Award Ceremony Designers & Artists Award Genomics 4 (DA4GA)

Tue, 30 Nov 2010 15:52:00 +0100

On December 8, 2010 the winners of the Designers & Artists Award Genomics 4 (DA4GA) will be presented by Robert Dijkgraaf. DA4GA is the contest where art, design and life sciences meet. DA4GA aims to promote Bio Art and make visible the significance and diversity of Genomics Research. Bio Art is an art practice in which the medium is living matter and the works of art are produced in laboratories and/or artists’ studios. Designers and artists have collaborated with various Genomics Centres to develop in total nine project proposals rated by a prominent jury from the arts, design and sciences: Robbert Dijkgraaf, Francine Houben, Geert Verbeke, Hub Zwart and Paul Voogt. Three winning proposals will be awarded with € 25,000, to be spend on its realization. The results will be exhibited at Naturalis in 2011. Hienke Sminia (NBIC, bioinformatics@school) together with the artists Bas Kools and Gunter Wehmeyer are participating in this contest on behalf of NBIC. Admission free, registration required via: da4ga@waag.org DA4GA is made possible by the Netherlands Genomics Initiative, Centre for Society and Genomics and Waag Society.

CWI-NISB Life Sciences seminar Erik van Dijk

Thu, 21 Oct 2010 00:00:00 +0200

The Life Sciences group at CWI organizes a weekly seminar in cooperation with the Netherlands Institute of Systems Biology (NISB). The seminar takes place in room L016 or L017 at CWI (new wing). The seminar is devoted to any aspects at the interface of mathematics or computer science and the life sciences. The seminar on December 10 will be presented by Erik van Dijk, as part of his internship. Title: Modeling tip cell selection during angiogenesis using Petri Nets and the Cellular Potts. More information can be found on: www.cwi.nl/en/node/2443

CWI-NISB Life Sciences seminar Séverine Urdy

Thu, 21 Oct 2010 00:00:00 +0200

The Life Sciences group at CWI organizes a weekly seminar in cooperation with the Netherlands Institute of Systems Biology (NISB). The seminar takes place in room L016 or L017 at CWI (new wing). The seminar is devoted to any aspects at the interface of mathematics or computer science and the life sciences. The seminar on December 17 will be presented by Séverine Urdy of the paläontologisches Institut und Museum der Universität Zurich, CH. Title: Computational models of shell growth: the next step? More information can be found on: www.cwi.nl/en/node/2443

NPC Progress Meeting 2011

Thu, 18 Nov 2010 15:36:00 +0100

The Netherlands Proteomics Centre (NPC) is organising its yearly NPC Progress Meeting on January 13^th 2011 in Mediaplaza in Utrecht.

Link with NBIC

Theme meetings
In the morning several NPC theme leaders will organise a theme meeting. NPC project members will receive an invitation from their theme leader for this session. Plenary session
All interested people are invited to attend the plenary session in the afternoon. The plenary session will be particularly special, because four outstanding international scientists are invited:

Anne-Claude Gingras, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada
Lukas Käll, Center for Biomembrane Research, Stockholms Universitet, Sweden (Machine learning techniques to assess confidence and increase yield for shotgun proteomics)
Roland Annan, Proteomics and Biological Mass Spectrometry Laboratory, GlaxoSmithKline (Biological Variability: A Cardiac Proteome Study in the SILAC Mouse)
Matthias Mann, Max Planck Institute of Biochemistry, Martinsried, Germany (High resolution, quantitative mass spectrometry: a toolbox for biomedical research)

Win €1000 travel grant
PhD students and postdocs are invited to present a poster. NPC project groups are expected to present at least one poster. The NPC will award the three best posters with a travel grant of €1000. The travel grant can be used for a journey abroad to attend a conference or summer school which is immediately related to the research. Poster titles should be submitted no later than 7 January 2011 via the website of the NPC. For more information, online registration and poster submission, please go to: www.netherlandsproteomicscentre.nl Attendance is free, but registration is required. In case you have any further questions, please contact the NPC office at progressmeeting@npc.genomics.nl or +31 (0)30 253 4564.

International Seminar: Molecular Networks in Cancer and Innate Immunity

Mon, 24 Jan 2011 19:50:00 +0100

Seminar by Ilya Smulevich (Institute of Systems Biology, Seattle, Washington, USA). He will discuss integrative methods in systems biology aimed at understanding cellular function and dysfunction through the study of the structure and dynamics of biomolecular networks in cells. In the study of the innate immune system, he will discuss the efforts in combining expression level time course data, epigenomic data sets measured by ChIPseq, computational prediction of transcription factorbinding sites, and other information, to infer and model transcriptional regulatory networks governing the innate immune response. In the case of The Cancer Genome Atlas (TCGA), he will discuss approaches to integrate multiple types of data, including genomic sequencing of tumor and germline DNA, genome wide DNA methylation, gene and microRNA expression with RNAseq, and copy number data. Strong statistical relationships among the multitude of features in these collective data sets can be used to study particular aspects of the disease including clinical outcomes involving tumor grade,metastasis, cell of origin, or clinical subtype.

Kickoff meeting: Cancer Systems Biology

Tue, 16 Nov 2010 15:24:00 +0100

On February 4, 2011, 3 NWO Systems Biology Centres will be organising a kickoff symposium on Cancer Systems Biology in collaboration with The Netherlands Consortium for Systems Biology. The NWO Centers involved are:

Cancer Systems Biology Center, NKI-AVL, Amsterdam
Center for Systems Biology and Bioenergetics, Radboud University, Nijmegen
The Systems Biology Centre for Metabolism and Ageing, University of Groningen

Registration is required before 10 December 2010. Attendance is free of charge. The number of available seats is limited, so register early! For more information, please find a pdf-file with the program below or visit the website mentioned below.

PCDI postdoc Retreat 2011

Wed, 01 Dec 2010 10:44:00 +0100

The PCDI Postdoc Retreat is a 3-day course, specifically targeting early career researchers in the Life Sciences focused on personal, professional and career development.

No matter how talented or passionate you are about science, positions in academia are scarce and only 1 out of 10 PhDs will eventually make it to a principle investigator. At the PCDI Postdoc Retreat you will hear what alternatives you have. And whether you choose for a career within academia or somewhere else, at the retreat you will find out what you can do to increase your chances to succeed. You will see that it involves more than your publication record and winning grants alone!

Together with 80 - 100 other postdocs and final year PhD students, you will discover what your career options are, what is important to you as regard to choosing your career and how to take charge of your future. Next to inspiring keynote lectures by successful PhDs in Life Sciences who followed different career paths, you will attend 3 training workshops to:

Discover your talents
Better present yourself
Enhance your transferable skills

Free participation for 25 NGI postdocs/PhD students http://www.pcdi.nl/postdoc-retreat-2011/retreat-2011-funding-registration.html For more information, please visit the website mentioned below.

FEBS-SystemsX-SysBio2011: From Molecules To Function

Fri, 17 Dec 2010 10:24:00 +0100

Systems Biology is one of the most prominent newly emerging interdisciplinary science areas. By connecting fields such as genomics, proteomics, cell biology, medicine, molecular biology, biochemistry and genetics, with mathematics, bioinformatics, engineering and computation, it enables discovery of yet unknown principles underlying the functioning of living cells. At the same time testable and predictive models of complex cellular pathways and eventually of whole cells are generated, which are useful for efficient experimental design and bioengineering and the network-based design of drugs and therapies. FEBS-SystemsX-SysBio2011 will cover essential and state-of-the-art aspects of SysBio from principles and methods through the modeling of living systems to applications in biotechnology and medicine. Many leading experts will participate as lecturers, tutors, black-board teachers and informal poster discussants, which will make FEBSX-SysBio2011an outstanding lecture course with an exquisite scientific program. It will open the doors for regular student training in Systems Biology in Europe, provide a basis for a human network of young Systems Biology experts, and provide a centre for other Systems Biology discussions between scientists and funders. Organizing Institutions: FEBS: The Federation of European Biochemical Societies is one of the largest organizations in European life sciences, with nearly 40.000 members distributed among 36 Constituent Societies and 7 Associated Member Societies in 43 countries. FEBS seeks to promote, encourage and support biochemistry, molecular cell biology and molecular biophysics throughout Europe in a variety of ways. SystemX.ch: The Swiss Initiative in Systems Biology is currently the biggest research initiative underway in Switzerland with the mandate to promote Systems Biology. It is a consortium with nine universities and three research institutions as partners. The Swiss National Science Foundation (SNSF) supervises and safeguards the quality of the research and the initiative as a whole.

TBI 2011: The Joint Summits on Translational Science (TBI & CRI)

Mon, 28 Jun 2010 09:45:00 +0200

AMIA is organising the 2011 Summit on Translational Bioinformatics (TBI). The TBI Summit will be part of the Joint Summits on Translational Science. Immediately following the TBI Summit, the Summit on Clinical Research Informatics (CRI) will take place at the same venue (March 9th-11th, 2011).

As in previous years, the Summit on Translational Bioinformatics will aim to highlight the trans-disciplinary nature of this now-burgeoning research field and provide a unique opportunity to bring together the finest minds in translational bioinformatics from the academia, industry, government and non-profit sectors. For more information about the summit and for registration and paper submission, please visit the conference website.

2011 Summit on Translational Bioinformatics (TBI)

Thu, 18 Nov 2010 15:22:00 +0100

The TBI Summit will be held on March 7th-9th, 2011, in San Francisco, California as part of the Joint Summits on Translational Science. Since 2008, the Summit has been recognized as a key venue for the exchange of ideas in translational bioinformatics. As in previous years, the Summit on Translational Bioinformatics will aim to highlight the trans-disciplinary nature of this research field and provide a unique opportunity to bring together the finest minds in translational bioinformatics from the academia, industry, government and non-profit sectors. The four tracks this year are focused on methodological innovations from bench to bedside, with a particular emphasis on clinical implications based on the latest in molecular and cellular biology innovations:

Concepts, Tools and Techniques to Enable Integrative Translational Bioinformatics
Integrative Analysis of Molecular and Clinical Measurements
Representing and Relating Phenotypes and Disease for Translational Bioinformatics
Bridging Basic Science Discoveries and Clinical Practice

Reflecting on the position of translational bioinformatics in medical research and ultimately in clinical care, the 2011 Scientific Program Committee and Advisory Committee strives to design a comprehensive scientific program with a complementary set of tutorials, lectures, panels, and posters that are designed to feature the latest innovative deployment and translation of biomedical informatics research products to biomedical research and clinical care.

Landelijke Reizende DNA-Lab Dag

Wed, 02 Mar 2011 13:28:00 +0100

High school teachers are invited for the DNA-Lab On The Road meeting on March 11. NBIC organizes workshops during this day. Below, you can find more information in Dutch. Vrijdag 11 maart 2011 vindt de tweede landelijke DNA-lab dag plaats in Hogeschool Domstad, Utrecht. De DNA-LAB DAG is een landelijke conferentie voor docenten en TOA’s over genomics, en over de Reizende DNA-labs in het bijzonder. Er zijn nog enkele plaatsen over. U kunt zich nog inschrijven. U hoort dan zo snel mogelijk of u terecht kunt. Schrijf u nu in! Deelname aan de dag kost 90 euro. Het programma duurt van 9.00u - 16.00u. Wat kunt u verwachten?

Evolutiebioloog Prof. Dr. Bas Zwaan vertelt over interacties tussen genetica en omgeving;
Dr. Marie-José Goumans, lid van De Jonge Akademie, spreekt over haar onderzoek naar het gebruik van stamcellen bij regeneratieve therapie voor het hart;
workshops met direct-in-de-klas-toepasbare ideeën en materialen;
workshops van de Reizende DNA-labs zelf.

Symposium: Bioinformatics for Metabolomics and Fluxomics

Thu, 27 Jan 2011 10:11:00 +0100

On March 11, 2011 a small symposium is organized at the VU University Amsterdam. Program: 9.00-9.30h: Predicting metabolic functions of Creatine Kinase: a multiscale "sloppy" modeling approach
Hannes Hetling, M.Sc., Ph.D. student Bioinformatics, Centre for Integrative Bioinformatics, VU University Amsterdam. 9.30-10.00h: Metabolomics studies for identification of drug induced side effects in rheumatoid arthritis
Wynand Alkema, Dr., Head of Bioinformatics EU, Merck Sharpe & Dohme. 10.00-10.30h: Burning fat - understanding the role of PPAR-delta in regulating systemic metabolism
Jules Griffin, Dr., Senior Lecturer in Biochemistry, University of Cambridge. 10.30-10.45h: Coffee break 10.45-11.15h: TBA
Thomas Hankemeier, Prof. Dr., Professor of Analytical Bioscience, University of Leiden, Scientific Director Netherlands Metabolomics Centre. 11.15-11.45h: Isotopic analysis of cellular glutamine metabolism: linking fluxes and enzymatic reactions
Joanne Kelleher, Prof. Dr., Emeritus Professor of Physiology, George Washington University School of Medicine and Health Sciences. Research Scientist / Lecturer, Department of Chemical Engineering, Massachusetts Institute of Technology. Associate Physiologist, Massachusetts General Hospital. This symposium is coupled to the PhD Defense of Thomas Binsl: Title of the thesis:
Fluxes of Life - Bioinformatics for Metabolic Flux Quantification in Isotopic Non-Steady-State Date and location:
March 11, 2011, Aula of the VU University Amsterdam, 13.45h Abstract:
Life is a continuous process and constantly asking for the right adjustments that ensure the survival of a life form under changing environmental conditions. A very suitable reflection of such dynamic changes can be found in the way of how food is broken down and transformed into energy. This is commonly known as metabolism and present in all living organism.
Although much is known about the interconnections of the breakdown products, there is a huge lack of knowledge with respect to metabolic fluxes, which describe the dynamic transformation of one breakdown product into another. This absence is a huge obstacle for modeling and understanding metabolism in humans, animals and microorganisms. Hence, this thesis is devoted to fluxomics, the study of metabolic fluxes. Fluxomics studies are quite complex and suffer from several bottlenecks such as non-intuitive mathematical models or difficult experimental situations. To address some of these impediments this thesis introduces multiple computer programs for the simulation and quantification of metabolic fluxes. The computer programs make it possible to investigate metabolism under a range of different conditions and were used to study the metabolism of the heart and gut.
The new insights achieved in the studies provide a potential basis for the development and testing of new drug candidates against Ischemic Heart Disease, which is the leading cause of death in the western world. In addition, they facilitate to achieve more control over our gut and may finally help to develop personalized nutrition to optimize digestion and health.

BioCafé RSG Netherlands: 'Scientific Poster Design'

Wed, 23 Feb 2011 09:49:00 +0100

The RSG Netherlands invites you to their BioCafé on March 14th, 16:00 in Utrecht. Subject: "Scientific Poster design" Do you want to know what it takes to make a good poster? Going for the poster-prize at upcoming conferences? hear the do's and don'ts at the next BioCafé. Marco Mok from DM Creative Communicatie will show us how to design an attractive scientific poster while paying attention to fonts, colours and images. Bring your own poster. At the end of the meeting there will be a discussion about each others work. Registration for this event is required, so please send an e-mail with your name, institute and whether you want to eat dinner with us after the the BioCafé. Where: Poort van Kleef (second floor of Café Carré), Mariaplaats, Utrecht This BioCafé is sponsored by Celgene. The RSG is supported by NBIC.

BioCafé RSG Netherlands: 'Scientific Poster Design'

Wed, 23 Feb 2011 09:49:00 +0100

Conference on Integrative Bioinformatics (IB2011)

Thu, 04 Nov 2010 12:52:00 +0100

The 2011International Symposium on Integrative Bioinformatics (IB2011) will take place from 21 to 23 of March, 2011 in Wageningen (the Netherlands). This seventh meeting on Integrative Bioinformatics will be of interest to bioinformaticians, computer scientists and all working in, or interested in the developing area of integrative bioinformatics. There will be opportunities to present and discuss methods, theoretical approaches, and their practical applications.

You are invited to register for the conference, and to send in an abstract for a presentation for the conference. Accepted abstracts will be invited for a presentation at the conference, and will also be invited to send in a full manuscript, to be published (after peer reviewing) in the Special IB2011 Issue of the Journal of Integrative Bioinformatics. The deadline for sending in an extended abstract was January 15th but has been extended with one week; submissions should not exceed 4 pages. Authors will be informed of acceptance before February 1st. There are also opportunities for presenting posters and software demonstrations at the Symposium. The deadline for sending in abstracts for posters or a software demo is February 15th, 2011.

The conference website is open for registration and abstract submission now, and can be found at www.bioinformatics.nl/ib2011/.

IB2011 is organized by Wageningen University, the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben and IMBio e.V.

Conference: Enabling Systems Biology: registrations now open!

Thu, 01 Jan 1970 01:00:00 +0100

The conference "Enabling Systems Biology" is a one-off conference focusing on the interface between computational approaches in systems biology with experimental techniques. A world-leading set of invited speakers will be talking, and there will be a number of talks drawn from the set of submitted abstracts. Registration deadline is March 1st 2011.

More information can be found at: http://www.enfin.org/page.php?page=esb

Confirmed Speakers are:

Ewan Birney (EBI, Cambridge, UK)
Christine Orengo (UCL, London)
James Adjaye (MPI, Berlin)
Giulio Superti-Furga (CMM, Vienna)
Geoff Barton (U. Dundee, Dundee)
Michael Boutros (DKFZ, Heidelberg)
Martha Bulyk (Harvard Medical School, Cambridge, US)
Gianni Cesareni (U. Tor Vergata, Rome)
Bertie Goettgens (CIMR, Cambridge, UK)
John Hancock (MRC Harwell, UK)
Jean-Karim Heriche (EMBL, Heidelberg)
Jaap Heringa (VU, Netherlands)
Henning Hermjakob (EBI, Cambridge, UK)
Edda Klipp (Humboldt University, Berlin)
Xuedong Liu (U Colorado, Boulder)
Tomi Makela (U Helsinki, Finland)
Aristidis Moustakas (Ludwig Institute, Uppsala)
Stuart Newfeld (Tempe, Arizon)
Erich Nigg (BioZentrum, Zurich)
Christos Ouzounis (Institute of Agrobiotechnology, Thessaloniki)
Bernhard Palsson (UCSD, San Diego)
Dietmar Schomburg (Technical University Braunschweig)
Eran Segal (Weizmann Institute, Jerusalem)
Peter Sorger (Harvard, Cambridge, US)
Alfonso Valencia (CNIO, Madrid)
Jaak Vilo (Quretec, Tartu)
Hans Westerhoff (University of Manchester, Manchester)
Ioannis Xenarios (SIB, Geneva)

The Enabling Systems Biology conference is organized by the European Network of Excellence ENFIN, which develops infrastructure for data integration, bioinformatics tools and assessment to enhance Systems Biology in Europe.

Conference: Comparative and Regulatory Genomics in Plants

Wed, 30 Mar 2011 14:59:00 +0200

Friendly reminder: the registration deadline is March 31st 2011. Full programme is available at http://bioinformatics.psb.ugent.be/crg_event/conference/programme The first international Conference on Comparative and Regulatory Genomics in Plants will be held at VIB - Ghent University, Belgium April 11-12, 2011. This conference will give an overview of the most recent developments in plant genomics and will discuss the integration of experimental high-throughput data with computational approaches to study gene functions, genome organization and transcriptional regulation. A panel of international invited speakers includes experts in the field of plant next-gen genome sequencing, genome evolution, comparative transcriptomics, ChIP profiling and plant regulatory networks. More information including invited + contributed speakers is available here: http://bioinformatics.psb.ugent.be/crg_event/conference/about

NBIC BioAssist Hackathon - April 2011

Mon, 14 Mar 2011 12:59:00 +0100

All BioAssist developers and developers involved in BioAssists task forces are invited to come to the BioAssist hackathon. It will be held April 13th and 14th in Voerstreek, Belgium. There are several interesting projects proposed and the participants will be encouraged to work with Agile development methods. The hackathon offers the chance to get familiar with some of the ongoing BIoAssist projects and can introduce Agile team development methods to developers who may normally work individually. For more information: https://wiki.nbic.nl/index.php/NBIC_Hackathon_April_2011

ISNB 2011: The 8th International Symposium on Networks in Bioinformatics

Fri, 25 Feb 2011 10:20:00 +0100

The 8th International Symposium on Networks in Bioinformatics (ISNB 2011) is scheduled on 14 and 15 April 2011 and is likely to continue its success from previous years in bringing different disciplines together to discuss ongoing research in bioinformatics and biology of networks. The focus of 8th International Symposium on Networks in Bioinformatics will be on biological networks such as metabolic networks, signal transduction pathways and genetic regulatory networks. This year we also aim to include topics like modeling of cells, tissues, gene regulation, from DNA to transcriptional behaviour and biomineralisation. We also want to invite researchers working on gene networks in plants (e.g. Arabidopsis), model organisms such as Drosophila and organisms with a relatively simple and basal body plan such as sponges and scleractinian corals. Understanding of these networks is crucial for understanding molecular and cellular processes in the organism or system under study. This field is subject of lively research and both experimental and computational approaches are used to elucidate the biological networks. The bioinformatics of biological networks involves a broad range of research and approaches. Research includes the identification of regulatory elements in DNA, developmental biology, genome context analysis, modelling and simulation of pathways, reconstruction of pathways from experimental data, visualization of pathways, and the representation of pathways in database, graphs and mark-up languages. Details about registration are available on http://isnb.amc.uva.nl/isnb2011/

Genome Imputation meeting

Thu, 31 Mar 2011 16:09:00 +0200

On April 14th the biobanking taskforce organises together with VU Amsterdam an Imputation day. During this day we will discuss several imputation pipelines used by VU, EMC and UMCG based on different software (Beagle, MACH, IMPUTE). The goal is to create a better understanding of the strength and weaknesses of the different pipelines and discuss collaboration in improving imputation pipelines within the Biobanking Taskforce. This day will also be the kickoff for the work on the imputation pipeline for the BBMRI Genome of the Netherlands project.

Sage Bionetworks Commons Congress Webcast

Mon, 11 Apr 2011 09:32:00 +0200

Join the online webcast webcast of the 2011 Sage Bionetworks Commons Congress on April 15^th&16^th. The free webcast will feature international thought leaders in research, industry, policy, patient advocacy, foundations and government charting a disruptive course forward on human data management and public engagement in biomedical research. More information at www.sagecongress.org

Date: April 15-16, 2011 beginning at 8:00 AM PDT
Webcast URL: http://bit.ly/htNpUR
Congress Agenda: http://sagecongress.org/WP/2011agenda The second Sage Bionetworks Commons Congress will be held in San Francisco on April 15-16, 2011. The theme will be the move towards personalized, patient-driven medicine, and the role that Sage Bionetworks can play in that transition. Expect reports from the Sage Federation, Working Groups, and exciting projects like SageCite, poster sessions and evening activities. The agenda is available on the linked web page and will be updated as the program is confirmed.

NBIC Conference 2011

Tue, 07 Sep 2010 14:45:00 +0200

Register for the: NBIC Conference 2011 on April 19 & 20 in Lunteren, the Netherlands! More information about the conference, a conference website and a registration form is available on the conference website: http://conference.nbic.nl. An impression of the NBIC Conference 2010 can be found here. NBIC Office: Femke Francissen
tel.: +31 (0)24 3619500
e-mail: office@nbic.nl

IOP Genomics Symposium 'Food for thought and Health'

Fri, 14 Jan 2011 14:30:00 +0100

On April 27 at 13 hrs. an IOP Genomics Symposium ‘Food for thought and Health’ is organized at the Grand Hotel Karel V, Utrecht. The symposium shows highlights of a number of IOP Genomics projects and potential value of the results for society and industry. The programme comprises the following topics:

A screening platform to understand energy metabolism;
Antibodies to combat neurological and neuromuscular diseases;
Biomarkers of ageing: why some people live longer than others;
Creating healthier food using nutrigenomics;
Inflammation in obesity-induced type 2 diabetes: new diagnostic markers and interventional targets.

A detailed programme will follow. Registration: Attendance is free of charge, but since participation is limited, registration is necessary. Save the date and register by sending an e-mail to iopinfo@agentschapnl.nl More information? Contact the IOP Genomics Programme Office: Tonnie Rijkers and Annelies van Ravestijn, by phone 088-6025496 or e-mail: iopinfo@agentschapnl.nl

Spring Meeting of the VOC "Robust Methods"

Wed, 04 May 2011 09:48:00 +0200

The Dutch/Flemish Classification Society (called VOC: http://www.voc.ac) organizes two scientific meetings per year. The 2011 Spring Meeting will be held on Friday May 13 in the centre of Antwerp and is on "Robust Methods". Keynote speakers are Stefan Van Aelst (Ghent University) and Marco Riani (Parma University). Those who would like to participate are welcome and are kindly requested to register by sending an e-mail to meeting@voc.ac with subject ‘Registration Spring Meeting 2011’ and including name and affiliation in the body of the e-mail. Participation is free, lunch is available for 10 Euros and must be requested upon registration. Registration deadline: May 10th.

We hope to welcome you in Antwerp.

2011 Galaxy Community Conference

Fri, 04 Feb 2011 13:33:00 +0100

We are pleased to announce the 2011 Galaxy Community Conference, being held May 25-26 in Lunteren, The Netherlands. This year the conference is co-organized by the Netherlands Bioinformatics Centre (NBIC). The meeting will feature two full days of presentations and discussion on extending Galaxy to use new tools and data sources, deploying Galaxy at your organization, and best practices for using Galaxy to further your own and your community's research. Overview
This event aims to engage a broader community of developers, data producers, tool creators, and core facility and other research hub staff to become an active part of the Galaxy community. We'll cover defining resources in the Galaxy framework, increasing their visibility and making them easier to use and integrate with other resources, how to extend Galaxy to use custom data sources and custom tools, and best practices for using Galaxy in your organization.

Additional topics include, but are not limited to:

Talks submitted by the Galaxy community
Integration of tools (including NGS analysis tools) and distributed job management
Deployment of Galaxy instances on local resources and on the Cloud
Management of large datasets with the Galaxy Library System
Using the Galaxy LIMS functionality at NGS sequencing facilities
Visualizing Data without leaving Galaxy
Performing reproducible research
Performing and sharing complex analyses with Workflows
An "Introduction to Galaxy" session, offered on May 24, for Galaxy newcomers

Registration
The conference fee is €100 on or before April 24, and €120 after that. The meeting is being held at the Conference Centre De Werelt in Lunteren, The Netherlands, which is also the conference hotel. You are encouraged to register early, as space at the hotel (and at the "Intro to Galaxy" session) is limited and is likely to fill up before the conference itself does. Go to the registration page.

Abstract submission
Abstracts are now being accepted for short oral presentations. Proposals on any topic of interest to the Galaxy community are welcome and encouraged. The abstract submission deadline is the end of February 28. More information about the abstract submission.

Sponsors
The 2011 Galaxy Community Conference is co-sponsored by the US National Science Foundation (NSF), and the Netherlands Bioinformatics Centre (NBIC). About Galaxy
Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biomedical research. Accessibility: Galaxy enables users without programming experience to easily specify parameters and run tools and workflows.
Reproducibility: Galaxy captures all information necessary so that any user can repeat and understand a complete computational analysis.
Transparency: Galaxy enables users to share and publish analyses via the web and create Pages--interactive, web-based documents that describe a complete analysis. Galaxy is open source for all organizations. The public Galaxy service (http://usegalaxy.org) makes analysis tools, genomic data, tutorial demonstrations, persistent workspaces, and publication services available to any scientist that has access to the Internet. Local Galaxy servers can be set up by downloading the Galaxy application and customizing it to meet particular needs. We are looking forward to a great conference and hope to see you in Lunteren!

The Galaxy and NBIC Teams

Workshop 'Toward Systems Biology'

Mon, 09 May 2011 11:24:00 +0200

Recent advances in experimental techniques for molecular cell biology have provided a wealth of information concerning numerous low-level mechanisms that participate in the life of a cell. It is, however, commonly recognized that in order to make use of this information and build models having predictive power for more complex systems, biological models should be elevated from the verbal and quasi-formal levels of description in which they are formulated today, and become closer to the standards of "harder" scientific and engineering disciplines. Of course, such an upgrading of modeling standards should involve conceptual innovations to deal with the specifics of biological systems in terms of complexity and experimental limitations. The goal of the workshop is to bring together potential participants in this systems biology endeavor, that is system-aware biologists together with researchers in domains that may provide a source of inspiration to this evolving field, most notably engineering disciplines like computer science, electronics and control as well as physics and applied mathematics. For more information, visit: www-tsb-workshop.imag.fr

ICCS 2011

Wed, 01 Dec 2010 11:07:00 +0100

The International Conference on Computational Science aims to bring together annually researchers and scientists from mathematics and computer science as basic computing disciplines, researchers from various application areas who are pioneering advanced application of computational methods to sciences such as physics, chemistry, life sciences, and engineering, arts and humanitarian fields, along with software developers and vendors, to discuss problems and solutions in the area, to identify new issues, and to shape future directions for research, as well as to help industrial users apply various advanced computational techniques.

The theme for ICCS 2011 in Tsukuba is "The Ascent of Computational Excellence in the Land of the Rising Sun", to mark the continued progress in computational science theory and practice, leading to greatly improved applications in science. This conference will be a unique event focusing on recent developments in methods and modelling of complex systems for diverse areas of science, scalable scientific algorithms, advanced software tools, computational grids, advanced numerical methods, and novel application areas where the above novel models, algorithms and tools can be efficiently applied such as physical systems, computational and systems biology, environmental systems, finance, and others.

9th International Conference on Chemical Structures (ICCS)

Mon, 17 Jan 2011 11:44:00 +0100

The International Conference on Chemical Structures brings together an international audience interested in handling chemical structures and related topics. Participants discuss research and development in the processing, storage, retrieval and use of chemical structures. The conference fosters cooperation among organizations and researchers involved in the merging fields of cheminformatics and bioinformatics and has a reputation of providing in-depth technical presentations with ample opportunities for one-on-one discussions with the presenters. Scientific Program
The 9th International Conference on Chemical Structures (ICCS) is seeking presentations of novel research and emerging technologies for the following plenary sessions:

Cheminformatics
Structure-Activity and Structure-Property Prediction
Structure-Based Drug Design and Virtual Screening
Analysis of Large Chemistry Spaces
Integrated Chemical Information
Dealing with Biological Complexity

For more detailed information about the program and abstract submission please visit the conference website. The deadline for the submission of abstracts is 31 January 2011. The nineth in the series of these respected triennial conferences will be held from 5-9 June, 2011 at the beautiful Conference Center in Noordwijkerhout, The Netherlands. The conference is jointly organized by:

Division of Chemical Information of the American Chemical Society (CINF)
Chemical Structure Association Trust (CSA Trust)
Division of Chemical Information and Computer Science of the Chemical Society of Japan (CSJ)
Chemistry-Information-Computer Division of the German Chemical Society (GDCh)
Royal Netherlands Chemical Society (KNCV)
Chemical Information and Computer Applications Group of the Royal Society of Chemistry (RSC)
Swiss Chemical Society (SCS)

The conference will start with a keynote address on Sunday afternoon followed by a traditional Rijsttafel dinner. Six plenary sessions and a poster session are planned during the remaining 3.5 days of the conference.

Workshop on Dynamic Distributed Data-Intensive Applications, Programming Abstractions, and Systems (3DAPAS)

Mon, 17 Jan 2011 09:43:00 +0100

To be held in conjunction with HPDC-2011. Part of the: 2nd International Emerging Computational Methods for the Life Sciences Workshop. There has been a lot of effort in managing and distributing tasks where computational loads are dominant. Such applications have after all, been historically the drivers of "grid" computing. There has, however, been relatively less effort on tasks where the computational load is matched by the data load, or even dominated by the data load. For such tasks to be able to operate at scale, there are conceptually simple run-time trade-offs that need to be made, such as determining whether to move data to compute versus keeping data localized and move computational tasks to operate on the data in situ, or possibly neither, and with data regenerated on-the-fly. Due to fluctuating resource availability and capabilities, as well as insufficient prior information about application requirements, such decisions must be made at run-time. Furthermore, resource, connectivity and/or storage constraints may require the data to be manipulated in-transit so that it is “made-right” for the consumer. Currently it is very difficult to implement these dynamic decisions or the underlying mechanisms in a general-purpose and scalable fashion. Although the increasing volumes and complexity of data will make many problems data load dominated, the computational requirements will still be high. In practice, data-intensive applications will encompass data-driven applications. For example, many data-driven applications will involve computational activities triggered as a consequence of independently created data; thus it is imperative for an application to be able to respond to unplanned changes in data load or content. Therefore, understanding how to support dynamic computations is a fundamental, but currently missing element in data-intensive computing. This workshop will operate at the triple point of dynamic, distributed and data-intensive (3D) attributes. It will also focus on innovative approaches for scalability in the end-to-end real-time processing of scientific data. We refer to 3D applications as those are data-intensive, need to support and respond to dynamic data, and, either are fundamentally, or need to be, distributed. We are interested in papers that span the spectrum from the design of cyberinfrastructure to support 3D applications, to novel application examples. We are also looking to bring researchers together to look at holistic, rather than piecewise, approaches to the end-to-end processing and managing of scientific data. 3DAPAS builds upon a 3 year research theme on Distributed Programming Abstractions (DPA), which has held a series of related workshops including but not limited to e-Science2008, EuroPar 2008 and the CLADE series. 3DAPAS will also draw on ideas from the ongoing 3DPAS Research Theme funded by the NSF and UK EPSRC. Submission deadline: February 15, 2011 http://sites.google.com/site/3dapas/

IWSG-Life 2011 (3rd International Workshop on Science Gateways for Life Sciences)

Wed, 16 Feb 2011 12:38:00 +0100

IWSG-Life’11 will bring together scientists from the field of life sciences, bioinformatics and computer science. The aim is to exchange experience, formulate ideas and introduce up-to-date technological advances in molecular and systems biology in the context of Science Gateways. We invite the submission of papers related to various aspects of molecular and systems biology and Science Gateways/Portals. For more information, visit: http://www.cpc.wmin.ac.uk/iwsg2011 Call for papers: There are three alternatives for researchers to present their work: talks, lightning talks, and demonstration sessions. Submission of a full paper may result in a talk, submission of an abstract may result in an lightning talk or a demonstration. Authors of best papers will be invited to submit a significantly extended and updated version of their paper into the Journal of Grid Computing for a Special Issue on Science Gateways. For more information, visit: https://sites.google.com/a/staff.westminster.ac.uk/iwsg-life2011/call-for-papers

Teacher Training Bioinformatics@school (kopie 1)

Thu, 12 May 2011 14:27:00 +0200

Since the first training was a succes, Bioinformatics@school will organize her second teacher training for high school teachers. This training will take place on the 8th of July in Groningen. More information will follow in Dutch: Ontwerp je eigen bioinformatica-opdracht!
Nascholing bioinformatica in de klas, woensdag 8 juni 2011, Groningen

Maak een stamboom
Vind genen in de databank
Bekijk een eiwit

WAAROM?
Of het nu over ecologie, evolutie of celbiologie gaat; elke tak van biologisch onderzoek maakt tegenwoordig gebruik van genetische databanken en programma’s om genen en eiwitten te vergelijken en weer te geven. Die databanken en programma’s zijn in het onderwijs goed te benutten! VOOR WIE?
Biologiedocenten die lesgeven in het voortgezet onderwijs aan de bovenbouw havo en vwo, en hun onderwijs willen verbeteren ten aanzien van de moleculaire onderwerpen DNA en eiwitten.
Een bijzonder kenmerk van deze nascholing is dat we ook expliciet leerlingen uitnodigen. Zo maken ook zij kennis met technieken die ze in life sciences zullen tegenkomen, en kunnen samen met docenten meedenken over lesmateriaal. HOE?
Voor leerlingen is de dag gratis, aan docenten vragen we €25,-. Dit is inclusief lunch, hapjes, drankjes en lesmateriaal. PROGRAMMA
09:30 Inloop met koffie en thee
09:45 Welkomstwoord
10:00 Lezing met opdrachten van een Groningse bioinformaticus, Dr. M. Noback
11:00 Pauze
11:10 Lezing met opdrachten van Hienke Sminia over bioinformatica als didactisch hulpmiddel
12:15 Lunch
13:15 Zelf een opdracht maken - met ondersteuning van NaviGene kunt u zelf aan de slag met programma’s en databanken.
14:45 Pauze
15:00 Vervolg: Zelf een opdracht maken
15:30 Afsluiting
16:30 Hapjes en drankjes Ook na deze dag gaat de nascholing door. U kunt contact houden met de organisatoren en de andere docenten om uw materiaal te optimaliseren en uit te wisselen. INSCHRIJVEN?
Meer informatie over de training en inschrijven kan via hienke.sminia@nbic.nl THUIS UITPROBEREN?
Zoek uit op welk chromosoom het gen voor amylase ligt en of dit om één of meerdere genen gaat.

Open http://www.ncbi.nlm.nih.gov/genome/guide
Dit is een overzicht van organismen waarvan het genoom bekend is. Klik op de regel naast ‘human’ op de M (map viewer).
Je ziet een overzicht van chromosomen. Vul linksboven ‘amylase’ in en klik op 'Find'.

Deze nascholing wordt u aangeboden door Bioinformaticaindeklas (www.nbic.nl) en Hanzehogeschool Groningen.

Opening Designers & Artists 4 Genomics

Mon, 23 May 2011 10:26:00 +0200

The official opening of the exhibition of the projects of the winners of the Designers & Artists Award Genomics 4 (DA4GA) will be on June 16, in Naturalis in Leiden. The opening starts at 16:00 and you can register for the exhibition by sending an e-mail to: opening@ncbnaturalis.nl, please mention ‘design’. The exhibition within the framework of LiveScience is open for visitors from June 17 until Januari 2011. On December 8, 2010 the winners of the Designers & Artists Award Genomics 4 (DA4GA) were presented by Robert Dijkgraaf. DA4GA is the contest where art, design and life sciences meet. DA4GA aims to promote Bio Art and make visible the significance and diversity of Genomics Research. Bio Art is an art practice in which the medium is living matter and the works of art are produced in laboratories and/or artists’ studios. Three winning proposals were awarded with € 25,000, to be spend on its realization.

4th Benelux next-generation sequencing meeting

Fri, 06 May 2011 00:00:00 +0200

This year we present the fourth BeNeLux NGS meeting. At this one-day annual meeting we expect approximately 200 scientists involved/interested in NGS to meet and discuss developments in the field, with a strong focus on practical issues like protocols, bioinformatics issues etc. In addition, a number of plenary presentations will be given by leading scientists in the field of NGS. For information and the registration form, please click here.

KAUST Workshop on quantitative biology: a matter of perspective

Mon, 28 Feb 2011 11:17:00 +0100

Twentyfive years ago, Cyrus Chothia and Arthur Lesk published a seminal paper that illustrated the promise of quantitative computational analysis of biological data. The occasion of this anniversary was used to gather experts in the field of computational biology to discuss the many challenges that must be overcome if we are to realize the power of quantitative computational biology in the life sciences. The KAUST workshop is planned in Rome on "Quantitative biology: a matter of perspective"

The official language of the workshop will be English.
Registraton cost is 30 Euro (reduced to 20 Euro for members of the Italian Bioinformatics Society http://www.bioinformatics.it provided they have regularly paid their annual subscription for 2011).
Attendance is limited. A first-come first serve scheme will be applied.
There is no provision for posters at the meeting site.

For further information, please visit http://www.biocomputing.it/quantbiol

9th Basel Computational Biology Conference "Multiscale Modeling"

Wed, 06 Apr 2011 09:05:00 +0200

The 9^th [BC]² Basel Computational Biology Conference "Multiscale Modeling" will take place on June 23 & 24, 2011 at the congress center Basel. Registration and poster submission are now open on the conference web site.

Poster submission
The organizing committee would like to invite all interested participants and conference attendees to consider presenting a poster. They are soliciting high-quality research posters in all aspects of computational biology, systems biology, bioinformatics, biophysics, modeling and simulation. Submission deadline for poster abstracts is May 15, 2011.

Registration
Online registration for the meeting is open now. Early registration deadline is May 15, 2011. Please visit the conference website for details and on-line registration: http://www.bc2.ch/2011/

BioCafe in Utrecht: "Bioinformatics: when ethics counts"

Tue, 28 Jun 2011 00:00:00 +0200

On Tuesday the 28th of June the PhD-students network RSG Netherlands is organizing another BioCafe with a new and exciting area of research in bioinformatics: "Bioinformatics: when ethics counts" .The BioCafé is planned in the same week and city as the NBIC PhD school course Comparative Genomics. Programme
The speaker of the BioCafe will be Dr. Jeantine E. Lunshof, a philosopher and bioethicist in the field of human genetics and genomics, and systems biology. She has been an ethics consultant of genetics department of Harvard medical school since 2006.

To know more about her and her achievements go to the following link http://www.bio.vu.nl/microb/personnel/jeantine_lunshof/index.html

The presentation will be given in a café in Utrecht (t.b.a.), where there will be ample opportunity to have informal talks with Dr. Jeantine, her experiences working in Harvard medical school. And last, but not least this BioCafe will provide you the platform to connect with your fellow young researchers within the field of Bioinformatics. Registration
Registration for this event is required, so please send an e-mail to rsg-netherlands@iscbsc.org with your name, institute and whether you want to join the dinner (at your own costs) after the BioCafé.

BioCafe in Utrecht: "Bioinformatics: when ethics counts"

Tue, 28 Jun 2011 00:00:00 +0200

3rd BioInformatics Industrial User Platform (BIUP) meeting

Thu, 23 Jun 2011 11:02:00 +0200

The BioInformatics Industrial User Platform (BIUP) is a group of Dutch companies that use bioinformatics expertise and tools in research and product development. BIUP members have a common interest in:

informal discussions between industrial parties that use bioinformatics tools for research and product development
an infrastructure for joined bioinformatics research (e.g. safe data repository)
stimulating relevant bioinformatics research
shaping the competences of the bioinformaticians of the future

At June 29 the third BIUP meeting will be organized. During this meeting extra attention will be given to the Dutch Tech Center (DTL) initiative. DTL offers a strategic framework of interconnected life science technology facilities (techcentres).

This meeting is open for delegates from industrial parties that use bioinformatics tools for research and product development. For more information about BIUP and registration for the meeting, please visit the BIUP website.

European Lab Automation Advances in Microarray Technology, Next-Gen Sequencing & AgriGenomics

Fri, 01 Apr 2011 16:45:00 +0200

Select Biosciences would like to introduce you to the Advances in Microarray Technology, Next-Gen Sequencing and AgriGenomics conference streams. Part of this year's inaugural European Laboratory Automation congress, which will be held at the Congress Center Hamburg (CCH), Germany, 30 June - 1 July 2011. The Advances in Microarray Technology stream will explore the very latest key topics in the application of microarray's in diagnostics, in particular the recent advancements in array platforms for biomarker discovery and signaling network analysis. With attendance of both novice users and experts alike, the conference will cover the most relevant and challenging issues in microarray development and use. The Next-Gen Sequencing stream will highlight many of the emerging technologies and techniques used for DNA sequencing and analysis. It aims to examine how they have been applied in genomic analysis and disease identification through speakers who are leaders in their fields. AgriGenomics will cover the latest tools and techniques being used to enhance growth in plants and crops as well as the use of genomic mapping to increase plant resistance to disease. Register here. * Registered conference delegates will be allowed access to all conference streams at European Lab Automation.

Lipari CompBio 2011: Biological Sequence Analysis and High Throughput Technologies

Wed, 09 Feb 2011 09:59:00 +0100

The dramatic rising of data being generated by high-throughput technologies,such as microarrays, ChIP-chip,ChIP-Seq data are opening a new universe of problems that will certainly provide great challenges in the coming years.The theme of the School: 'Biological Sequence Analysis and High Throughput Technologies' will describe and highlight a few of techniques and methods for the data analysis in the era of the Personalized Genomics. The main lectures will focus on the following key topics:

methods for high-throughput and parallel sequencing
data Integrationand knowledge inference from high-throughput Genomic Experiments

Three special lectures will survey applications in the field of human diseases and cellular development. A series of tutorial will also be given, with the intent to complement the main lectures. These will provide snapshots of other areas that are perceived of relevance to the theme of the School. They range from introductory topics to sequence analysis to structural biology. Two kinds of participants are welcome.

Students: Participants who are expected to do afternoon courseworks and take a final exam (The grades will be given following the ECTS grading scale). The course will involve a total of 24 hours of teaching. According to our university rules passing the final exam gives right to an equivalent of 6 ECTS credits in any Ph.D. program.
Auditors: participants who are not interested in taking the final exam.

Registration:
Registration is open. The registration fee is 450 Euros and covers course material, bus and hydrofoil Catania airport-Lipari-Catania airport and social event. Late registration is 550 Euros. Deadline for application is May 1, 2011. Applicants are asked to include a short curriculum vitae and specify two professors whom letters of recommendation will be asked to, if deemed necessary. For more information, please visit: http://lipari.dmi.unict.it/LipariSchool/Bio/index.php

Sixth Summer School on Advanced Statistics and Data Mining

Wed, 30 Mar 2011 14:51:00 +0200

The Technical University of Madrid (UPM) again organizes the summer
school on 'Advanced Statistics and Data Mining' in Madrid between July
4th and July 15th. This year's programme comprises 17 courses divided in
2 weeks. There are new 5 courses not previously offered in the previous
edition. Attendees may register in each course independently.

Registration is now open. Extended information on courses programme,
price, venue, accommodation and transport is available at the school's
website: http://www.dia.fi.upm.es/ASDM

NBIC HotTopics meeting: Gene regulatory interaction networks

Wed, 22 Jun 2011 09:10:00 +0200

The field of molecular biology is facing the challenge to bridge the data-knowledge gap. Clearly, the current data deluge is not automatically leading to new biological insight. Therefore it becomes unarguably clear that computational methods will be required to piece together the biological principles that underlie these enormous amounts of data. During this HotTopics meeting we will elaborate on the use of methods to elucidate and predict (gene) regulatory interactions from large biomolecular datasets, with special focus on recent novel biomolecular data types and ways of integrating them. Of particular interest are methods that employ a module based approach, i.e. summarization of data into modules and application of interaction inference between and within these modules. Keywords: regulatory interaction, networks, modules, high-throughput data You can find more information about the programme and registration here. NBIC HotTopics are a new series of NBIC meetings committed to bringing scientists together to discuss the concepts and methods on a hot topic in their research field. It should provide a platform to keep in touch with peers in the field and foster sharing of new insights, applications and collaborations. Therefore, the aim of the meeting is not to present the latest results of your own work, but rather to identify new trends and breakthroughs in the field in general.

7th ISCB Student Council Symposium 2011 - Call for Abstracts

Wed, 30 Mar 2011 09:36:00 +0200

Submit your abstract today to participate in the 7th Symposium of the International Society for Computational Biology Student Council on July 15th 2011 in Vienna! The Student Council Symposium aims at bringing together young computational biologists from all areas of research and parts of the world. As the central part of our symposium 12 student presentations will be selected from the submitted abstracts. This is your chance to present your work! They accept abstracts covering both scientific studies as well as novel tools and applications in the field of computational biology and bioinformatics. Travel Fellowships are available (see website) and awards will be given to best poster and best presentation. Submission website: http://bit.ly/iscbsc-scs7-sub
Travel Fellowship information: http://bit.ly/iscbsc-scs7-tsub
General information: http://bit.ly/iscbsc-scs7 Important dates:
January 31: Abstract and Travel Fellowship submission opens
February 15: Travel Fellowships submission opens
April 29: Abstract submission closes
May 6: Travel Fellowships submission closes
May 23: Travel Fellowship winners and Abstract acceptance notification

ISMB/ECCB 2011

Fri, 17 Dec 2010 10:41:00 +0100

The annual international conference on Intelligent Systems for Molecular Biology (ISMB) is the major meeting of the International Society for Computational Biology (ISCB). This year the conference is co-organised together with the European Conference on Computational Biology (ECCB). ISMB/ECCB bring together scientists from computer science, molecular biology, mathematics, statistics and related fields. Online registration for the ISMB/ECCB 2011 closes on July 1. NBIC is sponsoring the ISMB/ECCB 2011 and willl be present with a exhibition booth in the exhibition hall. We invite you all to visit us at our stand! Scheduled NBIC technology track presentations during the ISMB/ECCB 2011:

July 17, 11:45 - 12:10:
'Bringing bioinformatics to the classroom' by Hienke Sminia (NBIC)
July 18, 11:45 - 12:10:
'End user tools for data interoperability' by Christine Chichester (NBIC - BioAssist Engineering team)
July 18, 12:15 - 12:40:
'Enacting Taverna Workflows through Galaxy', by Kostas Karasavvas (NBIC-LUMC)

Below you can find the booklet where you can find tools, course material and expertise you can use from NBIC.

BIOCOMP'11 The 2011 International Conference on Bioinformatics and Computational Biology

Thu, 17 Mar 2011 14:22:00 +0100

This is the 12th annual offering of BIOCOMP conference. You are invited to submit a full paper for consideration. All accepted papers will be published in the BIOCOMP conference proceedings (in printed book form; later, the proceedings will also be accessible online).The proceedings will be indexed in Inspec / IET / The Institute for Engineering & Technology, DBLP / Computer Science Bibliography, andothers.) In the past, the proceedings have also been included in EICompendex/Elsevier. Like prior years, extended versions of selected papers will appear in special issues of journals and edited research books (so far, two books have been approved to be published by Springerbased on BIOCOMP'11 - these books will be indexed by Medline, Scopus,EMBASE, BIOSIS, Biological Abstracts, CSA, Biological Sciences and Living Resources, and Biological Sciences). Conference Web site:
http://www.worldacademyofscience.org/worldcomp11/ws/conferences/biocomp11 BIOCOMP'11 conference will be held simultaneously (same location and dates) with WORLDCOMP 2011 congress. For more information, refer to:
http://www.world-academy-of-science.org/ Important dates:
March 31, 2011 Submission of papers (about 5 to 7 pages)
April 20, 2011 Notification of acceptance (+/- 6 days)
May 7, 2011 Final papers + Copyright/Consent + Registration
July 18-21, 2011 The 2011 International Conference on Bioinformatics and Computational Biology (BIOCOMP'11) Those who have submitted papers during the month of February will receive the decision on their papers by the end of March 2011.

BIOKDD'11 / DEXA'11

Mon, 21 Mar 2011 17:11:00 +0100

2nd International Workshop on Biological Knowledge Discovery and Data Mining (BIOKDD'11)
held in parallel with
22nd International Conference on Database and Expert Systems Applications(DEXA’11) www.dexa.org With the development of Molecular Biology during the last decades, we are witnessing an exponential growth of both the volume and the complexity of biological data. For example, the Human Genome Project provided the sequence of the 3 billion DNA bases that constitute the human genome. And, consequently, we are provided too with the sequences of about 100,000 proteins. Therefore, we are entering the post-genomic era: after having focused so many efforts on the accumulation of data, we have now to focus as much effort, and even more, on the analysis of these data. Analyzing this huge volume of data is a challenging task because, not only, of its complexity and its multiple and numerous correlated factors, but also, because of the continuous evolution of our understanding of the biological mechanisms. Classical approaches of biological data analysis are no longer efficient and produce only a very limited amount of information, compared to the numerous and complex biological mechanisms under study. From here comes the necessity to use computer tools and develop new in silico high performance approaches to support us in the analysis of biological data and, hence, to help us in our understanding of the correlations that exist between, on one hand, structures and functional patterns of biological sequences and, on the other hand, genetic and biochemical mechanisms. Knowledge Discovery and Data Mining (KDD) are a response to these new trends. Paper submission details:
Authors are invited to submit electronically original contributions in English. Submitted papers should not exceed 5 pages in IEEE format www.ieee.org/web/publications/authors/transjnl/index.html. All accepted papers will be published in the proceedings of DEXA’11 Workshops with IEEE CSP. One of the authors of an accepted paper must register to DEXA’11 conference and present the paper at BIOKDD’11 workshop. For paper registration and electronic submission see http://confdriver.ifs.tuwien.ac.at/dexa2011/, starting from January 2011.

Extended versions of selected accepted papers will be published as chapters in a book, entitled Biological Knowledge Discovery Handbook: Preprocessing, Mining and Postprocessing of Biological Data, which will be published by Wiley, USA www.wiley.com.

Important dates:
Submission of Full Papers: March 30, 2011
Notification of Acceptance: April 26, 2011
Camera-ready Copies: May 23, 2011

Plant Genome Evolution Conference (Current opinion conference)

Wed, 31 Aug 2011 10:02:00 +0200

The first plant genome sequence, the one of the model organism Arabidopsis thaliana, was presented in December of the year 2000. The second one, of rice, followed more than a year later, in April 2002. The poplar genome, which was third, was only published in late 2006. However, due to the recent progress in next-generation sequencing technologies, the number of completely sequenced plant genomes is rapidly increasing. On top of that, also more and more functional genomics data are becoming available for plants. All this makes this an extremely fascinating era for plant science and, amongst other things, allows studying plant genome evolution at many different levels. Current Opinion in Plant Genome Evolution is the second in a new and exciting series of conferences sponsored by the timely and popular Current Opinion journals. These conferences provide a new level of direct interaction between the leaders in the scientific field and the attending delegates. Emphasis will be placed on latest unpublished results, extended discussion periods and direct interactions with leaders in the field.

The second Current Opinion Conference is dedicated to plant genome evolution. The conference will cover all areas of genomic and evolutionary research within this topic including new plant genome sequence projects, genome structure, genetic diversity, evolution, polyploidy, gene duplication, hybridization and heterosis, plants systems biology and bioinformatics. There are still a few seats available for the conference. Register here: https://conferences.elsevier.com/index.cfm

WABI'11, the 11th Workshop for Algorithms in Bioinformatics

Wed, 30 Mar 2011 15:04:00 +0200

They are pleased to announce the call for papers for WABI'11, the 11th Workshop for Algorithms in Bioinformatics. WABI will be part of ALGO 2011, and will be hosted by the Max-Planck-Institut für Informatik, Saarbrucken, Germany. The conference will run from Sept 5 to 7, 2011, and the submission deadline is May 10, 2011. They welcome papers on algorithmic work in bioinformatics, computational biology and systems biology. Please see their provisional website for details: http://pbil.univ-lyon1.fr/members/sagot/htdocs/wabi2011/wabi2011.html

Interactive workshop on Software Licensing Strategies

Mon, 27 Jun 2011 13:25:00 +0200

On September 8th 2011, the Netherlands Metabolomics Centre (NMC), the Technology Transfer Office of the University of Amsterdam and the Netherlands Bioinformatics Centre (NBIC) are jointly organising two workshops on Software Licensing Strategies, in co-creation with Leiden University Research & Innovation Services (LURIS). In the morning there will be an interactive expert workshop discussing best software licensing strategies for NMC and NBIC, and in the afternoon a more informative workshop aimed at researchers & programmers. The workshops are in principle open to other interested parties (space permitting) on confirmation by the organisers. Information about registration and detailed programme can be found here

SIB PhD Training Network, Workshop 2011, Bioinformatics in the Chalet

Tue, 24 May 2011 13:55:00 +0200

This workshop, based on a concept developed by Steve Stearns and John Maynard Smith, and shamelessly copied from the doctoral program in Ecology and Evolution, takes place in a beautiful small Alpine village (Chandolin). The beautiful and remote setting was chosen to allow you to focus while being able to enjoy the landscape and get to know your peers.

The main goal of this event is to develop the following skills:

expressing your scientific ideas through discussions in groups
thinking critically and expressing yourself clearly
turning a general idea into a research project
writing the research proposal and defending it

Target audience
PhD students of the SIB or PhD students doing a thesis in bioinformatics. A number of places are reserved for students from outside the SIB or Switzerland. Prerequisites: Background knowledge and interest in bioinformatics. Deadline for application: June 6, 2011 More information about the schedule, location and registration can be found here.

The Second International Workshop on Static Analysis and Systems Biology (SASB 2011)

Mon, 09 May 2011 11:26:00 +0200

A lot of biological models suffer from a high combinatorial complexity. Many methods have been proposed to break down this combinatorial complexity. Some of these methods are informal and are validated experimentally. By contrast, static analysis-based scalable formal methods increase the level of confidence by providing formal characterization of what is computed. Being automatic, easily reusable, and offering formal soundness criteria, static analyses can help designing models, testing models with respect to experimental data, and predicting the behavior of the system being modeled.
The goal of this workshop is to promote discussions and collaborations between biologists (modelers), computer scientists (in static analysis) and applied-mathematicians around the design and the use of static analysis methods for biological models. The second SASB will be co-located with SAS 2011 in Venice, Italy. Please visit the submission website. The program of SASB 2011 will consist mainly of presentations of refereed papers. Contributions are welcomed on all aspects about the use of static analysis methods in Systems Biology, including, but not limited to:

bottle-neck challenges for static analysis of biological models,
new static analysis frameworks,
modeling experiences using static analysis,
informal methods (that could be candidate to formalization and automatization).

All submitted papers will be peer-reviewed by the program committee. Submitted papers should not exceed 12 pages including bibliography, and follow the ENTCS guidelines. Submitted papers may include, in addition, an appendix containing technical details, which reviewers may read or not, at their discretion. Papers must be written and presented in English, and describe original work that does not substantially overlap with papers that have been published or that are simultaneously submitted to a journal, conference, or workshop with refereed proceedings. For more information, visit: www.di.ens.fr/sasb2011

RSG company visit: Genetwister

Fri, 16 Sep 2011 10:06:00 +0200

The PhD student network RSG Netherlands invites you to their second Company Visit on September 16th, at Genetwister in Wageningen. Genetwister is an innovative biotechnology company, which was founded in 1998. Initially their focus was marker discovery for diagnostics and tool development for genetic modification, but over the years this shifted and expanded towards high throughput marker discovery and practical application and development of both genomic breeding and green biotechnology tools. The accumulating information on biomarker, genetics and gene expression databases required the development of advanced software for data storage, data analysis and visualization. Therefore a bioinformatics group was established in 2004. For more information you can read the short profile (pdf) of Genetwister. During the visit you will learn more about the work that is done in this company with an emphasize on the role of Bioinformatics. The RSG likes to close of the visit with drinks in a nearby pub and there will the possibility to join for dinner as well.

Vist location: Genetwister: Nieuwe Kanaal 7b, 6709PA, Wageningen
Directions: http://www.genetwister.nl/contacteng.html Registration This visit provides the unique opportunity to get an inside look at this innovative biotechnology company! Please send an email to rsg-netherlands@iscbsc.org to register.

For those interested in joining the RSG for dinner afterwards (at your own costs), please mention this in the e-mail as well.

RSG company visit: Genetwister

Fri, 16 Sep 2011 10:06:00 +0200

EMBL Symposium Cancer Genomics

Sat, 16 Apr 2011 14:44:00 +0200

This symposium will provide an opportunity to learn about the rapidly progressing area of cancer genomics including presentations representing many of the major international cancer genome sequencing projects as well as the areas of cancer epigenomics, mouse cancer models and the developments in both computational and bioninformatics areas that are required to manage, interpret and present these substantial datasets. The meeting will bring together scientists from across these areas for a unique opportunity to interact and stimulate further integration of these efforts.

Discovery Festival

Tue, 20 Sep 2011 16:10:00 +0200

Discovery Festival is a nighttime festival with live scientific research, ultra short talks, science-related art, a high quality music programme, and a lot of mostly young and always enthusiastic scientists and artists. The broad and varied programme of activities include over 30 activities: live scientific research directly involving researchers in contact with the visitors, an art exhibition with selected bio-art related works, and a music programme on the top floor and in the main hall with dj’s and sound architects. Some highlights: Mobile Eye Tracker, Brain Computer Interface for Music, The Body Lab, Cardboard Robot Battle, Renkas (live), MacGyver Science, Citizen Science, Fellow (live) and many more. NBIC's contribution to the festival will be 'Foldit: Citizen Science'. Hannes Hettling, Punto Bawono and Hienke Sminia will guide you through the world of proteins and science. And challenging you to become a real scientist. Read more on the festival: http://www.discoveryfestival.nl Read more on Fold It: http://www.fold.it/ Read more on Citizen Science: http://discoveryfestival.wordpress.com/2011/09/12/citizen-science/

5th International Chemometrics Research Meeting

Mon, 28 Feb 2011 10:40:00 +0100

The Dutch Chemometrics Society invites you to the 5th International Chemometrics Research Meeting. The meeting is organized under the auspices of the Royal Netherlands Chemical Society. Following successful earlier meetings in 1994, 1998, 2002 and 2006 the format of the conference will be such that lectures reflect the current state-of-the-art in chemometrics and will be a starting point for extended discussions and exchanges of views. Like previous ICRM meetings, the scientific program consists of invited lectures of 50 minutes, and ample time for discussions. These discussions will be introduced by a discussant. At this 5th ICRM, also time has been reserved for contributed lectures. You are invited to submit abstracts for oral contributions, as well as for the two poster sessions. Abstracts can be submitted through the conference website. Submission deadline is May 1st 2011. The conference will cover the most state-of-the-art topics in the field of Chemometrics, including:

Multivariate data analysis, calibration and classification,
Multi-block and multi-way methods,
Process Chemometrics,
-Omics related Chemometrics.

The current program including abstracts and the CV’s of the presenters can be found on the ICRM website website: www.icrm2011.org/program/program.html. For more information, visit: www.icrm2011.org For registration, visit: www.icrm2011.org/registration/registration.html

Structural Bioinformatics meets Structural Biology

Tue, 27 Sep 2011 16:55:00 +0200

The Netherlands Society for Structural Bioinformatics organises the third meeting for researchers in structural bioinformatics on Tuesday 27 September 2011 (10:00-18:30). The invited speakers are:

Torsten Schwede about "Progress and challenges in homology modeling"
Alexandre Bonvin about "Modeling macromolecular interactions"
Tom Burnley about "Molecular dynamics in crystallographic refinement"
Ewald Edink about "Design and structures of AchBP inhibitors"

The meeting is hosted by the Netherlands Cancer Institute (NKI) in Amsterdam:
NKI, Room Z4, 1st floor, Plesmanlaan 121,1066CX Amsterdam. Registration for poster session A poster session will run for the whole day. Please register your poster before September 12th by sending an abstract to a.perrakis@nki.nl indicating if you want your poster to be considered for a short oral presentation.

Systems Genetics: from man to microbe, from genotype to phenotype

Tue, 12 Jul 2011 11:26:00 +0200

The availability of complete genome sequences from man and a wide range of other species, and the development of high-throughput technologies have led to the accumulation of biological data at an unprecedented scale. These data are different in nature as they come from various sources and they provide detailed information on the individual components of living cells. However, ample experimental and theoretical evidence indicates that extensive knowledge about the individual components is insufficient to describe the operation of complex cellular systems as a whole. Hence, a central challenge for biology and medicine is to reach a much deeper understanding of the operation of whole cells and cellular assemblies. The complex dynamic behavior of these biological systems is sustained by complex networks of interactions between the individual components. Thus, biological systems cannot be understood intuitively, and theory-based approaches are necessary to unravel this complexity. This insight has led to the emergence of Systems Biology, a holistic approach that is based on the view that biological systems are composed of two types of information: genes, encoding proteins that form the molecular machines that execute the functions of life, and networks of regulatory interactions that control the hierarchical flow of information from DNA to mRNA to proteins to molecular machines to metabolites and, ultimately, to phenotype. The present symposium “Systems Genetics: from man to microbe, from genotype to phenotype” focuses attention on the genetic aspects in Systems Biology. It brings together leading experts in the field, who will present key-note lectures and, in addition, will attend master classes in which they will share their experience with PhD students and post-doctoral researchers. Confirmed key-note speakers include:

Jun Wang (BGI, China) Sequencing, Sequencing and Sequencing
Matthias Heinemann (RUG, Netherlands) Stochasticity-induced phenotypic heterogeneity of clonal bacteria
Timothy J. Aitman (Imperial College, England) Whole genomes and epigenomes in the dissection of complex traits
Henk Stunnenberg (NCMLS, Netherlands) The BLUEPRINT of hematopoiesis: deregulation of the epigenome by oncofusion proteins in AML
Uwe Völker (University Greifswald,Deutschland) Integrated OMICs studies in the characterization of host pathogen interactions
Bas van Steensel (NKI, Netherlands) Chromatin domain organization of eukaryotic Genomes
Peter Lansdorp (Eriba Institute, Netherlands) Telomeres: from genes to patients
Alan D Attie (UW Madison, United States) Genetic Deconstruction of Type 2 Diabetes

For further information and registration see www.systemsgenetics.nl (Deadline for Posters and Abstracts is July 15th 2011)

Complete Genomics and VIB Bioinformatics Training and Services Facility Joint Seminar

Thu, 15 Sep 2011 16:24:00 +0200

Complete Genomics, a whole human genome re-sequencing service provider, and BITS, the VIB Bioinformatics Training and Services Facility, are pleased to invite you to a complimentary event including presentations from leading researchers. Discover how large-scale, accurate and affordable whole human genome sequencing helps researchers advance their understanding of the impact of genetic changes on cancer and other diseases. Complete Genomics is the complete human genome sequencing company that has developed and commercialized an innovative DNA sequencingplatform. The Complete Genomics Analysis Platform (CGA™ Platform) combines Complete Genomics' proprietary human genome sequencing technology with its advanced informatics and data management software. Complete Genomics offersthis solution as an innovative, end-to-end, outsourced service, CGA Service, which provides customers with data that is immediately ready-to-use for genome-based research. For more information about the agenda, click here. For registration, click here.

High Performance Cloud Computing Day

Tue, 26 Jul 2011 15:17:00 +0200

On Tuesday Oktober 4^th, 10:00 - 17:00, SARA & BiG Grid are organizing a special High Performance Cloud Computing Day. This event will be concluded with the festive launch of the new HPC Cloud infrastructure. Venue: Conference Halls, Science Park 125, Amsterdam
Language: English. Free admission Registration is open!
http://www.sara.nl/form/hpc-cloud-day-october-4-2011

The new National HPC Cloud: a user-friendly compute cluster for scientists.
Apply now! http://www.sara.nl/apply-for-new-national-hpc-cloud

Preliminary program
10h00 - 10h30
Opening and welcome by Jaap van den Herik, BiG Grid
‘HPC Cloud: Focus on your research’ by Floris Sluiter, SARA Computing and Networking Services

10h30 - 11h30 Theme: Bioinformatics
Short presentations by several researchers

11h30 - 12h00 Keynote
'Enabling clouds' by Ignacio Llorente, OpenNebula, DSA-Research Group Complutense University of Madrid

12h00 -13h30 Lunch and demo & poster market
(Live) demonstrations by researchers on the Cloud

13h30 -14h30 Theme: Finance & linguistics
Short presentations by several researchers

14h30 - 15h30 Theme: Earth Science
Short presentations by several researchers

15h30- 16h00 Tea break and demo & poster market
(Live) demonstrations by researchers on the Cloud

16h00 Keynote
‘1B core hours in the cloud’ by David Konerding, Google

16h45 Speech by Anwar Osseyran, SARA Computing and Networking Services
Festive launch of the new HPC Cloud infrastructure

17.15 Reception

For more information on the website of SARA www.sara.nl and BiG Grid www.biggrid.nl

8th CMSB Symposium

Thu, 25 Aug 2011 16:07:00 +0200

On Tuesday October 4, the Centre for Medical Systems Biology (CMSB) organises its 8th Annual Symposium, which will be held at the VU in Amsterdam. The symposium is free of charge.

Also this year there is a varied programme applying to the CMSB theme "Improving diagnosis, treatment and prevention of common and rare diseases". In the morning, there are four overview stories given by well-established CMSB researchers: Eco de Geus, Gisela Terwindt, Peter Heutink and Silvère van der Maarel. In the afternoon, there are three parallel sessions. In these sessions their researchers will present their findings covering the main CMSB research programme diseases Alzheimer’s disease, arthritis, depression, metabolic syndrome and migraine, the theme ‘societal aspects of genomics’, and platforms immunology and DIAL (data integration, analysis and logistics).

As their closing speaker, they are honoured to present Tune H. Pers. He is a computational biologist from the University of Copenhagen, and did his PhD in the Brunak research group at the Center for Biological Sequence Analysis at the Technical University of Denmark. During his doctoral studies, his main focus has been on the development of integrative methods that augment genetic analyses of complex traits. Tune Pers is currently employed as a research fellow at Children’s Hospital Boston and the Broad Institute of Harvard and MIT. He will talk about some of his recent work in the presentation “Integrative systems biology: elucidating complex traits”.

Registration is free of charge; please register at Boerhaave Nascholing via this link.

More Information: Petra van Overveld, p.overveld@lumc.nl / 071 526 9551

INSERM training workshops: genome-scale approaches to genetic and epigenetic regulation

Wed, 18 May 2011 10:30:00 +0200

The Institut National de la Santé et de la Recherche Médicale (INSERM) organizes two coupled training workshops on genome-scale approaches to genetic and epigenetic regulation. Participants can register to either workshop independently, or to both workshops. Target audience: researchers, physicians, post-docs, technicians, engineers and students in the domains of life science or bioinformatics. All conferences will be given in English. Registration deadline: June 1st, 2011. Detailed programs and registration forms can be found here. Email: ateliers@inserm.fr Training workshop 211: High-throughput approaches in epigenomics Organizers: Emmanuel Barillot (Institut Curie/INSERM/Mines ParisTech, Paris), Christophe Lavelle (CNRS, Muséum National d'Histoire Naturelle, Paris). Phase I (theory): October 10-12, 2011, Bordeaux (France). Phase II (practical): 2011, Paris, Montpellier, Nice/Marseille (France), and Darmstadt (Germany). Aims. Through its polymorphism, as evidenced by the heterogeneity of its physicochemical properties, chromatin is the support of an information — so-called "epigenetic" — which is superimposed to the genetic information — carried by DNA — to determine cell fate. While genetic sequencing, more and more efficient, provides data at a dizzying pace, the "epigenetic sequencing" is in turn becoming a priority in an attempt to gather all information necessary for the deciphering of cellular function. The challenge of this new quest is obvious when we know that, contrary to genetic information, epigenetic information varies from one cell to another (within the same organism) and in regard with the cell cycle, making the epigenome particularly difficult to establish. However, the first high-resolution epigenetical maps begin to emerge, including information as diverse (and complementary) as the position of nucleosomes, the presence of histone variants and their modifications, the distribution of transcription factors and remodeling factors, and location of DNA methylation. While these profiles accumulate, the need is urgent to develop analytical tools that allow efficient analysis of these data, in hopes of eventually cracking the epigenetic code. The objective of this workshop is to present the most recent techniques (mainly ChIP-seq) in this area, focusing on possible problems commonly encountered in their implementation. Beyond the "wet" technical aspects, a presentation of the most common bioinformatics tools for analysis (peak finding, differential analysis, integrative analysis of profiles, databases, ...) will also be provided. Training workshop 212: Bioinformatics approaches to decipher genome regulation from high-throughput data Organizers: Jacques van Helden (ULB, Belgium), Philipp Bucher (SIB/ISREC, Switzerland). Phase I (theory): October 12-14, 2011, Bordeaux (France). Phase II (practical): December 12-16, 2011, Marseille (France). Aims. Genome regulation plays a crucial role in embryonic development, adaptation of cells, tissues and organisms to their environment, and evolution. This regulation occurs at multiple levels: transcription, RNA maturation (splicing, degradation), micro-RNA, nucleosome occupancy, chromosome conformation. New high-throughput methods offer unprecedented ways to characterize regulatory elements at a genome scale: expression microarrays, ChIP-on-chip, ChIP-seq, RNA-seq, protein binding arrays, etc. Sequencing platforms become available in many institutes, but researchers generally feel some perplexity when they are first confronted to the terabases of novel data. New software tools re being developed to answer those new needs, but their utilization requires to understand the underlying principles, master the parameters, and interpret the significance of the result. The goal of this workshop is to provide researchers with a theoretical and practical training enabling them to apprehend the whole flow of data analysis, from data acquisition to biological interpretation of the results.

NBIC BioRange Project Meeting

Thu, 08 Sep 2011 11:19:00 +0200

The BioRange Project Meeting is an internal NBIC meeting, open only for BioRange researchers, with the aim at bringing together the researchers working in BioRange projects to exchange information about the research projects. The meeting is obligatory for all researchers who have a research position within BioRange, funded by NBIC. For more information and registration, please visit the meeting website.

NETTAB 2011 on "Clinical Bioinformatics"

Thu, 15 Sep 2011 16:45:00 +0200

NETTAB 2011 is the eleventh in a series of international workshops on Network Tools and Applications in Biology. NETTAB 2011 is focused on Clinical Bioinformatics and it is aimed at presenting the methods, tools and infrastructures that are nowadays available. It will also show some of the most interesting applications in this field. Invited Speakers:

Network Models of Mesophenotypes in Personal Genomics and Targeted Therapies. Yves A. LUSSIER, Institute for Translational Medicine, University of Chicago, USA
From Omics to Systems Biology - an Approach to Individualized Medicine. Thomas ILLIG, Institute of Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
ICT Architectures for Biobanks to Support Clinical Research. Jan-Eric LITTON, Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
Computing our Patients' Future Using Data from our Healthcare Institutions. Shawn N MURPHY, Harvard Medical School, Boston, USA

For more information about the programme and registration, click here.

Structure and Dynamics of Protein Networks

Sat, 16 Apr 2011 14:47:00 +0200

The general aim of the symposium is to explore the possible synergisms and cross-talk between the large-scale and classical approaches to biological networks. Understanding the molecular mechanisms of biological function largely relies on the systematic charting of the dynamics interactions taking place between the various components of living cells. Recent “OMICS” technologies contribute large biological networks covering entire proteomes. These networks are generally static as they fail to capture spatial and temporal dimensions that represent essential properties of living systems. Mechanistic and dynamic insights often come from focused smaller-scale approaches, such as those used in structural biology, biophysics or cell biology. This symposium brings together leading scientists from the “OMICS” field with leading structural and cell biologists to discuss scientific issues arising at the interface of these complementary fields. Possible avenues to populate current networks with dynamics and mechanistic insights that will ensure high levels of biological understanding and contribute to deciphering fundamental principles will be reviewed and investigated.

Comparative genomics of eukaryotic microorganisms: understanding the complexity of diversity

Thu, 10 Feb 2011 10:29:00 +0100

Comparative genomics is a rapidly developing field. Europe has been at the forefront of eukaryotic microbial genome sequencing and the analysis and comparison of these genomes. The first eukaryote sequenced, the budding yeast Saccharomyces cerevisiae, laid the foundation for the post-genomic era where we are dealing with this wealth of information. Many of the organisms are models for particular biological processes, others are used in industry, are pathogens of plants, animals and humans, are important in ecology, or largely contribute to our understanding of eukaryote evolution. In this conference we bring together the experts from around the world to meet and discuss with interested participants the current state of and future of comparative genomics of eukaryotic microorganisms. This conference will address the big evolutionary questions of what makes a eukaryote, how multicellularity arose, the evolution of reproduction, pathogenesis, and so on. Lineages of the Eukaryotic Tree of Life (TOL) that until now received only moderate attention, such as the Excavates, Archaeoplastids, Amoebozoa and Choanozoa, will be discussed, together with the better studied Chromalveolates and Fungi. There will be opportunities for participants to present both short talks and posters, which will be conducted interactively with plenty of time reserved for questions and discussions. In addition there will be interactive workshops on ‘Do It Yourself’ genomics, databases and bioinformatics. For more information about the program, visit:
http://events.embo.org/11-comparative-genomics/programme.html For registration, visit:
http://events.embo.org/11-comparative-genomics/application.html

NBIC HotTopics meeting: Multi-level omics integration

Thu, 15 Sep 2011 16:06:00 +0200

With the advancement of microarray and sequencing technology, many genomics researchers apply more than one profiling method for detection of molecular changes related to their phenotype of interest, e.g. cancer and complex diseases. To gain biological insight from these data, molecular phenotypes such as gene or protein expression are related to measurements at the DNA level such as copy number, SNPs or DNA methylation. Genome‐wide integration of different omics levels yields important insights into the genetic control of gene expression and is instrumental to the deciphering of disease mechanisms. Moreover, the diagnostic value of the integrated data for prediction of disease outcomes such as survival in cancer is probably higher than their individual values.

During this HotTopics meeting we will discuss different approaches for the joint analysis of multiple omics levels' data.

The aim is to identify advances, issues and challenges of these methods in the context of recent developments in genomics, transcriptomics, proteomics and metabolomics. In an open discussion we want to learn how to make the best out of these computational techniques for a better understanding of biology.

Keywords: multi level omics, integration, disease mechanisms You can find more information about the programme here. Registration for the meeting is closed! NBIC HotTopics are a new series of NBIC meetings committed to bringing scientists together to discuss the concepts and methods on a hot topic in their research field. It should provide a platform to keep in touch with peers in the field and foster sharing of new insights, applications and collaborations. Therefore, the aim of the meeting is not to present the latest results of your own work, but rather to identify new trends and breakthroughs in the field in general.

NCSB 2011 Symposium: the Full Systems Biology Cycle

Tue, 05 Jul 2011 11:53:00 +0200

The NCSB 2011 symposium is held in the third year of the nation-wide NCSB programme. The programme runs for a total of five years until the end of 2013. Hence, NCSB is now at the peak of its strength. This symposium will showcase the achievements of the systems biology approach across several biological research areas and also across the nation: it will be a Netherlands systems biology meeting. The “NCSB paradigm” is the iteration of predictive, quantitative modelling with biological experimentation, hence, integrating dry with wet research work. This cycle drives systems biology research. Presentations at the symposium will be selected on the evidence for the operation of this systems biology cycle: research which has (nearly) passed one or more times the SB-cycle. Abstract deadline: September 16, 2011 Participation is free of charge, however registration is required! For more information about the programme and registration, click here.

NMC Metabolomics Days 2011

Fri, 14 Oct 2011 10:56:00 +0200

You are cordially invited to take part in the NMC Metabolomics Days 2011. The first of the Metabolomics Days 2011 of the Netherlands Metabolomics Centre on November 1st, will have an international character, and is open to non-NMC members. The second day is only for NMC members. The conference center Engels is next to Rotterdam Central Station, on the Stationsplein 45. There are (expensive) parking facilities in the Engels garage. Please fill out the registration form (you can find this form below) and send it by return mail to j.p.poels@lacdr.leidenuniv.nl. Please note that after the drinks in the afternoon, the meeting will be for members only. If you would like to present a poster, guests can choose the first (international) day and NMC members either the first (if your work is not confidential) or the second (internal) day. The NMC poster template is enclosed. Enclosed, you can also find the program of the first day.

International Conference on Pattern Recognition in Bioinformatics

Wed, 09 Mar 2011 11:41:00 +0100

In modern biology, high-throughput measurement devices allow scientists to gather data at unprecedented rates. To make sense of this data, computational biologists and system biologists construct quantitative models, many of which depend on pattern recognition techniques. Their application is challenging due to the large volumes of data and background information, noisy measurements and target outputs, highly diverse data types etc.

The Pattern Recognition in Bioinformatics conference series aims to bring together researchers, practitioners and students from around the world to present and discuss recent developments and applications of pattern recognition methods in current bioinformatics, computational biology and systems biology. Authors are invited to submit full papers in relevant research areas. Papers should be submitted electronically through the conference website. We will work with Springer to publish accepted papers in its Lecture Notes in Bioinformatics series (LNBI). A limited number of Ph.D. student travel grants will be made available; please keep an eye on the website for more information.

Important dates:

Paper submission June 19, 2011
Author notification July 25, 2011
Camera-ready paper August 24, 2011
Poster abstract submission October 2, 2011

For more information: http://prib2011.org

RSG BioCafe: PubQuiz

Fri, 14 Oct 2011 14:45:00 +0200

RSG Netherlands is organizing an exciting and fun filled Pubquiz in Nijmegen on 2nd November. The quiz will span questions from different areas of bioinformatics and also from general areas, movies and songs. Join us in Nijmegen for this exciting event with other fellow young researchers and increase the horizon of your social network in the world of bioinformatics. Where: Universiteitscafé Piecken,Professor Bromstraat 54, Nijmegen
When: November 2nd nd, , from 17:30 onwards You can register for the meeting by sending an e-mail to: rsg-netherlands@iscbsc.org Find more information about the programme in the pdf-file below!

e-BioGrid Workshop 2011

Wed, 05 Oct 2011 17:14:00 +0200

e-BioGrid Workshop 2011: e-Science Infrastructure for Life Science Research
Requirements and frameworks Language: English
Participation: free. Please send an email to e-BioGrid if you would like to participate. The workshop reviews the requirements and framework solutions for e-science infrastructure in life sciences. What computing infrastructure works best for next-generation sequencing data analyses? Which job submission framework is most scalable? What works best for biologists? This and more .. The focus of this workshop is primarily on the needs for e-science and computing infrastructure in life science research, and what is available on the Dutch e-science infrastructure. We will review and discuss the matching of requirements and technological frameworks, and identify standards and priorities for developments where possible. Requirements are presented from the technology application areas next-generation sequencing, microarray technology, mass spectrometry, nanoscopy, medical imaging, and structural modeling. We zoom in on the available infrastructure and frameworks for job submission. Is Cloud computing the way to go for life sciences? For which software or data structures is Grid computing more suitable? We will elaborate on the developments in computing infrastructures with respect to current and upcoming data analysis and modeling requirements in life sciences. We invite programmers and bioinformaticians as well as projectleaders and principical investigators, from the life science application areas. For more information about the program, click here. The workshop is organised by the e-BioGrid project of BiG Grid and NBIC that helps Life Science programmers to use the Dutch infrastructure.

Meeting on Epigenetics/Epigenomics Technologies

Mon, 31 Oct 2011 16:39:00 +0100

Not all changes in the regulation of gene function in the cell are caused by variation in the underlying DNA sequence. Epigenetics is the study of gene regulation through other mechanisms, including DNA methylation, histone modifications and small/long RNA-mediated regulation. In this one-day seminar, you will:

Learn how you can leverage the proven data quality of Illumina array and sequencing technologies in your epigenetic/epigenomic studies
Hear ULB investigators, Dr. F. Fuks and his colleagues, explain how applying epigenetic/epigenomic technologies has advanced their research
Learn more about Illumina’s diverse portfolio of epigenetics/epigenomics tools and applications

Organisers: François Fuks, Laboratory of Cancer Epigenetics, ULB Erasme and Steven Van Hove, Illumina. Registration is free but places are limited. Register Now at: ffuks@ulb.ac.be

Bioinformatics Career Day

Mon, 05 Sep 2011 10:53:00 +0200

Bioinformatics bachelor students can get a glimpse of their future at the Bioinformatics Career Day on the 18th of November 2011 at Hogeschool Leiden. Graduates speak about their career; master education programs present their curriculum and future employers show their career possibilities hoping to attract the most promising students. This is the place to find out what a bioinformaticians career path at a company, university or institute looks like. Join the tour of the Leiden Genome Technology Center or be inspired by the talks of bioinformatic heavyweights prof.dr. Den Dunnen, prof. dr. Heringa, dr. Schaap, dr. Sanne Abeln en ir.ing. Den Hollander. The HBO teacher network LOBIN organizes this day for all 3rd and 4th year Dutch bachelor students in bioinformatics, but masters and alumni are welcome as well. In short, a day no student or future employer can afford to miss! Students and employers who want more information please contact Celia van Gelder at NBIC Education or look here. Programme
The programme of the Bioinformatics Bioinformatics Career Day can be found here.

Conference on stochastic gene expression from an experimental, theoretical and philosophical perspective

Thu, 03 Nov 2011 08:39:00 +0100

Stochastic gene expression (SGE) is involved in an evergrowing number of aspects of cellular life. It is typically an area of research needing modelization and interdisciplinary collaboration between biologists, bioinformaticians, physicists and mathematicians. SGE is an important aspect of cellular physiology that has to be integrated into systemic approaches and as such it is now the object of much attention of the international community. It raises a number of questions regarding its role in organisms, notably in developmental biology and could have profound consequences for biological theories: is it a "noise" that disrupts the operation of the genetic program, does it fits into a vision based on the theories of self-organization, or does it implies a conceptual framework change such as cellular Darwinism ? It is clear that the intrusion of probability in molecular biology is not straightforward. It calls into question not only the design of deterministic gene expression, but the whole tradition of biology, which has always been deterministic regarding the internal functioning of organisms. As in physics, the question inevitably arises of the status of probability in biology: is it a subjective probability (epistemic), dependent on a lack of complete information upon the studied phenomena and ultimately reducible or is it an objective (ontological) stochasticity dependent on the intrinsic nature of the living process, and thus irreducible? The emergence of stochastic gene expression therefore raises important questions about its implications not only for biological theories but also about its epistemological status. Furthermore, it causes reluctance among biologists for number of historical reasons that should be understood for being bypassed. For all those reasons they organized in the center Cavaillès (ENS-Paris) a multidisciplinary conference in French in 2008, entitled "Le Hasard au Coeur de la Cellule”. This conference brought together experimental and theoretical biologists, modelers, epistemologists and philosophers who addressed all those issues. This conference attracted a large audience and was a successful interdisciplinary exchange. The conference that they are now organizing aims at extending this initiative by giving it an international dimension. They plan to publish the outcome of this meeting. The holding of this conference will bring a new theoretical and epistemological dimension for research in this multidisciplinary field and create a unique opportunity for interaction between participants. For more information about the program and registration, click here.

BBMRI-NL second annual conference ‘Connecting Biobanks’

Mon, 23 May 2011 11:39:00 +0200

Since its launch in 2010, BBMRI-NL has made great progress in achieving its purpose of connecting biobanks. Over forty small scale Complementation Projects received funding, as well as several large scale collaborative Rainbow Projects. Dutch biobanks were enriched and harmonized, a necessity for European collaboration and essential for the future of biomedical science. The Dutch biobank initiative BBMRI-NL wants to commemorate these steps forward and gladly invites you to its second international conference ‘Connecting Biobanks’ on November 21, 2011 in Rotterdam. Please mark this date on your calendar! The conference will offer:

International keynote speakers in the field of pharmacogenomics and biobanks, as yet confirmed: Prof. Bartha Knoppers (Mc Gill University) and Prof. Bruce Psaty (University of Washington)
Masterclasses for selected researchers
Results from BBMRI Rainbow Projects
Poster presentations presenting BBMRI-NL Complementation Projects
Workshops
Award ceremony
Ample opportunity to interact with colleagues

Admission is free for non-commercial parties, but registration is required. For commercial parties the admission fee is € 100,-. For registration click here. Conference venue: Engels Grandcafe Restaurant Zalen. Date: 21 November 2011 (from 9.00 till 17.00, followed by drinks) BBMRI-NL is the Dutch project for biobank collaboration, linking over 140 existing Dutch biobanks. Within the 'hub and spoke' structure of the European Biobanking and Biomolecular Resources Research Infrastructure, BBMRI-NL is the Dutch national 'hub'.

Life Sciences Momentum 2011 - Science for Society

Thu, 07 Jul 2011 15:08:00 +0200

When it comes to keeping up with Dutch life sciences, there is no better way than by attending Life Sciences Momentum – for more than a decade the event of choice for anyone interested in the science, the business and the people of the Dutch life sciences field. Meeting new people, catching up with existing relations, exchanging ideas and making new plans – it is all about networking and interacting. This year's edition of Life Sciences Momentum puts the spotlight on the tangible benefits of life sciences research for patients, consumers, companies and our environment. In other words: Science for Society. What has been achieved, what can we expect on short notice and what are the future major developments? Thought-provoking presentations, interactive sessions and inspiring conversations will provide you with new insights on how today's science generates tomorrow's benefits. Registration if free of charge. Organised by the Netherlands Genomics Initiative

BITS workshop: Comparative Genomics in Eukaryotes

Tue, 18 Oct 2011 10:08:00 +0200

You are kindly invited to this workshop! During a whole-day hands-on
session, you will learn to perform the basic steps of gene family analysis
to construct a gene family phylogenetic tree, detect species-specific
duplicates, study orthologs and identify synteny. They will also look into
comparative sequence analysis to study promoter sequences and
identify conserved regulatory elements. More info and registration on www.bits.vib.be/compgen

Teacher Training Bioinformatics@school

Fri, 25 Nov 2011 00:00:00 +0100

The third edition of the bioinformatics@school-trainings for high school teachers organised by NBIC will take place in Nijmegen. The training explains how teachers can design their own bioinformatics assignment. More information will follow in Dutch: Ontwerp je eigen bioinformatica-opdracht!
Nascholing bioinformatica in de klas, vrijdag 25 november 2011

Vind genen in de databank
Maak een stamboom
Bekijk een eiwit in 3D

WAAROM?
Of het nu over ecologie, evolutie of celbiologie gaat; elke tak van biologisch onderzoek maakt tegenwoordig gebruik van genetische databanken en programma’s om genen en eiwitten te vergelijken en weer te geven. Die databanken en programma’s zijn in het onderwijs goed te benutten! VOOR WIE?
Biologiedocenten die lesgeven in het voortgezet onderwijs aan de bovenbouw havo en vwo, en hun onderwijs willen verbeteren ten aanzien van de moleculaire onderwerpen DNA en eiwitten.
Een bijzonder kenmerk van deze nascholing is dat we ook expliciet leerlingen uitnodigen. Zo maken ook zij kennis met technieken die ze in life sciences zullen tegenkomen, en kunnen samen met docenten meedenken over lesmateriaal. HOE?
Voor leerlingen is de dag gratis, aan docenten vragen we €75,-. Dit is inclusief lunch, hapjes, drankjes en lesmateriaal. PROGRAMMA
09.30 Inloop met koffie en thee
09.45 Welkom en inleiding door Hienke Sminia
10.00 Interactieve lezing over chromosomale mutaties door Drs. Wigard Kloosterman
11.00 Koffie- en theepauze
11.10 Interactieve lezing over bioinformatica als didactisch hulpmiddel door Hienke Sminia
12.30 Lunch
13.30 Oefenen met bioinformatica en in groepen werken aan een eigen lesopdracht
14.45 Koffie- en theepauze
15.00 Vervolg werken aan eigen lesopdracht
16.00 Nabespreking
16.30 Hapjes & drankjes
17.00 Voldaan naar huis INSCHRIJVEN?
Meer informatie over de training en inschrijven kan via hienke.sminia@nbic.nl THUIS UITPROBEREN?
Zoek uit op welk chromosoom het gen voor amylase ligt en of dit om één of meerdere genen gaat.

Open http://www.ncbi.nlm.nih.gov/genome/guide
Dit is een overzicht van organismen waarvan het genoom bekend is. Klik op de regel naast ‘human’ op de M (map viewer).
Je ziet een overzicht van chromosomen. Vul linksboven ‘amylase’ in en klik op 'Find'.

Lecture on Large-scale data processing with Hadoop MapReduce

Fri, 18 Nov 2011 09:51:00 +0100

BiG Grid and Amsterdam Information Retrieval (AIR) present a guest lecture by Dr. Jimmy Lin on the processing of large datasets using the open-source MapReduce implementation Apache Hadoop. If you are curious to see how Hadoop can help you with your processing needs, and are not afraid of some technical examples, then this should be a helpful and interesting talk for you. Jimmy will give special attention to Bioinformatics. Specifically: about doing de novo short read assembly using the De Bruijn graph approach on Hadoop. Jimmy received his Ph.D. at MIT and is an associate professor at the University of Maryland, holding several positions. He is currently on sabbatical at Twitter. Jimmy is author of the book 'Data-Intensive Text Processing with MapReduce', the most exhaustive source of information on MapReduce currently available. (See http://www.umiacs.umd.edu/~jimmylin/book.html) Apache Hadoop is an open source data-processing framework that is able to leverage the power of very large clusters of commodity computers. It's today's most widely used software for distributed data processing and provides a rich ecosystem of related tools, together with a large, enthusiastic, and helpful developer community. It has been used to win the 2009 edition of Jim Gray's Sort benchmark, and it is the processing framework powering Watson, IBM's supercomputer that won the game-show Jeopardy earlier this year.

BiG Grid and SARA offer access to a prototype Apache Hadoop service to scientists in The Netherlands, and will have a production-level service ready by the first quarter of 2012. This production service will offer more than 500 cores of processing power, and 500 terabytes of storage capacity, and will be made available for all scientists in The Netherlands. For more information contact us at evert.lammerts@sara.nl.

More information on:

Dr. Jimmy Lin: http://ischool.umd.edu/content/jimmy-lin-0
Hadoop: http://hadoop.apache.org/
Hadoop @ BiG Grid: http://www.sara.nl/project/hadoop

Directions to venue: http://www.amolf.nl/about-amolf/visitor/#c42

IEEE eScience2011 Workshop on “Computing Advances in Life Sciences”

Sun, 03 Jul 2011 17:08:00 +0200

Computationally intensive simulations and processing of large data sets have become a necessity in Life Science research. Full utilization of the available computing platforms has increased the demand for software optimized for performance, scalability and highthroughput. The workshop will bring together leading researchers to share their experiences in software development across all Life Science fields such as biology, biophysics, biochemistry, ecology, medicine, medical imaging, neuroscience, pharmacology and systems biology. The focus will be on discussions regarding methods, algorithms and frameworks for exploiting a wide spectrum of hardware resources such as clusters, grids and clouds; many-core and hybrid systems; GPGPUs, FPGAs and other non-traditional architectures. The workshop is part of the eScience2011 conference (www.escience2011.org, December 5-8, Stockholm). It is organized by the EU funded project ScalaLife and the HealthGrid association which are establishing community structures for provision of support to various aspects on computing in Life Sciences. Important dates:

Full Papers Due: July 1st, 2011
Author Notifications: August 17th, 2011
Presentation: December 5th, 2011

Submission guidelines: Authors are invited to submit papers with unpublished, original work of not more than 8 pages of double column text using single spaced 10 point size on 8.5 x 11 inch pages, as per IEEE 8.5 x 11 manuscript guidelines. The proceedings will be published by the IEEE Computer Society Press, USA and will be made available online through the IEEE Digital Library. Templates are available from here: www.ieee.org/web/publications/pubservices/confpub/AuthorTools/conferenceTemplates.html . Authors should submit a PDF or PostScript (level 2) file that will print on a PostScript printer. Papers conforming to the above guidelines can be submitted through the submissions page at https://www.easychair.org/conferences/?conf=cals2011.

4th International SWAT4LS Workshop - Semantic web applications and tools for life sciences

Tue, 25 Oct 2011 12:59:00 +0200

SWAT4LS is a workshop that provides a venue to present and discuss benefits and limits of the adoption of Web based information systems and Semantic technologies in biomedical informatics and computational biology. The 2011 edition of SWAT4LS will be articulated on a one day workshop, preceded by a one day hackathon and one day of tutorials. SWAT4LS provides an open and stimulating environment that brings together researchers, both developers and users, from the various fields of Biology, Bioinformatics and Computer Science, to discuss goals, current limits and real experiences in the use of semantic, web-based technologies in the Life Sciences and Biomedical Informatics. For more information about the programme and registration, click here.

SURFnet7, launchpad for the new way of working for researchers

Tue, 15 Nov 2011 10:14:00 +0100

On Wednesday December 7th, SURFnet is organizing a festive event "SURFnet7, launchpad for the new way of working for researchers" at Utrecht's Central Museum. This afternoon event is intended to show researchers and potential users the possibilities opened up by SURFnet7. As part of the GigaPort3 innovation programme, the existing network infrastructure will be upgraded, with the aim of giving the research and higher education sector access to a flexible and scalable network that they can easily use – anytime and anywhere. At the event, SURFnet and a number of other key players for the e-infrastructure will explain the possibilities of SURFnet7. They will celebrate the start of rollout of the SURFnet7 network. The prizes for the 'Enlighten Your Research' competition will also be presented. The event starts with lunch at 12.30 p.m. and concludes at 5.30 p.m., followed by drinks. Details of the programme: http://www.surf-academy.nl/programma/event/?id=437

You can register via the following link: http://events.surfnet.nl/wat_maakt_surfnet7_mogelijk_7_december_2011_middag.html

Benelux Bioinformatics Conference 2011

Fri, 10 Jun 2011 22:55:00 +0200

BBC11, the sixth BeNeLux Bioinformatics Conference, will be held in Luxembourg on December 12th and 13th, 2011.

BBC11 will discuss advances in bioinformatics and interrelated disciplines, and their wide-ranging applications in health and biotechnologies. BBC11 will deliver a cross-disciplinary scientific program of oral and poster presentations, as well as other opportunities to explore innovative ideas.

A key theme of BBC11 will be "Bioinformatics: Enabling Translational Biomedical Research". The programme includes invited talks and networking activities to promote the role of bioinformatics in finding better ways to prevent, detect and treat disease.

Invited speakers:

Thomas Lengauer, Max-Planck-Institut für Informatik, Germany
Burkhard Rost, Technical University Munich, Germany
Peter van der Spek, Erasmus Medical Center, The Netherlands
Ioannis Xenarios, Swiss Institute of Bioinformatics and Vital-IT

You can find more information about the BBC 2011 on the conference website: http://www.bbc11.lu/ Registration deadline: 27 November 2011
Abstract submission deadline: 28 October 2011 You can also follow the updates on twitter: https://twitter.com/BBCLux

Genome Browser Seminar

Mon, 14 Nov 2011 14:16:00 +0100

On December 19th, the NBIC BioAssist programme and the Biomics group at the Erasmus MC are organising a seminar on Genome Browsers. Next generation sequencing produces vast amounts of data. One possibility to represent this genomic information in a visual form - and thus to reveal its scientific meaning - is to use genome browsers such as ENSEMBL, UCSC, Generic Genome Browser. The main subjects include, but not limited to, the latest development of genome browsers, genomic data visualization, software and data integration. Please register with Leon Mei if you plan to participate. More information about the programme, including information on how to get to the venue: https://wiki.nbic.nl/index.php/Genome_Browser_Seminar_on_19-12-2011

e-Infrastructure colloquium

Fri, 20 Jan 2012 11:26:00 +0100

Putting Condor in a container: Adapting virtualization techniques to batch systems In a world that could aptly be described as "cloud crazy", it seems quaint and outmoded to be working with batch or grid systems. Despite appearances, the batch system and the cloud are not two discrete entries - rather, there is almost a continuum of techniques that blend and mix virtual machines, virtualization and batch systems. This talk will demonstrate the recent process we have made in porting virtualization techniques to the Condor ecosystem - without using virtual machines. The various techniques implement and discussed are organized into the categories of accounting, resource management, and isolation. To accomplish this, we use modern Linux kernel features such as cgroups and namespaces. The resulting system solves some age old problems in batch systems, and may pleasantly even the most experienced sysadmin. Dr. Brian Bockelman, Computer Science & Engineering, Universityof Nebraska, Lincoln, USA Register for this lecture by adding your name in the doodle www.doodle.com/uv27vqqthn5ssui6 The capacity is limited to 51 registrants, so be sure to register in time!

Interdisciplinary Seminar on Biological Networks

Wed, 21 Dec 2011 10:05:00 +0100

Networks are becoming increasingly important in core areas of biology and their study has important applications, for example, in personalized medicine and biotechnology. Mathematical and computational techniques play a key role in understanding these networks. This seminar covers some of the most relevant topics in this area. Target group: This seminar is intended for master students and beginning PhD students. It will be truly interdisciplinary, and students from mathematics, biology, bioinformatics, and computer science as well as other disciplines are welcome. The seminar covers aspects of graph theory, network analysis, algorithmics, combinatorial optimization, computational complexity, statistics, probability theory, and cell biology, and knowledge in at least one of these fields as well as interest in the others is a hard requirement for participation. The number of ECTS points depends on contribution and/or size of a project, but the maximum is 8 ECTS points. The seminar will take place on Tuesdays at Utrecht University, the exact place and time slot is still to be decided. The number of participants is limited to 20. If you are possibly interested in participating, please send an e-mail to gunnar.klau@cwi.nl with name, background, interests and preference for time slot. Motivation and topics: It has turned out that the complexity of life is rather due to complex interactions between molecules than to the complexity of single entities. Consequently, research in the life sciences has focused on studying systems of interactions such as regulatory, metabolic, signaling, and interaction networks. Mathematical and computational techniques play a key role in understanding these networks and this seminar focuses on some of their core contributions to network biology:

Introduction to cell biology and biological networks, basic graph theory
Network analysis. (Random) network models and their properties. Network motifs and modules.
Networks in inference: Protein function, disease genes, drug targets
Network modules. Clustering and bi-clustering.
Network mining: Active/dysfunctional subnetworks. Classification.
Network evolution and comparison. Alignment and queries.
Late-breaking results (from the top conferences RECOMB and ISMB)

Format: They will discuss original work on one topic in each class, which is presented by one or two students. Assignment of topics will take place in January. In addition, there is the possibility to do an additional small project on a topic of choice. Grades will be given based on the presentation, active participaction in interdisciplinary discussions, and a possible final project. For more information, click here.

SURF Onderzoeksdag

Mon, 09 Jan 2012 16:11:00 +0100

Together with the Netherlands eScience Center, SURF is organising the 'SURF Onderzoeksdag'. This research day will be held on February 9th 2012 in Media Plaza in Utrecht. The day aims at Dutch researchers and their supporters. At the SURF Onderzoeksdag researchers will show how ICT-methods can enrich scientific research and the presentation of scientific research. The latest national and international developments will be presented in keynote speeches and parallel sessions (mainly in Dutch!). Inspiring examples will demonstrate the role of ICT in text, data and image analysis and presentation. There will also be sessions about how ICT can help with the profiling of your own research and about the link between research and education. More information about the SURF Onderzoekdag can be found on www.surf.nl/ozdag

NCSB systems biology tutorial on parameter estimation

Mon, 16 Jan 2012 15:41:00 +0100

This one-day tutorial will give PhD students and postdocs a basic understanding of aspects of parameter estimation that are important in the Systems Biology practice. Fitting a model to given data by finding the appropriate parameter values is a common task in Systems Biology. Still, this often fails. In this course we discuss theoretical basics, existing methodologies, practical problems, and illustrative examples. This course is intended for a wide audience and does not require a strong background in mathematics or statistics. There will be a time window reserved for discussion of problems brought forward by the participants themselves. A short practical is included. For more information, visit the website.

International CSBB Symposium

Mon, 31 Oct 2011 18:55:00 +0100

The CSBB is organising a symposium, entitled “System Biology and Bioenergetics”, to be held on 13th February 2012 at the Radboud Auditorium, Nijmegen, The Netherlands. This is the second symposium in a series of symposia organised by the four Dutch Systems Biology consortia. It aims to bring together the members of these Dutch centres with each other and with other national and international systems biology researchers. Top experts from around the globe have been invited to highlight advances in energy metabolism, cancer, ageing and developmental mechanisms, through different systems biology approaches (see program). A session with laptop presentations will be organized during a “lunch-on-the-move”. Here, CSBB researchers will present their latest data and there will be ample time for discussion and networking. This symposium will be of interest to scientists and clinicians of all levels, from students to senior professors. Everyone is encouraged to attend. Registration is handled via PAO Heyendael: click here. Registration is open until 8th January 2012 (hotel information).

MidSouth Computational Biology Society's annual meeting (MCBIOS 2012)

Tue, 31 Jan 2012 15:51:00 +0100

The 2012 MCBIOS Conference, Making Sense of the Omics Data Deluge,
will be held February 17th and 18th in Oxford, MS on the campus of the University of Mississippi. The mission of MCBIOS is to foster networking and collaborationpromote the professional development of members and supporting our student members. Their objectives are:

Advance the understanding of bioinformatics and computational biology
Bring together scientists of various backgrounds and disciplines
Facilitate the collaboration of researchers with similar or complementary backgrounds to solve biological, health and/or medical problems
Promote education in bioinformatics and computational biology
Inform the general public on the results and implications of current research in bioinformatics and computational biology
Promote other activities that will contribute to the development of bioinformatics and computational biology MCBIOS Bylaws Current version.

For more information about the conference, visit their website.

YISB workshop 2012

Wed, 21 Dec 2011 09:25:00 +0100

YISB is organising a workshop to help young systems biologists bridge the communication gap that often exists in systems biology. Mathematicians want loads of data, time series, etc., but they don't know why it's hard to obtain this data. Biologists want a complete mathematical model which includes anything they have observed experimentally, but they don't see why it's hard to include anything. Therefore, they will shortly introduce mathematical modelling to biologists and biology to mathematicians, and they show a case study illustrating how these fields can complement each other.They'll also focuss on how to communicate your research to people outside your field. What details should you discuss, and which do you leave out? When you understand the other world a little bit better, it's time to start communicating. Not just communicating anything, you will be communicating your research with the other participants. You can present a specific research question from your research and discuss it with both biologists and mathematicians. For the research questions they ask you to submit an abstrect of your research and your question (see research question instructions). Finally, they'll show you where you could be in 10 years. What can systems biologists do in research, industry or pharmaceutics? Registration is open, and the workshop is free of charge. For more information, visit the site.

NBIC HotTopics meeting: Peptide and protein quantification using Mass Spectrometry

Sun, 22 Jan 2012 23:54:00 +0100

To date in addition to protein identification, quantification of abundances of proteins and peptides is common practice. In general there are stable isotope labeling, label-free and MSn approaches to obtain abundance levels of proteins using mass spectrometry. Each technique has its pro's and con's with differences in applicability and computational approaches. In the HotTopics Proteomics meeting an overview of these techniques will be shown, followed by the detailed presentation of the current state of the art of these three approaches. Finally the HotTopics Proteomics meeting will conclude by addressing the need for follow-up analysis using pathway or network discovery methods. Keywords: proteomics, peptides, quantification, statistics, mass spectrometry You can find more information about the programme and registration here. NBIC HotTopics are a series of NBIC meetings committed to bringing scientists together to discuss the concepts and methods on a hot topic in their research field. It should provide a platform to keep in touch with peers in the field and foster sharing of new insights, applications and collaborations. Therefore, the aim of the meeting is not to present the latest results of your own work, but rather to identify new trends and breakthroughs in the field in general.

3rd annual Visualizing Biological Data conference (VizBi 2012)

Tue, 31 Jan 2012 15:58:00 +0100

VizBi 2012, the 3rd international meeting on Visualizing Biological Data and the first in a series of EMBO conferences, will be held 6-8 March 2012 at the EMBL-Heidelberg in Germany. VizBi brings together scientists, illustrators, and designers actively using or developing computational visualization to study a diverse range of biological data. The conference features 22 invited talks that will review the state-of-the-art and challenges in visualizing data from genomes, transcripts, proteins, cells, organisms, and populations. Prior to the meeting (5 March), there will also be tutorials on several visualization tools. For more information about the conference, visit their website.

AMIA Summit on Translational Bioinformatics 2012

Tue, 31 Jan 2012 16:04:00 +0100

The American Medical Informatics Association (AMIA) is pleased to invite submissions for the 2012 Summit on Translational Bioinformatics (TBI), which will be held on March 19th-21st 2012 at the Parc 55 Hotel San Francisco, CA. The Summit will be part of the Joint Summits on Translational Science and will be immediately followed by the Summit on Clinical Research Informatics (CRI) at the same venue on March 21st – 23rd. Translational Bioinformatics focuses on applications of bioinformatics innovations within a clinical context and touches nearly all areas of biological, biomedical, and clinical research. Since 2008, the TBI Summit provides the premier forum for interacting with leaders in informatics at the interface of biology and health care. The 2012 TBI Summit will deliver a scientific program comprising a set of tutorials, lectures, panels, and posters that showcase the latest advances in applying informatics to biomedical research and clinical care. This year, they will have four tracks covering research that takes us from base pairs to the bedside, with an emphasis on clinical implications of mining massive data-sets, and on bridging the latest multimodal measurement technologies with large amounts of healthcare data:

Concepts, Tools and Techniques for Translational Bioinformatics
Integrative Analysis of multi modal measurements
Base pairs to Bedside
Informatics with Big Data

For more information about the conference, visit their website.

Webinar Bio-Informatics

Fri, 24 Feb 2012 08:59:00 +0100

Find out how much is possible with your genome data!

Genomics has matured to a standardized technique for analyzing bacterial activity in food products. With the reduction in costs of sequencing, microarray chips and generation of GC-MS data, the possibility of using these techniques are accessible to any company.

By using ~omics techniques, methods to enhance the viability of your (probiotic) production strain or remove spoilage organisms from your food product can be developed much faster and will be more sensitive in comparison to traditional methods.

NIZO food research supports genomics projects by providing pipelines for analyzing and integrating various genomics data sets.

In this free webinar they will present state-of-the-art bioinformatics tools and approaches that allow characterization, monitoring and prediction of bacterial strain functionalities related to food applications on the level of the genome sequence.

Topics covered during this 1 hr webinar are:
- (next generation) genome sequencing and annotation
- comparative genomics and genotype phenotype matching
- genome scale metabolic modelling and
- (16S) pyrosequencing of environmental samples For more information and registration, click here.

Symposium on Data Visualization (SARA and NLeSC)

Sat, 10 Mar 2012 16:24:00 +0100

On March 30, 2012, SARA and the NLeSC (Netherlands eScience Center) organize a symposium on data visualization, data exploration and collaboration. During this symposium the opening of the Collaboratorium, a new facility that is fully tailored to support cooperation, will take place.

The Collaboratorium offers researchers an excellent facility for multi-user presentations and (remote) communication with colleagues. It has strong possibilities for visual interpretation and exploration of large data sets, (Big) Data.

The facility stimulates cooperation and communication and is aimed at easy-accessible use, as well as the use of highly advanced applications. Besides a high-resolution (17 Mpixel) Multi-touch screen and facilities for video conferencing the Collaboratorium is also equipped with 3D stereo projection. It offers excellent opportunities for collaboration, joint ventures and technology transfer between science, government and industry.

The program is in preparation. Details will soon be published on the website.

After the plenary program, you can get an impression of the groundbreaking possibilities of the Collaboratorium during the informal reception at their address Science Park 140 (ICT Synergy Hub) at Science Park Amsterdam.

If you want to attend the event, you can already register.

CWI Life Sciences Seminar - Many-core Modularity Graph Clustering

Mon, 26 Mar 2012 19:23:00 +0200

The titel of the next CWI Life Sciences Seminar is: 'Many-core Modularity Graph Clustering', and will be presented by Bas Fagginger Auer (joint work with Prof. Rob Bisseling). Agglomerative clustering is an effective greedy way to quickly generate graph clusterings of high modularity in a small amount of time. In an effort to use the power offered by many-core CPU and GPU hardware to solve the clustering problem, they introduce a fast fine-grained shared-memory parallel graph clustering heuristic. As an application, they will consider this heuristic in the context of clustering a gene co-expression network repeatedly with varying edge weights.

NBIC HotTopics meeting: Detecting variations in the human genome using NGS

Thu, 22 Mar 2012 15:14:00 +0100

The new sequencing technologies are transforming the study of genomic variation. Detection of base-pair level and structural variants (SVs) and their association to human disease is a challenging and although various computational methods have been described for the detection of variations, no algorithm is fully capable of discovering all types of variants reliably. During this HotTopics meeting we will elaborate on the use of different experimental and computation approaches to call all types of variants across different size ranges. The comprehensive discovery, characterization and understanding the origins of genomic variants have important implications for studying human evolution and disease. The aim is to identify advances, issues and challenges of these methods in the context of recent developments in genomics, proteomics and metabolomics. In an open discussion we want to learn how to make the best out of these computational techniques for a better understanding of biology.

Keywords: variation detection, SVs, high-throughput data, NGS, human genome You can find more information about the programme and registration here. NBIC HotTopics are a series of NBIC meetings committed to bringing scientists together to discuss the concepts and methods on a hot topic in their research field. It should provide a platform to keep in touch with peers in the field and foster sharing of new insights, applications and collaborations. Therefore, the aim of the meeting is not to present the latest results of your own work, but rather to identify new trends and breakthroughs in the field in general.

TI Pharma Spring Meeting 2012 - Public Private: Perfect!

Sat, 10 Mar 2012 16:18:00 +0100

The first lustrum edition of the TI Pharma Spring Meeting will be held on Tuesday, April 17, 2012 at Media Plaza in Utrecht. At this meeting industrial researchers, academic scientists, regulatory experts, policy makers and more meet to discuss the latest advancements in drug discovery and development. TI Pharma would like to invite you for this interesting event. Scientific perspectives, the organizational implications of working alongside in complex research projects and networking are the core topics you can subscribe yourself for on their registration site. Fostering public-private interactions is what TI Pharma is all about, and forms the basis for this year’s theme ‘Public Private: Perfect!’. With two plenary lectures on PPP examples in the United Kingdom, poster sessions and a number of parallel sessions in which both research as well as other topics are discussed, they offer you an attractive program. Roadmaps for future public private partnerships in Pharmacotherapy and Neglected Diseases were recently presented to the Dutch government as part of the Life Sciences & Health ‘topsector’ innovation contract. With the discussions and interactions held at the Spring Meeting they aim to come to a next step in defining the public-private interactions in drug research for the future. The programme includes a parallel session about the Integration of Life Science Technologies, organized by DTL. More information and registration, click here.

NCSB Systems Biology Tutorial: Statistics with R

Tue, 21 Feb 2012 15:11:00 +0100

This is a one-day introduction to the possibilities of R for those who would like to use, or have already started using R for statistical data analysis.
The day will start with a lecture in which the philosophy behind the R-language will be explained. This will allow you to better understand the data structures in R. Also, you will be shown some of the advanced possibilities of R as well as where to find tutorials if you want to know more about those techniques. Subsequently there will be a computer tutorial where you can start either to learn working with R or, if you already have some experience, start to explore more advanced topics in R. The tutorial contains material from an introductory master course that is taught at the VU University.
Topics to be touched upon: R language basics, installing R and R-packages, finding help, editors for R, basic statistical tests, model fitting, reading/writing data from/to files, making publication-ready graphs, books and tutorials on the use of R.
For more information, visit the website.

16th Annual Conference on Research in Computational Molecular Biology (RECOMB 2012)

Tue, 31 Jan 2012 16:09:00 +0100

RECOMB 2012 will take place in vibrant and beautiful Barcelona from 21 to 24 April 2012. There will be a strong focus on the computational challenges arising from the extraordinary developments in high throughput technologies. Participants will enjoy a full agenda of keynote talks, paper presentations, and poster sessions, with ample opportunities to get a sample some of the city life of Barcelona. The meeting also overlaps with Sant Jordi (Saint George), on April 23, the patron of Catalonia, and one of the most important civic holidays in the country. RECOMB is a well-established scientific conference bridging the computational, mathematical, and biological sciences. The conference features keynote talks by preeminent scientists in the life sciences, together with presentations of refereed research papers in computational biology. The conference series aims at attracting research contributions in all areas of computational molecular biology, including: molecular sequence analysis; recognition of genes and regulatory elements; molecular evolution; protein structure; structural genomics; analysis of gene expression; biological networks; sequencing and genotyping technologies; drug design; probabilistic and combinatorial algorithms; systems biology; computational proteomics; structural and functional genomics; information systems for computational biology and imaging. The origins of the conference are in the mathematical and computational side of the field, and there remains a certain focus on computational advances. However, the effective application of computational techniques to achieve biological innovation remains a central aspect of the conference. For more information and registration, visit their website.

INBIOMEDvision Training Challenge 2012

Fri, 04 Nov 2011 12:59:00 +0100

From April 23rd to April 27th, 2012 the INBIOMEDvision Training Challenge will be held in a nice location close to Barcelona. During the Training Challenge 2 groups of 5 advanced students with expertise on different biomedical (informatics) fields will collaboratively work on a single case study. The call for student applications is now open! Application deadline: December 31st, 2011. Each student will be asked to submit a motivated case study - for example a topic from your PhD works that is suitable for a multidisciplinary approach and that focuses on more personalised healthcare. Among the case studies proposed, the organizing committee will select one case study per group. INBIOMEDvision will cover travel costs, accommodation and meals. No registration fee is charged. During the whole week INBIOMEDvision staff members from different areas of expertise will closely supervise and collaborate with the teams. At the end of the week both teams will present their results at a closing scientific event in Barcelona. A jury will select the winning team which will be rewarded with a prize. For more information and an online application form, please visit: www.inbiomedvision.eu You can also contact: Erik van Mulligen (e.vanmulligen@erasmusmc.nl) INBIOMEDvision is an initiative funded by the European Commission that aims to identify and disseminate common ground and possible synergies between Bioinformatics and Medical Informatics, and thus develop Biomedical Informatics (BMI) als a scientiic field that serves to progress in health care and biomedical research. BMI deals with the integrative management and synergic exploitation of the wide ranging and inter-related scope of information that is generated and needed in healthcare settings, biomedical research institutions and health-related industry.

NVTB Symposium - New developments in mathematical biology: DEB applications and epidemiology

Sat, 10 Mar 2012 16:34:00 +0100

The Dutch Society for Theoretical Biology (NVTB) is a biological society focussing on theoretical, mathematical and philosophical biology. The society comprises 200 members from several universities, institutes and other organisations. The main aim of the society is to stimulate and represent theoretical biology in its broadest sense in the Netherlands. A symposium about new developments in mathematical biology (DEB applications and epidemiology) will be held on April, 23. For more information, visit their website.

Netherlands Bioinformatics Conference 2012

Fri, 04 Nov 2011 13:41:00 +0100

On April 24 and 25, 2012 we will be organising the 7th edition of the Netherlands Bioinformatics Conference in Lunteren. More information is available on the conference webpage.

Bio-IT World Conference & Expo 2012

Tue, 31 Jan 2012 16:13:00 +0100

The 2012 Expo plans to unite more than 2,000 life sciences, pharmaceutical, clinical, healthcare, and IT professionals from more than 30 countries. The Expo provides the perfect venue to share information and discuss enabling technologies that are driving biomedical research and the drug development process. Since its debut in 2002, the annual Bio-IT World Conference & Expo has established itself as a premier event showcasing the myriad applications of IT and informatics to biomedical research and the drug discovery enterprise. Marking our 10th anniversary, the 2012 program will feature compelling talks from industry and academia on new trends in data generation, knowledge management, and information technology in life sciences and drug development. Bio-IT World Conference & Expo continues to expand with the addition of three new Tracks: Molecular Diagnostics Informatics, Open Source Solutions, and Cancer Informatics. Spanning three days, the meeting includes 12 parallel conference tracks and 16 pre-conference workshops. For more information, visit the website.

e-Infrastructure colloquium: E-Science Dictates E-Publication

Tue, 10 Apr 2012 16:36:00 +0200

Nanopublications as a Substrate for In-silico Knowledge Discovery

Admission free, No registration, Drinks afterwards! In a world of rapidly increasing complexity, interoperability of data is key and 'data publishing' will become the norm. New key technologies have altered our ability to generate massive data sets. And more data have been recognized as crucial data sources for research. Methods have been developed to mine massive data sets from different type of resources. These enormous strides in mining and measurement technologies have resulted in an exponentially growing flood of data: the 'data explosion’' in the life sciences. The increasing complexity also asks for collaborative environments to master the data sets and turn them into insights. Life sciences projects and programmes are increasingly multidisciplinary and international. This brings many complexities in terms of collaboration and data, information and knowledge management far beyond 'one's own laboratory'. The transition to 'e-science' also dictates innovative ways to publish, share and cite valuable datasets. Barend will cover the recent development around nanopublication in the Life Sciences. He will also address and elaborate on the skills a student of the future need to have.

by Barend Mons, LUMC, EMC, NBIC http://www.biosemantics.org/index.php?page=barend-mons
Barend Mons is a molecular biologist by training and received his PhD on genetic differentiation of malaria parasites from Leiden University. Subsequently he performed over a decade of research on malaria genetics and vaccine development in close collaboration with colleagues in developing countries. He served the research department of the European Commission in this field for 3 years as a seconded national expert and did gain further experience in science management at the Research council of The Netherlands (NWO). Barend was a co founder of three spin-off companies in biotechnological and semantic technologies. In the year 2000, Barend switched to the development of semantic technologies to manage big data and he founded the Biosemantics group. At present, Barend is Associate Professor in Bio-Semantics at the at the Department of Human Genetics at the Leiden University Medical Centre with an honorary appointment in the same discipline at the Department of Medical Informatics, Erasmus Medical Centre, University of Rotterdam, both in The Netherlands. He is also Scientific Director of the Netherlands Bioinformatics Center (NBIC), board member of the ELIXIR international board, an executive team member of the Open PHACTS IMI project and e-science integrator for the Life Sciences in the Netherlands e-Science Center. His research is focused on nanopublications as a substrate for in silico knowledge discovery.

e-infrastructure colloquia
This is the first lecture in a series of e-infrastructure colloquia, organized by BiG Grid, e-BioGrid, NBIC, SARA, Nikhef, EGI, NLeSC. Location
Science Park Amsterdam is easily accessible by public transport, train station Amsterdam Science Park. Paid parking for cars.
http://www.scienceparkamsterdam.nl/en/contact/how-to-find-us The following colloquia are on:

Wednesday 23 May at AMC, Amsterdam organized by e-BioGrid
Keynote by Roberto Barbera, University of Catania and INFN, Italy, followed by a panel discussion.
Thursday 21 June, Science Park Amsterdam organized by EGI

First International School on Semantic Web Applications and Tools in Life Sciences

Thu, 05 Apr 2012 17:04:00 +0200

It is a great pleasure to announce the first "International School on Semantic Web Applications and Tools for the Life Sciences" to be held in Aveiro (Portugal), from May 2nd to 5th, 2012. This school will provide advanced hands-on training in the use of Semantic Web technologies in research and enterprise. The format of the school will consist of focused keynotes, tutorials and hands-on sessions. Its content will include core Semantic Web technologies and aspects that complement them in practical applications.The school aims at bringing together practitioners, researchers and world leaders in the adoption and application of Semantic Web technologies in research, from academia, industry and small companies. The program of the school will include:

User Interaction and Semantic Web (Eric Miller, CognitiveAtlas)
Robust Ontology Design (to be confirmed)
Semantic Search (Michael Schroeder, GoPubMed)
Semantic Web Services (Luke McCarthy, SADI)
Semantic Web and large scale Life Sciences Knowledge Bases (Jerven Bolleman, Uniprot)
SPARQLing away at Data Integration using federated queries and SWObjects (Helena Deus, DERI)
Gene Disease Association (Dietrich Rebholz-Schugmann, EBI)

Please refer to the website for a detailed and updated program. Participants fees are €300 (before March 31st) and €350 (from April, 1st).The school will be limited to 40 participants. For registrations, please click here.

Spring 2012 NMC Metabolomics Meeting

Fri, 30 Mar 2012 15:36:00 +0200

The Netherlands Metabolomics Days offer a lecture programme with international key note speakers and a poster session. The first day May 7th is a closed meeting for NMC-members, the second day May 8th will be open to all national and international researchers and other people interested in metabolomics. Participation is free. For more information and registration, click here.

Great Lakes Bioinformatics Conference 2012 (GLBIO 2012)

Tue, 10 Jan 2012 15:22:00 +0100

The 7th Annual Great Lakes Bioinformatics Conference (GLBIO) is among the newest official conferences of the International Society for Computational Biology (ISCB). The conference provides an interdisciplinary forum for the discussion of research findings and methods. An important goal for the conference is to foster long term collaborative relationships and networking opportunities within the domain of computational approaches to biology. The program will include oral presentations, poster presentations, invited keynote speakers and tutorials. Keynote speakers:

Howard Cash, Gene Codes
Michael Lynch, Indiana University
Mercedes Pascual, University of Michigan
Russell Schwartz, Carnegie Mellon University

For more information about the program, submissions and registration, click here.

4th International Workshop on Semantic Web Information Management

Fri, 30 Mar 2012 12:28:00 +0200

As the World Wide Web grows, it is becoming more and more complex for humans to efficiently find and exploit the information we need. The underlying idea of having a description of data available on the Web, organized in such a way as to be used by machines for automation, integration and reuse across various applications, has been promoted by a number of research fields. The fourth International Workshop on “Semantic Web Information Management" (SWIM) aims to review the most recent data-centered solutions for the Semantic Web. In particular, the workshop’s ambition is to present and analyze techniques for semantic information management, taking advantage of the synergies between the logical basis of the Semantic Web and the logical foundations of conceptual modeling. Indeed, a leitmotif of these research areas is the proposal of models and methods to represent and manage appropriately structured data, permitting it to be easily machine-processable on the Web. The long-standing experience of the information modeling community can provide a significant contribution to the substantial problems arising in semantic data management using technologies such as RDF, RDFS and OWL. For more information about the conference, visit their website.

10th HealthGrid conference

Thu, 27 Oct 2011 14:14:00 +0200

The tenth HealthGrid conference will take place at the Academic Medical Centre of the University of Amsterdam from Monday 21st to Wednesday 23rd May 2012. It offers the opportunity to introduce and share novel ideas for the integration of grid, cloud and other e-infrastructures into the fields of biology, bioinformatics, biomedicine and healthcare, focusing on fundamental and practical aspects of middleware, technologies, applications and deployment issues. The conference programme will include high profile keynote presentations complemented by a set of selected papers, tutorials and demonstrations. A special session of invited talks will also retrospect the evolution and challenges of healthgrids during the last 10 years. Additionally, the conference is co-located and jointly organized with the 4th International Workshop on Science Gateways for Life Sciences. For more information about the programme, contributions and registration, click here.

HARMONY 2012: The Hackathon on Resources for Modeling in Biology

Wed, 18 Jan 2012 09:35:00 +0100

During this 5-day meeting (May 21 to May 25) around 70 researchers work on the development of different format standards (BioPAX, SBML, SBGN and SED-ML), interoperability and infrastructure. The start of the meeting will be a symposium open to interested scientists with tutorials and talks from three internationally recognized systems biologists, Gary Bader (University of Toronto, Canada), Nicolas Le Novere (EBI, UK) and Michael Hucka (California Institute of Technology, US). A reception and poster session will conclude the day allowing local researchers to exchange themselves with international systems biologists. The remaining part of the meeting is devoted to hands-on hacking and interaction between pople focused on practical development. For more information, visit the website.

International Symposium on Bioinformatics Research and Applications (ISBRA'12)

Mon, 23 Jan 2012 10:18:00 +0100

The International Symposium on Bioinformatics Research and Applications (ISBRA) provides a forum for the exchange of ideas and results among researchers, developers, and practitioners working on all aspects of bioinformatics and computational biology and their applications. Submissions presenting original research are solicited in all areas of bioinformatics and computational biology, including the development of experimental or commercial systems. For more information, visit the website.

4th International Workshop on Science Gateways for Life Sciences

Tue, 25 Oct 2011 13:03:00 +0200

New technologies and experimental methods in the field of life sciences have enabled researchers to create huge amounts of data in extremely short times. In turn, analysing this data demands a rise of compute power, storage, and data transmission. An enormous number of complex and sophisticated algorithms and tools have been developed to aid research. The demand for compute power and storage is met with a rise in provision of infrastructure and High-Performance Computing facilities and has resulted in the popularity of novel utility computing infrastructures, such as grid and cloud computing. Despite the increasing availability of resources, the broad uptake of these facilities and infrastructures is not following the same pace. The main reasons for this lie in the complexity of the human interface to these computing infrastructures. An approach to offer easy and intuitive access to computing infrastructures irrespective of their location is a Science Gateway. Science Gateways are frameworks (or toolsets) which incorporate applications, data and tools to enable running applications on Grid infrastructures. They also provide services to support, upload, search, manage and download (or share) applications and data. The gateways are integrated via portals or sets of applications. Gateways enable user communities to use compute and data resources through a common graphical user interface in an easy and intuitive way. As a result, users can focus on their applications instead of learning and managing the complex underlying infrastructure.

IWSG-Life2012 will bring together scientists from the field of life sciences, bioinformatics and computer science. The aim is to exchange experience, formulate ideas and introduce up-to-date technological advances in molecular and systems biology in the context of Science Gateways.

For more information, click here.

Science Gateways for Semantic-Web-Based Life Science Applications

Wed, 23 May 2012 00:00:00 +0200

Science Gateways for Semantic-Web-Based Life Science Applications
by Roberto Barbera (University of Catania and INFN, Italy)
followed by a panel discussion "Data analysis for the masses with cloud?" The colloquium is part of the programme of HealthGrid/IWSG-Life. Panelists:

Roberto Barbera, University of Catania and INFN, Italy
Shantenu Jha, Rutgers State University of New Jersey, US
Péter Kacsuk, MTA-SZTAKI, Budapest, Hungary
Tony Solomonides, NorthShore University Health System, US
Henri Vrooman, Erasmus MC - University Medical Center Rotterdam, The Netherlands
Nancy Wilkins-Diehr, San Diego Supercomputer Center, University of California, San Diego, CA USA

Abstract
e-Infrastructures have been built in several areas of the world but, despite the investments made by the European Commission and by other funding agencies, both at national and international level, the total number of its users is in the order of magnitude of 104, much less than O(107), which is the order of magnitude of the number of GÉANT users, or even O(106), which is the is the order of magnitude of the number of researchers in Europe. The reasons for this, investigated by several surveys (e.g., the EU-commissioned eResearch2020 one), are related to the complexity for non-IT-expert users of the Grid security, the little adoption of standards to let different middleware be interoperable among each other, and the lack of general frameworks to build easily customizable high-level user interfaces. In this keynote speech, I will report on the work done at INFN, in the context of several EU projects, to develop a standard-based and middleware-independent framework to build new-generation Science Gateways supporting Identity Federations. About Roberto Barbera
Prof. Roberto Barbera was born in Catania (Italy) in October 1963. He graduated in Physics "cum laude" at the University of Catania in 1986 and since 1990 he holds a Ph.D. in Physics from the same University. Since 2005 he is Associate Professor at the Department of Physics and Astronomy of the Catania University. Since his graduation his main research activity has been done in the domains of Experimental Nuclear and Particle Physics. He has been involved in many experiments in France, Russia, United States and Sweden to study nuclear matter properties in heavy ion collisions at intermediate energies. He is author of several book chapters, more than 170 scientific papers published on international journals, and more than 400 proceedings of international conferences. He is editor of the International Journal of Distributed Systems and Technologies and referee of Journal of Grid Computing, Future Generation Computer Systems, and BMC Medical Informatics.
Since 1997 he has been involved in CERN experiments and he is currently one of the members of the ALICE Experiment at LHC. Within ALICE, he has been the coordinator of the Off-line software of the Inner Tracking System detector and member of the Off-line Board. Since late 1999 he is interested in Grid Computing. He is member of the Executive Board of the Italian INFN Grid Project, of the Executive Committee of the Italian Grid Infrastructure (the Italian National Grid Initiative) and of the Scientific & Technical Committee of GARR (the Italian National Research and Education Network). Between 2005 and 2009 he has been the Director of two large Grid Projects (TriGrid VL and PI2S2) funded by the Sicilian Regional Government and by the Ministry of University and Research, respectively. At European level, he has been involved with managerial duties in many EU funded projects and he is currently the Coordinator of the EPIKH Marie Curie Action. In 2004, he created the international GILDA Grid infrastructure for training and dissemination that he coordinates since the beginning. He is currently involved in the design and implementation of Science Gateways for various Virtual Research Communities. About Location
Academic Medical Center of the University of Amsterdam (AMC).
The AMC is located in the south of Amsterdam, being asily reached by train, subway and bus. The trip from Amsterdam Center by public transportation takes ~20min. See more information here. About e-Infrastructure colloquia
This colloquium is organized by e-BioGrid. Admission: registration is required, no fee.
e-Infrastructure colloquia series are organized by BiG Grid, e-BioGrid, NBIC, SARA, Nikhef, EGI, NLeSC. The following colloquium is on:
- Thursday 21 June, Science Park Amsterdam organized by EGI

Belgian-Dutch Conference on Machine Learning & Workshop on Predictive Modeling for the Life Sciences

Fri, 02 Mar 2012 11:10:00 +0100

The 21st edition of the annual Belgian-Dutch Conference on Machine Learning (BeneLearn) will be organized in Ghent, in conjunction with a workshop on Predictive Modeling for the Life Sciences (PMLS). This joint event takes place on the 24th and 25th of May 2012 at the Faculty of Bioscience Engineering of Ghent University. BeneLearn serves as a forum for researchers in machine learning, knowledge discovery, pattern recognition, data mining and diverse application domains. Organised for nearly 22 years in a row, it has traditionally been an important opportunity for the dissemination of new ideas and for intensifying the collaboration between the different machine learning groups in Belgium and the Netherlands. To this end, it aims at bringing together promising young researchers in the course of their PhD and more established names. For more information, visit the website.

NVTB annual meeting

Sat, 10 Mar 2012 16:40:00 +0100

The annual meeting of the Dutch Society of theoretical biology (NVTB) will this year be held on Thursday and Friday, May 24 and 25 in Schoorl. Registration is open already. They have two invited lectures:Professor Martin Scheffer (WUR) will speak about 'Resilience Revisited' and Prof. Dr. Bela Mulder (AMOLF) about 'Survival of thealigned: modelling self-organisation in the plant cortical microtubule array'. For more information and the program, visit the website.

BioBusiness Event

Thu, 05 Apr 2012 16:57:00 +0200

BioBusiness Event is the annual business & network meeting for professionals in the Life Sciences & MedTech sector. The objective of this event is to provide a platform and to be a meeting place for entrepreneurs, investors, managers, business developers, scientists, consultants and other parties interested in business creation and innovation in Life Sciences & MedTech. The key elements of BioBusiness Event are:

Keynote speakers
Interactive Infomarket
Meet the Expert
Meet the Recruiter
Masterclass BioBusiness pitch presentations and Award
Diverse parallel sessions, workshops and Roundtable discussions
Niaba ALV

For more information, visit their website.

New Style VOC Conference

Tue, 31 Jan 2012 15:42:00 +0100

The Dutch/Flemisch Classification Society, VOC, is an interdisciplinary society that aims at communicating scientific principles, methods, and applications of ordination and classification. The VOC is a member of the International Federation of Classification Societies. The VOC would like to invite you to attend its first new style conference. Contributed papers can be submitted on topics such as classification, clustering, scaling, data analysis, machine learning, pattern recognition, statistical modeling, and applications of classification and data analysis. PhD students are encouraged to actively participate; therefore, the conference fee is kept very low. Important Dates / Deadlines:

March 30: deadline for abstract submission.
April 15: notification of acceptance of presentation.
May 11: deadline for inscription of non presenters.

For more information, visit the conference website.

Workshop Software Licensing and Valorization

Fri, 25 May 2012 00:00:00 +0200

Many software projects in the life sciences are written as "open source". But do we actually know what that means? What is "open source"? Is it different from "Public Domain?" What is a License? And how and when do I choose one? Do I need to claim copyrights? Can open source software be monetized or otherwise valorized? Can open source and closed source software be working together?

Legal issues surrounding software are not the specialty of bioinformatics programmers, nor from their (biology-oriented) group leaders. It is, however, for both of these groups very important to have a basic understanding about software licensing. To inform as many people as possible, NBIC and NMC together are organizing a one day workshop on Software licensing and valorization.

This workshop is organized together with NMC and Technology Transfer Offices. In the morning session a lecture will introduce you to software copyright and what a license can and can not do, with examples of existing open source licenses. A second lecture will add a valorization perspective: open source in company practice. In the afternoon session we will discuss licensing issues around software projects from participants in the workshop. Participants are encouraged to contact us with their own experience and questions. For more information and the registration form check here.

Thesis defense

Fri, 11 May 2012 09:35:00 +0200

Jumamurat Bayjanov (Radboud University) is defending his thesis Genome-scale integrative genotype-phenotype analysis of Lactococcus lactis and Lactobacillus plantarum. The work described in his thesis is part of the NBIC research programme BioRange.

NCSB Workshop

Mon, 14 May 2012 09:33:00 +0200

NCSB organizes a workshop on June 7^th about "Parameter Estimation and Uncertainty Analysis in Systems Biology". Speakers are:

Hans van Beek (VU / NBIC)
Gunnar Cedersund (Linköping University, SE)
Andreas Raue (University of Freiburg, DE)
Joep Vanlier (TUE / CMSB)
Vladislav Vyshemirsky (University of Strathclyde, Glasgow, UK)

Registration
Registration is free; first come, first served. Deadline for registration is June 1^st. You can register here:www.ncsb.nl/congress/public More information and contact
More information about the workshop can be found the NCSB-website: www.ncsb.nl/workshop/uncertainty-analysis, or you can contact Natal van Riel (n.a.w.v.riel@tue.nl) of TU Eindhoven. The workshop information is also available in de NBIC course overview.

SIB PhD Training Network and Doctoral Program in Population Genomics Joint Summer School 2012

Mon, 02 Apr 2012 14:48:00 +0200

Population Genomics and Bioinformatics share many common interests at the interface of modern integrative biology, which may generate enormous quantities of complex data, often through multiple sources. Efficient and accurate analysis of such data can only be accomplished through appropriate computational methods.
Working together, bioinformaticians and population genomics scientists develop advanced approaches to study biological variation. This collaboration is imperative to establish new hypotheses and models to strike a new path towards the understanding of biology at the population level.

In order to give PhD students access to the state-of-the-art bioinformatics techniques and the biological questions that population genomics has prompted, the interdisciplinary Doctoral Program in Population Genomics and the SIB are organizing a joint Summer School simply entitled “Bioinformatics and Population Genomics".
The objective of this course is to teach PhD students how to integrate, manage, and analyse experimental genomics data using advanced bioinformatics tools.

Theoretical approaches and their practical application covered during the week by renowned speakers will be of interest to both population genomics and bioinformatics PhD students from Switzerland or abroad.

The summer school will take place in Adelboden, a charming, small village in the Bernese Oberland (Swiss Alps). The beautiful and remote setting, along with the challenging program, were chosen to promote and enhance the communication and interaction amongst teachers and students. Lectures and hands-on sessions will provide the necessary environment to generate lively and informative discussions and initiate new synergies among the young investigators. For more information, click here.

RSG BioCafe: How to handle your supervisor

Fri, 11 May 2012 13:07:00 +0200

Prof. Bart Noordam will give a talk at the Vrije Universiteit of Amsterdam on the subject “How to handle your supervisor”, as part of the RSG BioCafé. A small reception will take place after the talk. Registration via email (rsg-netherlands@iscbsc.org) is required.
Registration deadline: Friday June 8th, 2012
Event website:http://www.iscbsc.org/rsg/rsg-netherlands/biocafe-how-handle-you-supervisor-june-18th-2012 About Bart Noordam
Prof. Bart Noordam, Ph.D. (1964) is co-author with Patricia Gosling of the book “Mastering Your Ph.D.: Survival and Success in the Doctoral Years and Beyond”, rated as a must reading for Ph.D. students and supervisors of all times. After a scientific career of ten years that culminated with a position as department head of the scientific research institute FOM-AMOLF and a professorship at the VU University Amsterdam, Bart Noordam worked for management consultants McKinsey & Company (where he was involved in restructuring former government organizations and developing plans for European pension funds, among other things). He was able to further hone his skills in analytical research and management from 2002 to 2005 as director of FOM-AMOLF (200 employees), and from 2005 to 2008 when, as director, he established an auditor’s office with statutory responsibility for the provinces of Flevoland, Noord-Holland, Utrecht and Zuid-Holland. From February 2008 to April 2009 he was director of the Imaging Department of ASML. He was appointed dean of the Faculty of Science of the UvA effective 1 May 2009. About RSG Netherlands
The Regional Student Group (RSG) Netherlands is a student organization whose mission is to promote scientific and social networking among Ph.D. students in the fields of Bioinformatics and Computational Biology. The group organizes on a regular basis events open to the Ph.D. community, ranging from informal lectures by renowned Dutch scientists to workshops on hot topics for the Ph.D. students, such as effective elaboration of presentations and posters and successful grant writing.

2012 Galaxy Community Conference (GCC2012)

Wed, 28 Mar 2012 12:11:00 +0200

Galaxy makes it easy to perform analysis interactively through the web, on arbitrarily large datasets. With hundreds of tools there are few limits on what can be done. Now with NGS tools & workflows for short-read mapping, ChIP-seq, RNA-seq, metagenomics, and pileup analysis (including numerous Illumina-, SOLiD-, and 454-specific tools), trackster browser, collaborative pages, and support for Galaxy in the Cloud. Galaxy is distributed under a BSD-like license. The Galaxy Community Conference will run for two full days, and be preceded by a full day of training workshops. GCC2012 will have things in common with previous meetings (see GDC 2010, GCC 2011), and will also incorporate new features, such as the training day, based on feedback we received after the 2011 conference. GCC2012 is hosted by the University of Illinois at Chicago, the University of Illinois at Urbana-Champaign, and the Computation Institute. For more information about the conference, click here.

Advanced Statistics and Data Mining Summerschool

Mon, 23 Apr 2012 09:35:00 +0200

This summerschool is organized by the Artificial Intelligence Department of the Computer Science Faculty of the Univ. Politécnica de Madrid. This summerschool is currently in its 7th edition. It is an intensive course aiming at providing attendees with an introduction to the theoretical foundations as well as the practical applications of some of the modern statistical analysis techniques currently in use. The summerschool takes 2 weeks and is divided into 12 courses. Each subject has theoretical classes as well as practical classes in which each technique is put into practice with a computer program. Students may register only in those courses of their interest. A leaflet with all the school details is available here in PDF format. Visit also their website for more information.

RenGen 2012 - Regulatory Genomics Special Interest Group

Fri, 11 May 2012 12:59:00 +0200

Regulatory genomics involves the study of the genomic 'control system,' which determines how, when and where to activate the 'blueprint' encoded in the genome. Regulatory genomics is the topic of much research activity worldwide. Since computational methods are important in the study of gene regulation, the ISMB Regulatory Genomics Special Interest Group - RegGenSIG - focuses on bioinformatics for regulatory genomics. An important goal of the SIG is to foster a collaborative community wherein scientists convene to discuss difficult research problems in all areas of computational regulatory genomics. RegGenSIG 2012 will include presentations and posters that cover the broad spectrum of topics important to regulatory genomics research, and a joint panel discussion with the Alternative Splicing SIG. RegGenSIG will bring together experts in experimental methods and computational methods to consider sequence-based reconstruction of regulatory networks and prediction of gene expression. Topics to be addressed in the SIG include the following:

inference of gene regulatory networks,
utilization of information pertaining to epigenetics, chromatin structure, and histone modifications,
determination of the roles of regulatory RNAs,
prediction of transcriptional regulation from RNA-seq data and ChIP-seq data,
pattern discovery in sequences, and
sequence based modeling of gene expression.

For more information, visit the website.

Brazilian Symposium on Bioinformatics 2012

Tue, 31 Jan 2012 16:16:00 +0100

The 2012 Brazilian Symposium on Bioinformatics (BSB 2012) is an international conference which covers all aspects of bioinformatics and computational biology. BSB 2012 is organized by the special interest group in computational biology of the Brazilian Computer Society(SBC). Since 2005 the BSB proceedings have been published in the series Lecture Notes in Bioinformatics (LNBI) by Springer Verlag. BSB 2012, together with the Brazilian School on Bioinformatics (Escola Brasileira de Bioinformática - EBB), will be held at the College of Computing of Federal University of Mato Grosso do Sul in Campo Grande, a city situated in the Center-West region of Brazil. In addition to regular technical sessions with oral, poster presentations, the conference program will feature invited plenary talks by world-leading researchers. For more information about BSB 2012, visit the website.

The Helsinki Summer School on Mathematical Ecology and Evolution 2012: Theory of Speciation

Thu, 03 Nov 2011 08:45:00 +0100

The Acadamy of Finland is pleased to invite students and young researchers to the summer school Theory of Speciation to be held between 19 and 26 August 2012 in Turku, Finland. The core program of the school consists of five series of lectures:

Sergey Gavrilets: Population genetics of speciation
Nick Barton: Multilocus models of speciation
Sander van Doorn: The role of sexual selection in speciation
Eva Kisdi: The ecology of speciation
Daniel Bolnick: Theory and empirical speciation research

All young researchers working in mathematical ecology/evolution can apply from all countries, especially from Europe and the Mediterranean. The school is aimed at PhD students of biology with sufficient theoretical background and at PhD students of mathematics with interest in ecology and evolution, but they also welcome advanced undergraduates and postdocs. The deadline for applications is 15 April 2012. There is no fee for registration. For more details and application, see http://wiki.helsinki.fi/display/huippu/mathbio2012

3rd International Workshop on BIOKDD'12 and 23rd International Conference on DEXA’12

Mon, 23 Jan 2012 14:05:00 +0100

The 3rd International Workshop on Biological Knowledge Discovery and Data Mining(BIOKDD'12) is held in parallel with the 23rd International Conference on Database and Expert Systems Applications (DEXA’12). With the development of Molecular Biology during the last decades, they are witnessing an exponential growth of both the volume and the complexity of biological data.For example, the Human Genome Projectprovided the sequence of the 3 billion DNA bases that constitute the human genome.And, consequently, they are provided too with the sequences of about 100,000 proteins. Therefore, they are entering the post-genomic era: after having focused so many efforts on the accumulation of data, they have now to focus as much effort, and even more, on the analysis of these data. Analyzing this huge volume of data is a challenging task because, not only, of its complexity and its multiple and numerous correlated factors, but also, because of the continuous evolution of their understanding of the biological mechanisms. Classical approaches of biological data analysis are no longer efficient and produce only a very limited amount of information, compared to the numerous and complex biological mechanisms under study. From here comes the necessity to use computer tools and develop new in silico high performance approaches to support them in the analysis of biological data and, hence, to help them in their understanding of the correlations that exist between, on one hand, structures and functional patterns of biological sequences and, on the other hand, genetic and biochemical mechanisms.Knowledge Discovery and Data Mining (KDD) are a response to these new trends. Paper submission details Authors are invited to submit electronically original contributions in English. Submitted papers should not exceed 5 pages in IEEE format. All accepted papers will be published in the proceedings of DEXA’12 Workshops with IEEE CSP.One of the authors of an accepted paper must register toDEXA’12 conference and present the paper at BIOKDD’12 workshop. For paper registration and electronic submission starting from January 2012, click here. For more information, visit the website.

European Conference on Computational Biology (ECCB) 2012

Tue, 31 Jan 2012 16:24:00 +0100

ECCB'12 - the European Conference on Computational Biology - is the key European computational biology event in 2012 uniting scientists working in a broad range of disciplines, including bioinformatics, computational biology, biology, medicine, and systems biology. ECCB'12 will take place 9-12 September 2012 in Basel, Switzerland. Participation at ECCB'12 will be the prime opportunity to learn about cutting-edge research in computational biology and bioinformatics and to network with other members of our community. ECCB'12 will be organized in association with the 10th [BC]2 Basel Computational Biology conference - the annual scientific symposium of the SIB Swiss Institute of Bioinformatics. For more information about ECCB'12, visit their website.

NBIC co-organises a workshop at ECCB2012

Mon, 23 Apr 2012 09:29:00 +0200

NBIC, SIB, EBI and BTN (Bioinformatics Training Network) organise a one-day workshop related to bioinformatics training for life scientists on September 9, 2012 in Basel, as part of the ECCB2012 conference.

The title of the workshop is: “Bioinformatics Training for Life Scientists - Showcases and Challenges from tutors’ perspectives”. The workshop contains sessions about the challenges that tutors face and about successful showcases. Furthermore, it represents a platform where those involved in bioinformatics training to life scientists can meet, confront and share experiences, as well as discuss future directions and collaboration in joint efforts. The tentative program of the workshop is available at http://www.eccb12.org/WS4. We encourage everyone to participate and share their training experiences with training by sending in an abstract for the Showcases Session. See at the workshop website for more information.

Workshop: Host-associated Microbiota 2012

Thu, 10 May 2012 09:20:00 +0200

The Host-associated Microbiota workshop 2012 takes place at the University of Basel in Switzerland on September 12th - 14th, 2012. Young scientists like master students, Ph.D. students or postdocs are invited to interact with leaders in the field of host-associated microbiota and microbial ecology. The major aim of this workshop is to provide a synthesis of the emerging research on evolutionary and ecological patterns governing the complex interactions of hosts and microbiota across different biological systems. For more information and registration, visit the website.

CTMM Annual Meeting

Thu, 13 Sep 2012 09:39:00 +0200

The Center for Translational Molecular Medicine (CTMM) is organizing its annual meeting on September 13th. Please check the calender on their website for more information.

Symposium Systems Biology of Energy Metabolism and Ageing

Fri, 10 Feb 2012 15:31:00 +0100

The symposium is third in a series organized by the Systems Biology Centres in the Netherlands. The first symposium, about Cancer Systems Biology, was held in Amsterdam early 2011. The second will be organized in Nijmegen on February 13, 2012 and will focus on Systems Biology and Bioenergetics (www.csb-bioenergetics.nl). The symposium in Groningen will highlight advances in Systems Biology of Energy Metabolism and Ageing, across species and bridging bottom-up and top-down approaches. Keynote speaker (confirmed): Alexander van Oudenaarden, Massachusetts Institute of Technology / Hubrecht Institute. The symposium will be followed by the biannual meeting of the International Study Group of Systems Biology, to be held on the isle of Ameland, one hour away from the city of Groningen, on September 25-28, 2012. For more information, visit the website.

International Study Group for Systems Biology 2012

Fri, 10 Feb 2012 15:44:00 +0100

The International Study Group of Systems Biology (ISGSB) organizes biannual workshops where new developments in systems biology research are discussed between PIs, postdocs and PhD students. The Study Group is specialized in the ‘bottom-up’ branch of Systems Biology, which concerns the detailed molecular mechanisms that lead to emergent biological properties. New developments in technology and modelling, however, bring the genome-wide top-down approach ever closer to the bottom-up approach. The ISGSB stimulates intensive interaction between the different approaches to systems biology. The meeting will be held on the isle of Ameland in the Wadden Sea. The Hotel Resort Amelander Kaap is close to the dunes and the sea and provides an excellent environment for intensive scientific discussions in a relaxed atmosphere. Topics will include:

Metabolic and regulatory networks
Multiscale modelling
Stochastic processes
Single cells
Structural organization
Medical systems biology
Synthetic biology
Ageing
Evolution
Advances in experimental and computational tools

On Sept 24, 2012, they are also organizing a satelite symposium on Systems Biology of Energy Metabolism and Ageing. For more information, visit the website.

NGS Data Management: Sequencing Systems, Storage and Analysis

Sat, 24 Mar 2012 09:42:00 +0100

Next-generation sequencing (NGS) platforms play an increasingly prominent role in biological research. In the coming year, we can expect the amount of sequence data generated to exceed the entire data generated in the past decade. To use NGS at maximum capability, we must address IT tools of data management, storage, and analysis. NGS Data Management convenes hardware/software engineers, database architects, storage managers, systems integrators and analysts, as well as biological researchers and bioinformaticists. This track will provide perspectives from each specialty, emphasizing how they can be integrated into a cohesive, comprehensive team to manage the sequencing data deluge. For more information about the conference, click here.

Alan Turing Year Conference

Sat, 12 May 2012 16:33:00 +0200

The ATIA ( Alan Turing Institute Almere) conference is a Dutch-language conference. The organization committee decided so as 95% of the guests and speakers are native Dutch speakers. Of course, keynote speaker Michael Wooldridge will give his presentation in English. English presentations
In order to make the conference accessible to all guests from different countries, ATIA is asking the speakers to write their digital support ( Powerpoint or Prezi) in English. Morning programme: 9.30 – 12.30
During the morning programme ATIA will take you from AI backgrounds and possibilities towards AI applications in the medical domain and show their role in this process.
In between the different parts of the programme the guests will see some maine parts of a BBC documentary on Alan Turing’s life. Afternoon programme: 13.30 – 17.00
ATIA has asked all speakers to make sure their lecture matches the Ted Talks formula:
an 18-minute speech, no desk, and a minimum amount of slides. During this short speech they will describe to the public the AI possibilities and decision support systems within life science and health service. Evening programme: 19.30
During the evening the theatre company University Players Hamburg will perform “Breaking the Code”, a play about Alan Turing’s life. 'The University Players' is founded by Dietrich Schwanitz and is part of the Anglistik and Amerikanistik Departments at the University of Hamburg.The play is performed in the Kleine Zaal of the Almere Theatre and starts at 8.00 p.m. Theatre menu: 18.00
Restaurant Waterfront offers the conference guests a 3-course theatre menu for the special price of € 25,00, on reservation only. To attend the conference:
Click here to go to page “inschrijven” and follow the instructions.
You need any help, have questions or remarks? Please contact us by mail at info@ati-a.nl or by phone ++31365345985.

PRIB 2012 - The 7th IAPR International Conference on Pattern Recognition in Bioinformatics

Wed, 28 Mar 2012 12:07:00 +0200

Pacific Symposium on Biocomputing's 18th annual event (PSB 2013)

Tue, 31 Jan 2012 16:27:00 +0100

This is an invitation to submit proposals for sessions for the 18th Pacific Symposium on Biocomputing (PSB) 2013, to be held January 4-8, 2013 on the Kohala Coast, The Big Island of Hawaii. PSB will bring together top researchers from the US, the Asian Pacific nations and around the world to exchange research for the presentation of work in databases, algorithms, interfaces, natural language processing, modeling and other computational methods, as applied to biological problems, with emphasis on applications in data-rich areas of molecular biology. PSB has been designed to be responsive to the need for critical mass in sub-disciplines within biocomputing. For that reason, it is the only meeting whose sessions are defined dynamically each year in response to specific proposals. PSB sessions are organized by leaders in the emerging areas, and targeted to provide a forum for publication and discussion of research in biocomputing’s "hot topics." In this way, PSB provides an early forum for serious examination of emerging methods and approaches in this rapidly changing field. For more information, visit the website.