NBIC news

The Power of RNA seq

Thu, 23 May 2013 14:19:00 +0200

The NBIC Research PhD School for Bioinformatics and Computational Biology was announced to the NBIC Faculty during the Netherlands Bioinformatics Conference (NBIC2013) in April this year. The NBIC research school will thrive on the cooperation with related universities and research groups, and local graduate schools. ‘The power of RNA-seq’ course will be one of the first activities ‘avant la lettre’. This introductory course is organised by the Wageningen University graduate school Experimental Plant Sciences (EPS) and NBIC for both PhD students of EPS & WUR staff and national NBIC participants.

Date: June 5-7th, 2013
Venue: Wageningen University, the Netherlands
Organised by: Graduate School Experimental Plant Sciences (EPS) & NBIC
Keywords: designing your RNA-seq experiment, sequencing, mapping, quality control & statistics, RNA-seq data analysis pipeline, transcript identification, differential expression, special applications of RNA-seq, extracting biology.

This 3-day course consists of lectures in the morning and extensive hands-on computer practicals in the afternoon using Galaxy, R and webtools. You'll learn about all aspects of RNA-seq during the morning lectures, but also the context, applicability, power and expected results of RNA-seq experiments are covered. During the practicals you'll learn the basic steps an RNA-seq pipeline consist of, how to interpret your data and to put the results to use in your research project.

There are still seats available and you can register via the application form.

Contact: Patrick Koks (education@nbic.nl)

Still some seats left for Variant Detection and Interpretation

Thu, 23 May 2013 14:12:00 +0200

Thera are still a few seats left for next week's course "Variant Detection and Interpretation in a Diagnostic Context”. This advanced NGS course will be held for the second time and is this year organised in Rotterdam. The course is accredited by VKGL for the Laboratory Specialist Clinical Genetics track for 6 credit point per day.

Date: May 27-29th, 2013
Venue: Erasmus MC, Rotterdam, the Netherlands
Organised by: NBIC, EMC, LUMC, UMC St. Radboud, CGD
Keywords: Lab methods, Read Mapping, Variant Calling, Quality Control, Annotation of Variants, Computational Predictions, Evaluation and Reporting of results, Validation, Clinical Interpretation & Relevance, Legal & Ethical issues.

The mixed programme aims at implementing and applying NGS techniques as a diagnostic tool in the clinic and targets all aspects involved. The course is intended for bioinformaticians, researchers and molecular & clinical geneticists. The varied programme consists of lectures and hands-on workshops and will appeal to those analysing, using or applying NGS techniques and results thereof for the genetic diagnosis of patients. The course is intended for people with experience in (NGS) data analysis or the application of NGS-based diagnostic tools.

Registration: http://www.nbic.nl/education/nbic-phd-school/enrolment/genomreseqappform2013/

Contact: Patrick Koks (education@nbic.nl)

NBIC Research School for Bioinformatics & Computational Biology

Thu, 16 May 2013 13:51:00 +0200

Activities to set up the NBIC Research PhD School for Bioinformatics and Computational Biology are gaining momentum. The NBIC Research School aims to offer a vibrant national environment for the scientific development and education of integrative bioinformatics and computational (systems) biology. The research school should sustain and foster the close research community that NBIC has built over the years. ‘The power of RNA-seq’ course will be one of the first activities ‘avant la lettre’. This introductory course is organised by the Wageningen University graduate school Experimental Plant Sciences (EPS) in close collaboration with NBIC. for both PhD students of EPS & WUR staff and national NBIC participants. The research school should underpin the integrative and cross-disciplinary activities within the Dutch Techcenter for the Life Sciences (DTL) and closely liaise with DTL’s Data Integration and Stewardship Centre (DISC). During the NBIC faculty meeting preceding NBIC2013, it was decided to include the computational aspects of systems biology in the main focus of the research school, which will yield a tight-knit, homogeneous community in bioinformatics and computational biology. One of the main missions of the research school will be organising NBIC2014 and beyond. It is currently looked into what sustainable format the workshop may be organised in the years to come.

EBI Roadshow on its way from Amsterdam to Maastricht

Thu, 16 May 2013 13:41:00 +0200

In April the first two days the EBI Roadshow were hosted by the group of Antoine van Kampen at the AMC. Aldo Jongejan coordinated the local organisation of the training modules which covered the topics Introduction to databases, Sequence Alignment, Ensembl and ArrayExpress. The AMC Research Council sponsored 12 seats for AMC researchers.

In total 26 participants joined the lectures of the EBI delegates Andrew Cowley, Amy Tang and Denise Carvalho-Silva. The roadshow evaluation gave positive feedback like “Good overview of all possible options there are, now I have more insights in all the EBI stuff. Now I understand all the basics about Ensembl it is very easy to go into more details after this course and to explain the database(s) to other people now.”

The second part of the EBI Roadshow will be organized 1-3 July in Maastricht by the group of Chris Evelo with local organizer Egon Willighagen, and it will introduce the advanced uses of the gene and genomes databases, small molecule resources, the protein sequence databases, and interaction and pathway databases at EBI (a.o. UniPROT, ENSEMBL, CHEMBL, IntAct and Reactome). The roadshow in Maastricht will be extended with two course days (July 4-5 ) provided by the department of Bioinformatics-BiGCaT at Maastricht University in collaboration with the DiXa FP7 project on systems biology approaches in toxicogenomics. The second part (DiXa) of the course focuses on real data analysis using pathway and network approaches with links to the databases covered in first part (EBI Roadshow). Tools that will be used include WikiPathways, PathVisio and Cytoscape. Take a look at the course webpage for full details!

Register now for 3rd edition Life Science Information course

Thu, 02 May 2013 11:23:00 +0200

The amount of Life Science data available in the public domain is a vast and growing resource for bioinformatics research. There are over 20 million papers in PubMed and over 1600 biological databases. In many cases finding and applying the information from these resources is far from trivial. Luckily, you can now register for the 3rd edition of the NBIC PhD course on Managing and Integrating Life Science Information. Following this course will show you new techniques for working with these distributed resources, including using the Semantic Web, linked data and scientific workflows. It will also focus on methods for using or linking your own data into this large distributed web of resources. The course is organized on 17-21 June 2013 in Leiden UMC and coordinated by Marco Roos and Katy Wolstencroft. More information about the course is available on the course website or in the pdf-flyer below. You can register through the NBIC course enrolment form.

Bioinformatics in Berlin

Mon, 29 Apr 2013 13:20:00 +0200

July 19-23 the international conference ISMB/ECCB 2013 is organised in Berlin. Two workshops at this conference are co-organized by people from the NBIC network. Driven by the impact of technology in diverse areas, bioinformatics is becoming increasingly interdisciplinary, and in parallel so too are the audiences seeking bioinformatics training. That’s why Celia van Gelder (CMBI Nijmegen, NBIC) and her international colleagues in bioinformatics education are organising a workshop to bring awareness to the bioinformatics training needs of these new audiences. The workshop will consist of presentations on the topics of 1) how a medically trained audience thinks and learns about bioinformatics and the opportunities for new tools for the clinical setting; and 2) opportunities and strategies for providing bioinformatics training to an engaged, savvy public. Hienke Sminia (NBIC) will share her experiences with activities and exhibits for the general public (from ages 5 to 99). Marco Roos (LUMC) is co-organizing another workshop which explains what bioinformaticians need to know about digital publishing beyond the PDF. The aim of this workshop is to inform participants of ISMB/ECCB 2013 of changes and new opportunities in scientific communication. It addresses guidelines and tools that enable contributions to be exposed in machine-readable formats, ready for evaluation, interoperation, reuse, and attribution. In addition two Technology Track sessions will highlight aspects of digital publishing, one focussing on the ‘Open Pharmacological Space’, and one on Research Objects and Nanopublications as means to organising and exposing your methods and results in a digital form. NBIC partners associated with the Interoperability Task Force play a prominent role in organising these events and developing these standards More information about the workshops can be found on the conference website of ISMB/ECCB2013.

An inspiring place

Mon, 29 Apr 2013 12:01:00 +0200

Performing part of your PhD research in another lab is a good way to broaden your experience and enlarge your network. And to spend some time in another country. But it may lead to tangible results as well. Take the case of David van Dijk who visited the Weizmann Institute in Israel in 2010 using a NBIC Travel Grant. The result: a wet lab debut, two publications and a postdoc position.

David van Dijk performed his PhD research in the group of Peter Sloot at the University of Amsterdam. Although he already pondered the idea of visiting a lab abroad, things started moving when two PhD students from the group of Eran Segal (Weizmann Institute) came to Amsterdam. Van Dijk: "I was so impressed by their work that I decided to visit the Segal group. My supervisor Peter Sloot supported the idea and together we approached Eran Segal and got a positive response. Being a PhD student in bioinformatics, applying for a NBIC Travel Grant seemed the most logical thing to do."

Machine learning
He already knew Segal's work from the literature. "In my view, this group is one of the leading groups in computational biology. Segal's background is in artificial intelligence, just like mine, and he specializes in applying machine learning to biological problems. In addition, his lab is special because he runs both a dry and a wet lab and that was very appealing to me." With a background in informatics, the wet lab was unchartered territory to van Dijk, but this offered him the chance to explore that type of research as well. "I was lucky to team up with Lucas Carey, a biologist, who taught me how to perform wet experiments. This was really exciting. A computer is familiar to me, but I had never worked in a wet lab before."

Tuning the noise
Van Dijk's research at first focused on modelling and simulating stochastic gene expression. His debut in the wet lab consisted of measuring gene expression in yeast. "Our initial idea was to measure single-cell gene expression of a set of genes with sequence differences in their promoters to establish whether and how the promoter sequence influences the variability or noise in gene expression of a certain cell population. Using a computer model we were able to simulate gene expression and subsequently predict how the promoter can suppress 'noise'. A number of our model predictions, we tested in the wet lab by inducing specific DNA mutations in the promoter sequences." Interesting findings that resulted in two papers, one in PLoS Biology and the other in Genome Research. "Both papers deal with 'tuning' the noise in gene expression", van Dijk explains. "We found that gene expression noise is not a constant, but can be very precisely regulated by altering the DNA sequence of the promoter. To us, the eye-opener was that there are multiple strategies to activate a gene to the same expression level, but the resulting noise level showed large differences. Next to the gene expression level itself, is gene expression noise a quantitative value that is encoded in the promoter sequence. Evolution created a 'choice' to enhance gene expression with or without a lot of noise."

Postdoc position
The Weizmann Institute is a great environment for a scientist, says van Dijk. "It is a beautiful and very inspiring place to work. There are a lot of interesting lectures to attend and there are always internationally renowned scientists visiting the institute." No wonder, van Dijk decided to stay longer and thanks to an EMBO scholarship to follow up on his NBIC Travel Grant, he was able to spend almost a year in Israel. "Peter Sloot deserves credit here as well, he was very supportive of my stay at the Weizmann." And right now, he is back there again. "After my visit, Eran Segal offered me a postdoc position, which I gladly accepted! I am already busy with some new exciting projects here. In the future, I would like to set up an academic career back in the Netherlands."

Carey LB, van Dijk D, Sloot PMA, Kaandorp JA, Segal E (2013)
Promoter Sequence Determines the Relationship between Expression Level and Noise.
PLoS Biology 11(4):e1001528. doi:10.1371/journal.pbio.1001528

Dadiani M, van Dijk D, Segal B, Field Y, Ben-Artzi G, Raveh-Sadka T, Levo M, Kaplow I, Weinberger A, Segal E
Two DNA-encoded strategies for increasing expression with opposing effects on promoter dynamics and transcriptional noise
Genome Res. 2013. doi:10.1101/gr.149096.112 Text by Esther Thole.

Photo impression NBIC2013

Mon, 22 Apr 2013 11:43:00 +0200

Last week the bioinformatics community in the Netherlands gathered in conference centre De Werelt for the 8th edition of the Netherlands Bioinformatics Conference (NBIC2013). For the ones who were there last week and like to look back, or for the ones who want to see what they have missed:

A photo impression of NBIC2013
A story about NBIC 2013 based on Tweets: Storify

Anwesha Dutta won Application Showcase Competition

Thu, 18 Apr 2013 15:17:00 +0200

Anwesha Dutta from BiGCaT at Maastricht University has won the Application Showcase of NBIC2013 by demonstrating how you can use CyTargetLinker to build biological regulatory networks in Cytoscape. The Application Showcase is a characteristic part of the yearly Netherland Bioinformatics Conference. It offers (bio)informatics researchers to demonstrate the software application they have developed to answer biological questions. Two industrial parties, GenDX and Genalice, also participated in the showcase and demonstrated their software. Only the applications developed in an academic group were part of the competition.

Poster award for Sepideh Babaei

Thu, 18 Apr 2013 15:05:00 +0200

This year, the poster session at the Netherlands Bioinformatics Conference (NBIC2013) was organized for the first time in the evening. It was scheduled from 20:000 till 22:00 offering ample of time to watch and discuss research results with a beer in one hand. After ten o-clock people were still discussing science between the posters in the conference hall. A jury chaired by Lex Overmars of the RSG Netherlands decided the best presentation was given by Sepideh Babaei from the Delft Bioinformatics Lab with her poster on “Recurrent Mutations in Context of the Spatial Organization of the Genome”.

Tom Hendriks gave best lecture at NBIC2013

Thu, 18 Apr 2013 12:04:00 +0200

Today – the day after – we are looking back on a lively edition of the yearly Netherlands Bioinformatics Conference. Last two days conference centre De Werelt was again home town for the bioinformatics community in the Netherlands. Parallel sessions with oral presentations by bioinformatics researchers formed the core of the scientific programme. At the end of the conference the best lecture was awarded with a prize. Tom Hendriks, a student of Dr. Tina Ritschel from the Computational Discovery and Design group at the Radboud University Medical Centre in Nijmegen, received the prize for his talk “Do the puzzle pieces fit? Docking Experiments on Binding Affinity of Papain Inhibitors”.

Panter released

Thu, 11 Apr 2013 16:02:00 +0200

Mathijs Kattenberg (VU) has released an Open Source version of Panter to the NBIC software repository. Panter stands for the Persons and Address Informationsystem NTR and provides a user interface to the address and research administration database of the Netherlands Twin Register. The application is written in C# and uses an MS-SQL server as database store. An open source edition is provided via NBIC under the GPLv3 license. The system Panter was designed for studies of extended twin families which are registered with the Netherlands Twin Register, but it is applicable to any longitudinal study involving participants that need to be tracked over longer periods of time. Longitudinal studies need to keep track of a variety of administrative information on their participants: the addresses of participants, the relationships among participants and the participation in various research projects. In a register these changes may be dynamic and can vary over time.

The administrative functions provided by Panter include importing new individuals and families or adding new family members, address management (tracing twins and families who have moved), documenting the participation status of individuals (moved, not willing to participate, ill, deceased), and storing information on questionnaire mailings, responses to mailings and reminders, approaching nonresponders and approaching subjects for other than survey projects, such as biobank studies.

Panter is at its heart extremely flexible in handling persons and relations. Panter has no intrinsic notion of types of relations, for example, biological parents versus stepparents. New relations among participants are easy to add and old relations can be made inactive, still retaining the information on the past existence of this relationship. Selection of subjects can be based on individual characteristics or on relations among participants. Panter was set up to make it easily adaptable for other environments. The solutions built into Panter present a flexible approach to accommodate pedigrees of arbitrary size, multiple biological and nonbiological relationships among participants and dynamic changes in these relations that occur over time, which can be implemented for any type of multigenerational family study. Panter has been designed and built to accommodate new developments in genetic epidemiological research. Typical examples of such developments are increasing data collections, both in sample size and dimensionality, and the need to integrate data in collaborative studies.

In short, Panter facilitates research by offering a smooth handling of administrative processes and unrestricted options for relations among participants. Panter is available via the NBIC repository: https://trac.nbic.nl/panter/

Misty and inspiring Winter School

Fri, 05 Apr 2013 15:31:00 +0200

March 2013 NBIC organized a Winter School in collaboration with the SIB Swiss Institute of Bioinformatics. Nineteen participants from five different nationalities gathered in Kandersteg (CH) for a week of interesting lectures and discussions at the intersection of bioinformatics and medicine. The lectures were very much appreciated, including the contributions from the Dutch teachers as illustrated by the feedback of participants: “very good talkers, especially Frank van Harmelen gave a very inspiring talk on semantic web (which is not that easy)” and “Talking to an expert also from the medical area, Han Brunner, who actually has interactions with patients was a great experience, made things even more interesting.” The social programme on Wednesday included skiing and hiking in the – unfortunately misty – landscape of Switzerland. The NBIC/SIB Winter School is part of the NBIC PhD school aimed at training and education of bioinformatics and life science researchers.

Netherlands hosts first ELIXIR nodes workshop

Fri, 05 Apr 2013 14:38:00 +0200

Representatives of ELIXIR Nodes came together in Noordwijk, Netherlands, for a successful two-day workshop on 21-22 March. The event was organised by NBIC, which is leading the Dutch ELIXIR Node (DTL-DISC).

Over 50 participants came together to discuss several key issues including how each Node planned to respond to the review carried out by ELIXIR's Scientific Advisory Board, which took place in late 2012. Delegates also held fruitful discussions on possible areas of future collaboration between Nodes. The workshop also saw discussions on how industry can be engaged in the development of ELIXIR and what the current interactions were between ELIXIR Nodes and the other ESFRI Biological and Medical Sciences Research Infrastructures.

NBIC NGS course portfolio complete

Tue, 05 Mar 2013 10:13:00 +0100

With the 'Metagenomics Approaches and Data Analysis’ that was held in Leiden recently, the NBIC NGS course portfolio has now reached its completion. The NGS courses form the major component of the Life Sciences (LS) track of the NBIC PhD School. The LS track was initiated by NBIC’s NGS Taskforce and the BioWise programme, and all courses are co-organised with other organisations. The LS Track is targeted at a broad audience of bioinformaticians and life sciences researchers and aims at disclosing the full spread of Next Generation Sequencing (NGS) applications.

The NGS Course Portfolio now consists of:

one basic NGS course (coordinated by LUMC)
4 advanced courses:

RNAseq Data Analysis, co-organised with LUMC and AMC
Genomic Resequencing: Variant Detection and Interpretation in a Diagnostic Context, co-organised with the Centre for Genome Diagnostics (CGD) and UMC Radboud
De novo assembly from NGS data, co-organised with WUR
Metagenomics Approaches and Data Analysis, co-organised with LUMC, UMC Radboud and NIZO Food Research.

In its short life, the advanced NGS courses programme has already attracted 180 participants. Approximate half of the participants are PhD-students in the Netherlands. Others include post-docs, people from industry and hospitals, and many people from abroad. Several NBIC BioAssist programmers have made substantial contribution to these courses: Jeroen Laros and Martijn Vermaat from LUMC, Rutger Brouwer from ErasmusMC, and Jan van Haarst from WUR.

All NGS courses will be provided on a yearly basis. We are also planning to implement new courses (e.g., Epigenomics) based on the request from the academic and industry community. We welcome your suggestions on how to improve or extend our course portfolio. For more information & (pre-) registration for the NGS courses please see the PhD-school on the NBIC website.

Recon 2: Metabolic reconstruction by consensus

Fri, 01 Mar 2013 13:30:00 +0100

Just as all roads lead to Rome, all biological pathways point the focus on metabolism. Studying human health and disease requires thorough understanding of metabolism and as a result, numerous efforts have been dedicated towards metabolic reconstructions that bring together biochemical, genetic and genomic knowledge in a structured manner. Such reconstructions are essential to bottom-up systems biology analyses and enable mechanistic investigations of the genotype-phenotype relationship.

Several global human metabolic reconstructions have been generated, as well as a number of cell-type specific reconstructions. Of the global reconstructions, Recon 1 is probably the most widely used. To make the most of the various reconstructions and to incorporate newly developed metabolic models and data - without duplication efforts - a large group of researchers, including former NBIC PhD student Miranda Stobbe, decided to pool resources and generate a community-driven consensus human metabolic reconstruction using available sources. This has resulted in Recon 2, the most comprehensive human metabolism resource to date. Recon 2 is publicly available at: http://humanmetabolism.org/

Thiele I, Swainston N, et al.
A community-driven global reconstruction of human metabolism
Nature Biotechnology, advanced online publication 3 March 2013, doi:10.1038/nbt.2488

NBIC Young Investigator Award 2013 is looking for nominees

Thu, 28 Feb 2013 16:50:00 +0100

During the NBIC 2013 on April 16, NBIC will present the NBIC Young Investigator Award 2013. The winner will be awarded with a cash prize of 2.500 Euro. The award ceremony is planned on Day 1 of the conference (April 16th, 2013) and will include an honorary lecture by the recipient of the award. You can now nominate candidates (PhD’s). They must meet the following criteria:

The candidate must have conducted his/her research primarily in a Dutch institute.
The primary result on which the award will be based will be the PhD thesis written by the candidate. Therefore, the final version of the thesis of the candidate should have been submitted to the PhD committee at the candidate's university between January 1, 2012 and February 28, 2013 at the latest.

Other criteria that might be considered by the award committee are:

The candidate significantly contributed to the idea of the research;
The research of the candidate resulted in novel or improved bioinformatics methodologies;
The research of the candidate advanced life sciences research;
The candidate independently conducted the research;
The research resulted in a scientific publication, software application or database;
The work of the candidate has given broad visibility of bioinformatics in the life sciences field;
The candidate has otherwise significantly contributed to bioinformatics or the bioinformatics community in the Netherlands.

Each nomination must be accompanied with:

Name and affiliation of candidate
Motivation for nomination by group leader of candidate
Curriculum Vitae of the candidate
A URL to the final version of the PhD thesis (preferably to the PDF of the printed version)

You can submit your abstract via the YIA submission form.

More information about the NBIC YIA at the NBIC2013 website.

CIMP, BRAF, FOX

Thu, 14 Feb 2013 15:38:00 +0100

In colon cancer, a subset of tumours called the CpG island methylator phenotype (CIMP) is characterized by high levels of cancer-specific methylation. Associations have been established between CIMP and BRAF mutation, but the underlying mechanisms remain unclear. In attempt to tackle this issue, Eddy van Roon (Erasmus MC Rotterdam) and colleagues, including NBIC Faculty member Judith Boer, studied genome-wide methylation differences between colorectal tumours carrying a BRAF mutation and BRAF wildtype tumours. They succeeded in identifying new BRAF-mutation specific methylation changes in colorectal cancer, including validated differential methylation of forkhead box (FOX) transcription factors. The authors also found methylation-dependent silencing of FOXD3 and enrichment of several cancer-related pathways, including the PI3 kinase and Wnt signalling pathways.

van Roon EH, Boot A, Dihal AA, Ernst RF, van Wezel T, Morreau H, Boer JM
BRAF mutation-specific promoter methylation of FOX genes in colorectal cancer.
Clin Epigenetics. 2013 Jan 16;5(1):2

NBIC2013: Call for Abstracts

Thu, 31 Jan 2013 11:09:00 +0100

The 8th edition of the Netherlands Bioinformatics Conference 2013 (NBIC2013) will be the last edition organized by the NBIC office. We invite you all to join this conference, which is thé place to be when you want to meet senior and junior researchers of the bioinformatics network in the Netherlands. Registration is open now, and you can submit abstracts untill March 4th. Abstract submission
You can submit an abstract for an oral presentation, a poster presentation and for a demo during the application showcase for the NBIC2013 programme. Abstracts can also be submitted for the two satellite meetings: the Metagenomics Satellite track, the NSBM Spring Meeting 2013 and for the parallel Data & Technology session. Submit your abstract via the conference website. Date:         16 & 17 April 2013
Venue:       De Werelt, Lunteren, the Netherlands
Website:    http://www.aanmelder.nl/nbic2013. Programme

5 keynote speakers, a.o. Alexander van Oudenaarden, Janet Thornton, Uwe Sauer, Roeland van Ham and Jeroen Raes
Satellite meetings: Spring meeting of the Netherlands Society on Biomolecular Modelling (NSBM) & Metagenomics Satellite Track
Parallel sessions of contributed lectures
Parallel workshops
Poster presentations
Industry meeting (BIUP)
RSG Retreat on April 15th

Key dates

deadline for abstract submission Monday March 4, 2013
notification of selection for oral presentations: Friday March 22, 2013
registration deadline: April 1, 2013

About NBIC2013
The Netherlands Bioinformatics Conference 2013 (NBIC2013) is the 8th edition of the annual conference organized by the Netherlands Bioinformatics Centre (NBIC). NBIC2013 discusses the latest developments in bioinformatics and interrelated disciplines, and their wide-ranging applications in life sciences & health, agriculture, food & nutrition and industrial biotechnology. NBIC2013 offers a cross-disciplinary scientific program of (poster) presentations, application demonstrations and workshops, as well as other opportunities to exchange innovative ideas.

More information
Contact: Femke Francissen, e-mail: femke.francissen@nbic.nl

Learn about Alignment, Ensembl and ArrayExpress at AMC

Mon, 21 Jan 2013 13:52:00 +0100

April 9 and 10, AMC Amsterdam (Antoine van Kampen) and NBIC organize a two day EBI Roadshow. Topics were selected by consulting the research community and comprise an introduction to databases and to Ensembl, Sequence Aligment and ArrayExpress. You can find more information in the course description. In the summer of 2013 a second EBI Roadshow will follow in Maastricht (Chris Evelo), with topics like advanced Ensembl, interactions & pathways and small molecules in bioinformatics (a.o. ChEMBL). If you are interested please mail to education@nbic.nl to be put on a pre-registration list. Related news

EBI Roadshow 2013 hosted by Amsterdam and Maastricht

Get up-to-date with developments in bioinformatics and medicine

Mon, 21 Jan 2013 13:09:00 +0100

For researchers working at the interface of bioinformatics and medicine, the NBIC/SIB Winterschool provides an excellent opportunity to learn about new developments in the areas of cancer genomics and treatments, GWAS studies, analysis of medical records and ontologies, drug testing and design. Participants will attend lectures, discuss case studies and papers and have hands-on computer practicals. Read more...

SARA & NBIC collaborate in the cloud

Mon, 21 Jan 2013 11:40:00 +0100

During NBIC's de novo Assembly course in Wageningen this January, all practicals were carried in SARA's HPC cloud, with great success! All 42 participants were running jobs concurrently both on individual Virtual Machines with pre-installed software for the course and on the NBIC Galaxy server (also in the SARA cloud). Operation was smooth and flawless as was acknowledged by teachers and participants, who were hardly aware of the special environment as one wrote “Computers worked very well!”. A big “thumbs-up” for SARA cloud support! SARA and NBIC plan to further expand this collaboration in training, a.o. in the context of DTL-DISC.

NBIC's flying course circus

Mon, 21 Jan 2013 11:31:00 +0100

On January 8^th-9^th, the first NBIC course of this year was held in Wageningen. 42 (!) participants from the Netherlands and some neighbouring countries visited the first issue of the “de novo Assembly from NGS data” and learned how to juggle with heaps of NGS data. Over 90% of the participants said they could apply what they've learned in their research: “Very informative and useful”! This week, from January 21^st till 25^th, the second NBIC course of this year, “Pattern Recognition” is running in Amsterdam. Participants will learn how to perform the most intricate tricks with high volume life sciences data. This course will be followed shortly by the “Metagenomics approaches and data analysis” course in Leiden on February 6^th-8^th, focussing on the analysis of sequence data from whole ecosystems. Some seats are still available! Please register if you would like to participate!

Metagenomics popular amongst high school teachers

Fri, 18 Jan 2013 16:26:00 +0100

Together with foundation Leve DNA! and high school Kandinsky College in Nijmegen, NBIC is trying to make metagenomics accessible for other high schools. In this project two pupils have taken samples from the Waal river. Leve DNA! has sequenced the 16s rRNA in these samples. NBIC and two teachers of the Kandinsky College are now developing educational material based on these results. A first teacher workshop on this subject was held on January 12 during the NIBI-conference for biology teachers. Participants got to know what metagenomics is and how they can analyze the results with MG-RAST. All 20 teachers were very enthusiastic about this new field of research and eager to try it in class with their students.

BioCafé and Course

Thu, 10 Jan 2013 14:55:00 +0100

RSG Netherlands, the network of junior researchers in bioinformatics, invites you for the Bio-Café on 21st January, 2013 in Amsterdam. The Bio-Café includes a contest which challenges your bioinformatics and general knowledge. Registration by e-mail is required.

The Bio-Café is part of the social programme of the Pattern Recognition course organised by the NBIC PhD school January 21-25, but also open for junior researchers who are not participating in the course. There are still some seats available for the course! You can register through the enrolment form.

Changed access to national e-infrastructure

Fri, 21 Dec 2012 13:59:00 +0100

Many bioinformatics researchers in the Netherlands have become familiar with the BiG Grid e-Infrastructure over the past six years. The access to the e-Infrastructure (grid, cloud, hadoop, etc.) has been organized through the BiG Grid project. SARA, Nikhef, CIT-RUG and Philips Research have been instrumental in operating the e-Infrastructure and providing various kinds of support to researchers. The BiG Grid project ends at 31 December 2012 and you can read the project achievements in the stories (in Dutch) of users at the BiG Grid website. SARA, which is expected to be part of SURF from January 2013, will be responsible for the e-Infrastructure from January 1, 2013. At Sara’s website is briefly explained the most important changes for researchers who want to apply for access to the national e-infrastructure, including the application procedure. As of 1 January 2013 SARA will be part of the SURF Foundation. From that date on SARA will carry a new logo and a new name: SURFsara. The services and accompanying support for science and industry from their location in Amsterdam will continue without changes. The website www.sara.nl will be moved to www.surfsara.nl. People at SURFsara can be reached through an email address with surfsara.nl, but the sara.nl addresses will temporarily stay available.

The aim of the merger is to achieve greater synergy within the national e infrastructure by making it part of a single organisation (SURF). The merger will above all benefit researchers at higher education and research institutions. Scientific research nowadays involves both an increasing need for large modelling and simulation and an increasing number of large and complex datasets. This ‘Big Data’ demands large-scale computing capacity, extensive data storage facilities, visualisation facilities and high-quality user support, combined with advanced network facilities. The combination of facilities created by the merger will provide for all this on a long-term basis.

Metagenomics Research of Skin Bacteria in public media

Fri, 14 Dec 2012 13:43:00 +0100

The results of metagenomics research of bacteria on human skin have reached the editors of the popular news website NU.nl (in Dutch) and the newspaper BioNieuws. Recent advances in sequencing technologies have enabled metagenomic analyses of many human body sites. Several studies have catalogued the composition of bacterial communities of the surface of human skin in healthy volunteers. Skin injury will disturb the host tissue and its commensal microbiota, but the dynamics of this process have not been studied before. A recent paper in Genome Biology of Zeeuwen et al describes the analysis of the microbiota of the surface layer and the deeper layers of normal skin. The authors from the UMC St Radboud, NIZO food research and Wageningen University, including NBIC Faculty Sacha van Hijum, investigated the dynamics of skin microbiota following skin barrier disruption by tape stripping as a model of superficial injury. The results of this study could in the future help in more accurately predicting the wound healing process based on host factors and the microbiome of deeper skin layers. Patrick LJM Zeeuwen
Microbiome dynamics of human epidermis following skin barrier disruption
Genome Biology 2012, 13:R101 doi:10.1186/gb-2012-13-11-r101

Apply now for funding for PCDI Postdoc Retreat 2013!

Fri, 14 Dec 2012 13:23:00 +0100

The Postdoc Career Development Initiative (PCDI) supports postdocs and final year PhD students at career orientation and realizing young researchers’ potential. On 13 - 15 March 2013, PCDI’s best known event, the annual Postdoc Retreat, will be held for the 9^th time. Aim of this three-day course is to support you in making the next step in your career: identify your skills and talents, develop a vision on science, improve your transferable skills and learn about the variety of career paths in Life Sciences within and outside academia. The programme includes inspiring lectures, training workshops, meet & greet with potential employers and a forum discussion with prominent persons in Life Sciences. The PCDI Postdoc Retreat is a unique career development course in the Netherlands. As it is exclusively open to postdocs and final year PhD students in Life Sciences, you can expect tailored activities, immediately relevant to your career stage. Over 900 early career scientists already took part in the PCDI Postdoc Retreat, including more than 85 participants from NGI-centres. Funding for 50 NGI postdocs/PhD students to attend
The Netherlands Genomics Initiative wants to actively encourage her young researchers to participate. NGI will sponsor participation for the very last time, up to a maximum of 50 sponsorships of the registration fee (max 5 per centre). This NGI funding will be assigned on a first come first served basis. NGI sponsored participants of earlier editions of the PCDI Postdoc Retreat cannot reapply for NGI funding for 2013. NBIC is one of the NGI Centres. If you want to make use of this opportunity to apply for a NGI-sponsored seat, please fill out the registration form attached and mail it to hegge@genomics.nl. Before sending, it should also be signed by the director of the NGI Centre (Ruben Kok for NBIC). Registration closes on 19 February 2013 or whenever the maximum number of participants has been reached. So register NOW!

GOBLET: Combining efforts in training and education

Fri, 14 Dec 2012 10:37:00 +0100

GOBLET – A global initiative towards combining efforts in bioinformatics training and education November 28^th 2012, the formal kickoff meeting of GOBLET (Global Organisation for Bioinformatics Learning, Education and Training) was hosted by NBIC in Amsterdam. The GOBLET MoU has now been signed by 22 international organisations and societies. GOBLET's mission is to coordinate world-wide bioinformatics training activities: to share, not duplicate, effort; to share, not duplicate, cost; to work together in a mutually respectful way towards common solutions and a sustainable future. You can read more at www.mygoblet.org.

NBIC advanced NGS courses for impact

Thu, 13 Dec 2012 16:25:00 +0100

Next Generation Sequencing is expected to have an even greater impact in 2013 and to find its way into more and more labs and applications. NBIC is offering high-level courses on different applications of NGS in addition to the joint NGS data analysis course with LUMC and EMC. Two new courses are organised at the beginning of 2013. Together they cover a substantial part of the NGS application range and will impact your NGS analysis proficiency and ability to apply NGS in your research:

“de novo assembly from NGS data”, January 8-9th, 2013, Wageningen
“Metagenomics approaches and data analysis”, February 6-8th, 2013 Leiden.

Our courses are co-organised with researchers from Wageningen UR, Leiden UMC, CMBI, NIZO Food Research and Keygene. Seats are still available for both courses and our courses are open for researchers in bioinformatics & life sciences from the Netherlands and abroad.

For more information, please contact Patrick Koks at education@nbic.nl.

Groningen and Chromosome 5

Thu, 13 Dec 2012 15:40:00 +0100

The Chromosome Centric Human Proteome Project (C-HPP) has the goal to detect and catalogue protein gene products and link them to their original chromosome location. C-HPP is organized teams for each chromosome with participation of world leading proteomics and bioinformatics laboratories. The Analytical Biochemistry group at University of Groningen headed by Rainer Bischoff was recently invited to join the C-HPP initiative taking responsibility for Chromosome 5. The Chromosome 5 team is further supported by Dirkje Postma’s (UMCG) group, which is internationally leader in COPD, asthma and lung cancer research, Manfred Wuhrer’s research group (LUMC, VU) which has extensive glycoproteomics expertise and the group of Henry Lam (HKUST, Hong Kong) with considerable bioinformatics expertise.

Register now for NBIC/SIB Winterschool 2013 in the snow!

Thu, 13 Dec 2012 15:16:00 +0100

From 10-15 March 2013, PhD students working at the intersection of bioinformatics and medicine can meet each other in the snow in Kandersteg, Switzerland, for the NBIC/SIB Winterschool. Bioinformatics has an essential place in the interplay of genomics, drug discovery and clinical diagnostics, and can thus bring new insights to the physicians’ daily work. This winter school, organized by NBIC and the Swiss Institute of Bioinformatics (SIB), will span four main hot topics in the intersection of bioinformatics and medicine: cancer genomics and treatments, GWAS studies, analysis of medical records and ontologies, drug testing and design. Check out the course webpage for more information about the programme and the registration procedure.

Pig genome reveals genes that made domesticated pigs longer

Thu, 06 Dec 2012 14:33:00 +0100

Since having been tamed and domesticated some ten thousand years ago, pigs have been getting longer. Researchers from the universities of Wageningen, Uppsala, Copenhagen and Edinburgh and led by professor Leif Andersson (Uppsala University) and NBIC faculty member professor Martien Groenen (Wageningen University) published details of the genetic origins of this remarkable change in an article in PNAS (Proceedings of the National Academy of Science).

The PNAS paper was simultaneously published with the Nature article about the sequencing of the pig genome. On November 15^th the international ‘Swine Genome Sequencing Consortium’ published their findings of the swine genome in Nature. The consortium was headed by Prof. Martien Groenen from Wageningen University, Prof. Larry Schook from the University of IIlinois and Prof. Alan Archibald of the University of Edinburgh. The swine genome is an important milestone research on pig evolution, pig breeding and due to the similar physiology of the pig with humans also as a model for biomedical research.

Rubin et al.
Strong signatures of selection in the domestic pig genome
Proc. Natl. Acad. Sci. USA, 15 November 2012

Groenen et al.
Analyses of pig genomes provide insight into porcine demography and evolution.
Nature 491:393-398

Trait project enforced with Bioinformatics Research Assistant

Mon, 12 Nov 2012 10:37:00 +0100

In October a new Bioinformatics Research Assistant, Pravin Pawar, joined the CTMM TraIT project. He has started in the TraIT work package that is focused on experimental data and he is currently deployed at the OncoProteomics laboratory in VUmc. The Bioinformatics Research Assistant works in the team that supports the collection, storage, analysis, archiving and securing of the data generated in the CTMM’s 21 research projects. CTMM and NBIC work together to make this position possible, and both CTMM TraIT and NBIC are looking forward to the results that our collaboration will bring.

Galaxy on cloud

Thu, 08 Nov 2012 11:54:00 +0100

Collaboration between NBIC and the e-BioGrid team resulted in a new service: NBIC Galaxy on Cloud. The migration of Galaxy to the cloud allows end-users (bioinformaticians, biologists or clinical researchers) to run their Galaxy tools and workflows on the BiG Grid High Performance Computing (HPC) cloud at SARA. The Dutch cloud version of Galaxy enables processing of big data volumes and the high speed network connection provides rapid data transfers.The application scales dynamically with increasing workload.

The NBIC Galaxy is used for genomics and proteomics data analysis. End users can easily use the web based interface to run sophisticated methods and algorithms without worrying about the local installation, maintenance, or data backups. Various NBIC BioAssist teams are also using this service to collaborate and provide integrated data analysis pipelines to end users in the life sciences and other national programme’s like the Netherlands Proteomics Centre and Ecogenomics centre.

The NBIC Galaxy on cloud is suitable to run complicated genomics and proteomics data analysis algorithms and it can deal with large amounts of data like de novo assembly task of middle to large genomes. In addition, the NBIC Galaxy support team and the BRS-team, can help end- users from non-commercial parties to do better science by allowing them to explore and analyse their full datasets on the server in a consistent manner. Furthermore, life scientists can be trained on this server during the Galaxy and Sequencing courses to work with state-of-the-art datasets and tools.

For more information, please send a mail to nbicgalaxy-admin@trac.nbic.nl

VarioML: lightweight option for variation data

Thu, 08 Nov 2012 11:42:00 +0100

In the global effort to unify genetic variation databases, covering human and model organism data, many obstacles still have to be scaled. Integrating data from the numerous different databases is difficult due to the lack of a single standard. Instead of trying to design a unifying format in a top-down manner, a large group of international variant experts, including NBIC Faculty member Morris Swertz (University Medical Centre Groningen) opted for a lightweight framework that allows users to compose interoperable use-case specific micro-standards around a limited number of generalized concepts. The group specifically focused on improving data entry into and data exchange between locus-specific databases (LSDB), of which currently more than 4,000 are around. Their efforts resulted in VarioML, which allows researchers, clinics and diagnostic laboratories to share human variation data in a straightforward and unambiguous manner. The open-ended nature of VarioML ensures that future extensions and adjustments can easily be incorporated.

Byrne MG, et al.
VarioML framework for comprehensive variation data representation and exchange
BMC Bioinformatics 2012, 13:254

Duplicates are not the same (anymore)

Tue, 06 Nov 2012 10:57:00 +0100

Gene duplication is a common phenomenon and plays as important role in evolution, because after duplication, the resulting paralogs each go their own way. They accumulate different mutations and start to exhibit differences in expression patterns. To find out more about the extent of divergence between paralogs and to study the influence of epigenetic modifications on this process, Lidija Berke and colleagues from Utrecht University focused on the role of the epigenetic mark H3K27me3 on the evolution of gene expression patterns in the model plant Arabidopsis thaliana. The results show an association between H3K27me3 (trimethylation of histone H3 at lysine 27) and the extent and manner of divergence between paralogs. Paralogs that are both targeted by H3K27me3 exhibit low expression levels, but a high coding sequence divergence. In contrast, pairs in which only one gene is targeted by this mark show the highest divergence in expression patterns and upstream regulatory sequence. Particularly for transcription factors, the difference in expression patterns is pronounced. According to the authors, this analysis demonstrates the importance of epigenetics in the evolutionary fate of genes.

Berke L, Sanchez-Perez GF, Snel B.
Contribution of the epigenetic mark H3K27me3 to functional divergence after whole genome duplication in Arabidopsis
Genome Biology 2012, 13:R94

Tool: CLI-mate

Tue, 23 Oct 2012 09:14:00 +0200

To inform as many people as possible about the large list of bioinformatics tools available, we will monthly present a tool in the news. This month we put the spotlight on CLI-mate. CLI-mate is a service to facilitate developers in creating user-friendly interfaces for a command line tool. CLI-mate was developed at the Department of Human Genetics, Leiden University Medical Center (LUMC). In the agile development environment of bioinformatics, many command line tools are created quickly to fill in gaps between complex information processes. A command line interface (CLI) is sometimes sufficient for the task, but it limits adoption by a broader audience. Therefore it’s often necessary for the developer to create a wrapper that provides a more user friendly interface. The CLI-mate interface generator makes this easy: it can generate different wrappers: one of them is turning the program into a Galaxy tool.

2nd Autumn School Bioinformatics Essen-Nijmegen

Tue, 16 Oct 2012 11:43:00 +0200

Gert Vriend (UMC St Radboud Nijmegen) for the second time organizes an Autumn School in collaboration with Daniel Hoffmann of the University of Duisburg-Essen around the theme “Biomolecular Structure and Function – Computational Approaches”. The course is intended for PhD and MSc students who are interested in computational approaches to study biomolecules, their structure, interactions and mechanisms. The Autumn school starts November 26 at the campus in Essen. The first week will focus on methods based on physical models of biomolecular systems. Topics include molecular dynamics simulation and related methods, biomolecular electrostatics, protein-protein-docking and matching, and datamining on sequences and structures. The second week of the school will take place in Nijmegen and will deal with methods that make empirical knowledge available for modelling proteins. Topics of this week include homology modelling, ligand docking, computational solutions for structural analysis with X-ray, NMR, SAXS, or Cryo-EM. If you want to participate you are requested to do a self-assessment before returning the application form. On the website of the Autumn School you can find more information about the programme and the admission procedure.

TNO and Sanquin in NBIC consortium

Thu, 11 Oct 2012 16:43:00 +0200

The NBIC consortium has been extended with two new partner organisations: TNO and Sanquin. TNO is an independent research organisation whose expertise and research make an important contribution to the competitiveness of companies and organisations, to the economy and to the quality of society as a whole. TNO’s unique position is attributable to its versatility and capacity to integrate this knowledge. Sanquin Blood Supply Foundation ensures the safe and efficient blood supply in the Netherlands. Sanquin also develops and produces pharmaceutical products, conducts high-quality scientific research, and develops and performs a multitude of diagnostic services.

The power of combining

Tue, 09 Oct 2012 08:55:00 +0200

Being able to predict the clinical outcome in individual breast cancer patients is essential to ensure each patient gets the right therapy (and is spared unnecessary treatment). Both clinical data and gene expression data are used to derive predictors of clinical outcome. However, combining the two sources to build a single prediction model remains rare and the few examples where it has been tried have yielded inclusive results on prediction performance. Together with colleagues from the Netherlands Cancer Institute and the Academic Medical Centre Amsterdam, Martin van Vliet (Delft University of Technology) performed an extensive comparison of three integration strategies as well as using five classifiers of varying complexity without integration data types. They used a dataset of breast cancer samples of which both gene expression profiles and clinical data are available to develop predictors, which were subsequently validated using four independent breast cancer datasets. Their main conclusions are that combining the two data types increases the performance of all five classifiers and that the late OR integration strategy generates the best overall result of the three strategies tested. van Vliet MH, Horlings HM, van de Vijver MJ, Reinders MJ, Wessels LF
Integration of clinical and gene expression data has a synergetic effect on predicting breast cancer outcome.
PLoS ONE 7(7): e40358. doi:10.1371/journal.pone.0040358

Bioinformatics in public

Mon, 08 Oct 2012 10:41:00 +0200

The bionformatics@school project not only visits schools and trains teachers; it also promotes bioinformatics to the general public. September 28, for instance, Hienke Sminia (NBIC) and Punto Bawono (VU) were at the Discovery Festival in Amsterdam (NEMO) to show how proteins can be folded and how multiple sequence alignments can be constructed, using citizen science games as Fold.it and Phylo. Coming weekend on Saturday 13^th Hienke will demonstrate bioinformatics at the Kunstnacht in Nijmegen. An ideal opportunity to show your friends and family how interesting your job is.

EBI Roadshow 2013 hosted by Amsterdam and Maastricht

Mon, 08 Oct 2012 10:26:00 +0200

Together, Antoine van Kampen (AMC), Chris Evelo (UM) and Celia van Gelder (NBIC) have successfully applied for hosting 5 days of EBI Roadshow modules in early summer 2013. Maastricht University will host 3 days covering Ensembl, interactions & pathways and small molecules in bioinformatics (a.o. ChEMBL). The other 3 days are hosted by the Academic Medical Centre (AMC) in Amsterdam, covering Introduction to databases, Sequence Alignment, Ensembl and ArrayExpress. If you are interested in a specific module or topic please mail to education@nbic.nl to be put on a pre-registration list.

3rd NBIC Pattern Recognition Course: Registration open now!

Fri, 05 Oct 2012 15:26:00 +0200

On January 21-25 2013, the 3^rd edition of the Pattern Recognition course of the NBIC PhD school will take place in Amsterdam. Perry Moerland has taken over the coordination for this course from Dick de Ridder, who has organized the 1^stand 2^nd edition of this course in Delft in 2009 and 2011. The course introduces theory and tools from the fields of pattern recognition and machine learning to solve bioinformatics problems. After the course, you have an overview of basic pattern recognition techniques and are able to recognize what method is most applicable to classification problems you will encounter. Registration is open now! You can register through the enrolment form.

Education tool enthused teachers at international conference

Fri, 05 Oct 2012 14:55:00 +0200

Hienke Sminia of the Bioinformatics@school project developed the instruction guide NaviGene to help biology teachers to use bioinformatics in their lessons. Friday September 21, she presented NaviGene during the European didactic research conference EriDob. Her talk was received well and some international participants already showed their interest for the guide. The EMBL and the Berlin Research institute (MDC) are going to use parts of the NaviGene in their bioinformatics teacher training programme. If you are also interested in the instruction guide NaviGene, you can directly download the Dutch and English version from the NBIC website.

Maastricht UMC+ partner in NBIC consortium

Thu, 27 Sep 2012 16:57:00 +0200

Maastricht UMC+ signed the partner agreement with NBIC and became partner in the NBIC consortium. Maastricht UMC+ is the name of the collaboration between the Academic Hospital Maastricht (AzM) and the Maastricht University. Research of Maastricht UMC+ takes place in five research schools: Caphri (Public Health & Primary Care), CARIM (cardiovascular diseases), GROW (oncology & development biology), MHeNS (mental health & neurosciences) and NUTRIM (Nutrition, Toxicology and Metabolism). Maastricht UMC is the 8th University medical Centre in the NBIC Consortium.

Dairy details

Mon, 17 Sep 2012 09:23:00 +0200

For those who are familiar with the strong and mostly unpleasant odour of sulfur-containing compounds, it may come as a surprise that such compounds are also the source of many of the characteristic flavours of much-loved fermented dairy products like cheese and yoghurt. Important flavour components such as dimethyl sulfide (DMS) and methanethiol are formed during the fermentation process when lactic acid bacteria break down the sulfur-containing amino acids cysteine and methionine.

To the dairy industry, insight into the regulation of this degradation process may offer clues to a rational control of flavour profiles of dairy products. To this end, Mengjin Liu (FrieslandCampina Research) and colleagues from academia including NBIC Faculty members Roland Siezen and Christof Francke, performed a genome-wide in silico analysis to systematically evaluate the regulatory interactions that control the expression of genes associated with cysteine and methionine metabolism in all sequenced species of the order Lactobacillales. The results suggest that the reaction network can be subdivided into five modules, with the family Streptococcaceae appearing to have a distinctly different modular composition compared to the three other families. The authors propose to include the reaction network built on their analysis into a quantitative metabolic network model, in order to develop rational strategies towards flavour control strategies in fermented food products.

Liu M, Prakash C, Nauta A, Siezen RJ, Francke C
Computational analysis of cysteine and methionine metabolism and its regulation in dairy starter and related bacteria.
J Bacteriol. 2012 Jul;194(13):3522-33

PropSeg: determining copy number alternations

Tue, 11 Sep 2012 09:18:00 +0200

Copy number alternations (CNAs) frequently occur in cancer and therefore tools that allow detection of (recurrent) CNAs are of high interest to cancer researchers. Originally developed to detect single nucleotide variants (SNVs), capture sequencing has proven its worth in deriving gene copy numbers as well. To assess changes in copy numbers from capture sequencing data, most approaches rely on determining log-ratios between test and control samples, but these methods are not well suited to deal with the large variety in coverage that is inherent to sequence data, resulting in information loss. These ratio-based approaches also suffer from outliers and are unable to handle homozygous deletions. Guillem Rigaill (Netherlands Cancer Institute, Amsterdam) and colleagues in the group of NBIC Faculty Lodewyk Wessels propose a proportionality model, in which the test sample coverage is modelled as a linear function of the control sample. A major advantage of this new statistical approach is that completely deleted regions are no longer ignored in the analysis. They tested their approach by determining the copy numbers for a set of 600 genes from nine breast cancer cell lines. The new method, called PropSeg, outperformed other log-ratio based methods, while demonstrating high concordance with SNP array results. The code for the new algorithm is available from http://bioinformatics.nki.nl/ocs

Rigaill GJ, Cadot S, Kluin RJC, Xue Z, Bernards R, Majewski IJ and Wessels LFA
A regression model for estimating DNA copy number data applied to capture sequencing data
Bioinformatics 2012, Jul 13

Inspiring interviews with keynotes

Fri, 31 Aug 2012 15:49:00 +0200

During the seventh edition of the Netherlands Bioinformatics Conference (April 24-25) keynote lectures were presented by renowned (inter)national bioinformatics scientists. Here you can find personal interviews with them, in which they explain their fascinating research.

New tool: PhenoLink

Mon, 27 Aug 2012 10:02:00 +0200

In the ongoing quest to understand the relationship between genotype and phenotype, being able to quickly prioritize and visualize potential links and relations has become a true survival skill for those who are taking on the very large and very noisy ~omics datasets to dig for well hidden treasures. To support these efforts, Jumamurat Bayjanov and colleagues (CMBI, Radboud University Nijmegen Medical Centre) have developed PhenoLink, a web-tool that effectively deals with high noise levels and imbalances in phenotype data. PhenoLink can be used on a wide variety of ~omics data. Identified links are visualized, which facilitates prioritizing these links as well as finding relations between features and between phenotypes, and identifying outliers in phenotype data. The authors applied PhenoLink on a set of 42 Lactobacillus plantarum strains to identify relationships between the presence/absence of genes and phenotypes defined by sugar utilization and nitrogen-dioxide production. In addition to known relationships, PhenoLink generated novel gene-to-phenotype relations in a well-studied strain (L. plantarum WCFS1).

Bayjanov JR, Molenaar D, Tzeneva V, Siezen RJ, van Hijum SA
PhenoLink--a web-tool for linking phenotype to ~omics data for bacteria: application to gene-trait matching for Lactobacillus plantarum strains.
BMC Genomics 2012;13:170

‘Distiguished’ Scientist Siezen visits UC Davis, California

Mon, 27 Aug 2012 09:39:00 +0200

Roland Siezen of the Bacterial Genomics group at the CMBI (UMC St. Radboud) in Nijmegen will visit the Food Science and Technology Department of the University of California, Davis, USA. Host scientist will be Dr. Maria Marco. Roland Siezen will be accompanied by NBIC PhD student Lex Overmars of the CMBI, Nijmegen. You can follow Roland and Lex by reading their blog. The visit is part of the Distinguished Visiting Scientist stipend has been awarded by NGI-NBIC to Prof. Dr. Roland Siezen for the period 2010-2013. He will visit international host institutes to set up new collaborations in genomics and bioinformatics of food- and health/disease-related bacteria, in particular in relation to microbial diversity. This will also involve exchange and developments of bioinformatics tools and databases. These host institutes at universities in South Africa and USA are of high international reputation, with excellent scientific infrastructure and computational facilities.

Gunnar Klau Extraordinary Professor at VU University

Fri, 17 Aug 2012 14:11:00 +0200

NBIC Faculty Gunnar Klau is instated as Extraordinary Professor of Bioinformatics and Operations Research at VU University Amsterdam. The appointment is shared between the Faculty of Sciences (Bioinformatics) and the Faculty of Economics and Business Administration (Operations Research). Prof. dr. ing. Gunnar W. Klau is group leader at the Centrum Wiskunde & Informatica (CWI), since 2008. Throughout his career, Dr. Klau has devised problem solving algorithms, using advanced techniques from Operations Research, often in combination with other areas from applied mathematics, thus making fundamental contributions to the area of bioinformatics. You can read more about this news on the website of CWI.

CBS-KNAW partner in NBIC consortium

Thu, 16 Aug 2012 14:06:00 +0200

CBS-KNAW signed the partner agreement with NBIC and became partner in the NBIC consortium. The Fungal Biodiversity Centre (Centraalbureau voor Schimmelcultures: CBS) - an institute of the Royal Netherlands Academy of Arts and Sciences (KNAW) and situated in Utrecht - maintains a world-renowned collection of living filamentous fungi, yeasts and bacteria. The Institute's research programs principally focus on the taxonomy and evolution of fungi as well as on functional aspects of fungal biology and ecology, increasingly making use of molecular and genomics approaches. With CBS-KNAW the total number of partner organisations in the NBIC Consortium adds up to 34.

New tool: GO-Elite

Thu, 16 Aug 2012 13:38:00 +0200

Alexander Zambon (UC San Diego) and colleagues, including NBIC Faculty member Chris Evelo, have developed a new tool to perform over-representation analysis on structured ontology annotations, pathway databases or biological IDs. Numerous over-representation tools are already available, but many of these are limited in scope, lack interchangeability or quickly become outdated because they are linked to only one resource. GO-Elite provides users with a flexible pathway analysis tool that uses the relationships between pathways, ontology species and gene ID systems to generate a minimally non-redundant set of results. Results from GO-Elite can be visualized on WikiPathways or as networks. GO-Elite is available as a web interface, GenMAPP-CS plugin and cross-platform application.

Zambon AC, Gaj S, Ho I, Hanspers K, Vranizan K, Evelo CT, Conklin BR, Pico AR and Salomonis N
GO-Elite: a flexible solution for pathway and ontology over-representation
Bioinformatics 2012 28(16):2209-2210 For more bioinformatics tools, please check the NBIC tools list.

Tight leash on ammonia

Thu, 16 Aug 2012 13:31:00 +0200

In low-GC Gram-positive bacteria four regulators, GlnR, TnrA, GltC and CodY, manage the transcriptional control of the enzymes involved in central nitrogen metabolism. Based on an extensive analysis of the genomes of all species belonging the class Bacilli, which includes well-known families such as Bacillaceae, Lactobacillaceae and Staphylococcaceae, Tom Groot Kormelink (Kluyver Centre for Genomics of Industrial Fermentation) and colleagues found that the GlnR regulon is the most constant of the four. Furthermore, GlnR appears unaffected by the absence/presence of the other three regulators. According to the authors, constraining the import of ammonia- and amino-containing compounds is primarily regulated by GlnR, as is the production of intracellular ammonia. Tight control of ammonia levels is important to limit futile cycling by diffusion of ammonia out of the cell, which fits with the proposed role of GlnR, the authors state.

Groot Kormelink T, Koenders E, Hagemeijer Y, Overmars L, Siezen RJ, de Vos WM, Francke C
Comparative genome analysis of central nitrogen metabolism and its control by GlnR in the class Bacilli.
BMC Genomics 2012, 13:191

Disagreeing databases

Tue, 14 Aug 2012 12:08:00 +0200

For those studying metabolism, pathway databases have become essential resources as they bring together the still expanding amount of information on metabolic networks. The number of available databases is increasing, but unfortunately the level of agreement between databases on a particular network or pathway is surprisingly low. For example, a comparison of 5 pathway databases that describe the human metabolic network revealed agreement on only 3% of the reactions described. As information from databases is used by researchers to for example, interpret their findings or design new experiments, mistakes easily propagate.

To shed some light on the causes of this lack of consensus, Miranda Stobbe (Academic Medical Centre, Amsterdam) and colleagues took the well-known and much studied TCA cycle as their reference point. They compared the description of the TCA cycle as provided by 10 human metabolic pathway databases. To their surprise, they found that none of these databases offered an entirely correct description, that is: a description that agrees on all aspects with the available literature. Furthermore, between these 10 databases, consensus exists on only 3 reactions. The authors combine their analysis of the databases with an extensive literature study to come up with an improved description of the TCA cycle in the WikiPathways database. They point to differences in the way databases retrieve information and in the curation process as potential sources for the inconsistencies found. However, it should not be ignored that part of the problem may be that the biochemistry of the TCA cycle, in spite of decades of intensive study, is simply not as clear-cut as previously thought, the authors add in their discussion.

This project is part of the NBIC BioRange I program.

Stobbe MD, Houten SM, van Kampen AH, Wanders RJ, Moerland PD
Improving the description of metabolic networks: the TCA cycle as example.
FASEB J. 2012 Jun 1

“High-level” bioinformatics

Fri, 10 Aug 2012 13:46:00 +0200

Marlou Snelleman of CMBI in Nijmegen brought bioinformatics to a "higher level" by giving a workshop in Nepal. The workshop - “Bioinformatics and computational analysis of Biomolecules” - was organized in July as part of the HOPE-project: Have yOur Protein Explained (HOPE). The Centre for Molecular and Biomolecular Informatics (CMBI) organized the workshop in collaboration with the Biotechnology Society of Nepal (BSN). More than 65 participants attended the workshop enthusiastically. The participants were provided with the basics of proteins and amino acids: hydrophobicity, structure, properties, mutation, structures, functions etc. They were also trained in bioinformatics tools, such as YASARA view, BLAST and HOPE. The workshop was given twice at two different locations: the National Academy of Science and Technology (NAST) in Khumaltar, and for the Regional Students outside valley at Pokhara University in Pokhara.

Veni and Vidi

Fri, 10 Aug 2012 09:19:00 +0200

July 2012, Jeroen de Ridder (Delft University of Technology) received a Veni grant for the proposal “Searching for new disease genes”. De Ridder will use the Veni grant to study a new analysis technique - based on scale space, a concept from image processing - in order to distinguish important mutations in tumours from unimportant ones. A Vidi was granted to Patrick Kemmeren (University Medical Center Utrecht), to study the regulatory circuits of genetic interactions. Veni and Vidi are part of NWO's prestigious Talent Line programme, which offers scientists at various stages in their career the possibility to do ground-breaking research. On the NWO website you can find:

NBIC tools in the spotlight

Fri, 03 Aug 2012 16:05:00 +0200

To inform as many people as possible about the large list of bioinformatics tools available , we will monthly present a tool in the news. This month we put the spotlight on the NBIC Galaxy Server. NBIC Galaxy is based on the Galaxy system developed by the Center for Comparative Genomics and Bioinformatics at Penn State University. Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biomedical research.
NBIC BioAssist task forces use this server to build and publish their workflows. This server is maintained as an academic best effort and anyone is welcome to use it. The Galaxy wiki provides more information about Galaxy.
You can directly start analysing your data at the NBIC Galaxy.

Royal Tropical Institute (KIT) partner of NBIC

Mon, 30 Jul 2012 15:40:00 +0200

Royal Tropical Institute (KIT) signed the partner agreement with NBIC and became partner in the NBIC consortium.

The Royal Tropical Institute (KIT) in Amsterdam is an independent centre of knowledge and expertise in the areas of international and intercultural cooperation. KIT carries out research on its four themes: Health, Sustainable development, Culture and Knowledge transfer. KIT Biomedical Research is a widely recognized international expert centre working in the field of detection, diagnosis and treatment of infectious diseases. KIT is the 33^rd partner in the NBIC consortium.

Nanopublication approach leads to new initiatives

Mon, 30 Jul 2012 14:48:00 +0200

CWA's nanopublication approach to data stewardship and interoperability has recently received rapidly growing interest from both the academic community and the private sector. This led to several new initiatives. One of them is nanopub.org, a 'sandbox' environment for data owners to 'play around' with turning their data into nanopublications. The ever growing demand for professional follow up on CWA academic initiatives also led to a unique collaboration in a Public Private Partnership (called Euretos) between LUMC, NBIC/DISC and the Phortosgroup, coordinated by Phortos Consultants, in which public and private partners collaborate to professionally develop a professional and sustainable nanopublication ecosystem. The Concept Web Alliance (CWA) is a global collaborative community addressing the increasing problems associated with information overload and the interoperability of data. NBIC is one of the initiators of CWA, which was launched on May 8, 2009 and has already been joined by over 90 participants from academia and the private sector worldwide.

Individual pathways, similar response

Thu, 12 Jul 2012 16:48:00 +0200

For many organisms, glucose is the primary source of carbon and of energy. The availability of cellular glucose drives many key biological processes, including growth and metabolism. Even in simple organisms like yeast, the glucose regulatory system has evolved into a complex network of monitoring glucose levels and relaying information to relevant mechanisms in metabolism and gene expression. Although glucose regulation has been studied extensively with yeast (Saccharomyces cerevisiae) as a model organism, a detailed view on how the various pathways are connected, the pathways' underlying hierarchy and the contribution of individual components is still lacking.

Eva Apweiler (UMC Utrecht) and colleagues generated gene expression profiles of DNA deletion mutants under high glucose growth conditions and subsequently used the data to relate the deleted gene to all transcripts that exhibited a significant change in response to the deletion. Overall, their analysis shows that the glucose signalling pathways in yeast are highly interconnected. As a result, disruption of any individual pathway leads to one main transcriptional response that mimics either a high or a low glucose response. This response appears to be mainly mediated by regulation of the biosynthesis of storage carbohydrates.

Apweiler E, Sameith K, Margaritis T, Brabers N, van de Pasch L, Bakker LV, van Leenen D, Holstege FC, Kemmeren P
Yeast glucose pathways converge on the transcriptional regulation of trehalose biosynthesis
BMC Genomics 2012, 13(1):239

Early Birds ECCB are invited to register for Workshop

Thu, 12 Jul 2012 15:31:00 +0200

Early rate registrations for the ECCB2012 in Basel should be received by August 1st, 2012. Those of you who will visit the ECCB are reminded of the Workshop Bioinformatics Training for Life Scientists. This workshop demonstrates Showcases and Challenges from tutors’ perspectives. The full programme is now available: http://www.eccb12.org/WS4. The workshop is meant for both experienced and beginner trainers, as well as researchers involved in training. Celia van Gelder from NBIC is co-organizer of the workshop and explains the advantages in attending the workshop: “You will get inspiration for your own training and be acquainted with training methods that are effectively used by expert trainers. In addition, you will have the opportunity to connect to the network of trainers & organizers (BTN) and you will be recognized by and become part of the training community. Hope to see you in Basel!” You can register for the ECCB and the workshop through the ECCB website.

NBIC opens pre-registration for Life Sciences Courses

Thu, 12 Jul 2012 14:54:00 +0200

The NBIC Education programme BioWise has opened a pre-registration form for its Life Sciences courses. This way you can pre-register for courses that are not open for registration yet. Your pre-registration gives BioWise some insight in the popularity of the planned and upcoming Next Generation Sequencing courses. You will receive a notification when more detailed information on a course is available or as soon as the actual enrolment form is open.

Barend Mons appointed as professor at LUMC on behalf of NBIC

Tue, 10 Jul 2012 16:01:00 +0200

Dr. Barend Mons, scientific director of NBIC, has been appointed as professor in Biosemantics at the Leiden University Medical Center. The chair is established by the Netherlands Bioinformatics Centre (NBIC).

Mons: “I feel honored with this appointment, not only for me personally, but also because it is the acknowledgment of the growing impact of the fledgling discipline of Biosemantics. This recognition will also serve the adoption of the semantic web approach to knowledge exchange and discovery in the international arena and it signifies the leading role of Dutch researchers in this field. I feel very privileged to work with all the wonderful and pioneering people in the Biosemantics groups”.

The Biosemantics group is a structural collaboration between two research groups on this topic in Leiden (LUMC) and Rotterdam (EMC). The groups focus on “in silico knowledge discovery” in the life sciences. The Rotterdam group is medically oriented and the Leiden group is more focused on basic human genetics. The overall aim is to structure data and information into computer readable formats (in silico), in order to reason over multiple big data sets and to recognize novel patterns (knowledge discovery).

Examples of computer readable structured data formats are Concept Profiles, Knowlets and Nanopublications. Recently, The Value of Data, a visionary paper proposing a next generation data-publishing model in Nature Genetics had been published by Mons et al. The approach is championed by one of the major projects of the Innovative Medicines Initiative (IMI) called Open PHACTS. A start has been made with the Concept Web Alliance to set up an international nanopublication sandbox database, called: the ‘nanopub’.

Ruben Kok, managing director of NBIC: “NBIC has established this chair in Biosemantics, because the discipline will be crucial for ‘reading’ and interpreting the growing amount of life science data”. Furthermore the semantic web approach pioneered by the Biosemantics group and the Concept Web Alliance in which NBIC is involved in a leadership role will be crucial in the wider field of semantic interoperability of data for many other purposes that those of the Biosemantics research groups. The technology is essentially discipline-neutral and can be used across the ‘red’, ‘green’ and ‘white’ sectors in biology and even beyond life sciences. Hence this will be a crucial field to include in the developments of DTL and DISC.

Insight into Leukemia and Bloodtransfusion

Mon, 09 Jul 2012 13:22:00 +0200

A NWO Free Competition grant is awarded to Anton Feenstra for a project that uses theoretical methods to get insight into Leukemia and Bloodtransfusion.

Leukemia is caused by disruption of the cell division and differentiation of blood stem-cells. A complex network of genes that regulate each other, but also many other genes, normally ensures that this process is conducted in an orderly manner. Applying powerful modelling and analysis methods from theoretical computer science provides better understanding of how this network of genes functions. This insight allows medical reseracher to develop better treatment of leukemia, and enables safer and cheaper blood transfusion.

The project awarded with the NWO-grant is a collaboration between the groups of Bioinformatics (Feenstra, Heringa, Bonzanni) and Theoretical Computer Science (Fokkink, Bonzanni) of the VU in Amsterdam. They will work with the groups of Receptor Biochemistry (Martine Smit, VU Faculty of Science, Chemistry) and Bertie Göttgens (Cambridge Institute for Medical Research) for the experimentally verification of predictions from the models.

Grid Computing an essential tool for discovering the Higgs

Fri, 06 Jul 2012 13:04:00 +0200

CERN announced the discovery of the Higgs in ATLAS and CMS. A summary statement listed the 3 essential tools "the accelerator – the experiments – Grid computing". A significant achievement that BiG Grid can feel proud of. The Netherlands, specifically SARA and Nikhef, provide one of the ATLAS Tier-1 Computing Centers through the BiG Grid project. Read more on the BiG Grid website.

NBIC partner in Open PHACTS consortium

Tue, 03 Jul 2012 14:29:00 +0200

NBIC has joined the Open PHACTS project as new consortium member. The Open PHACTS consortium is building a semantic data integration platform for pharmacological data, to give answers needed to identify new drug targets and pharmacological interactions. The Open PHACTS platform will provide a user-friendly tool to answer the critical pharmacology questions defined by nine major pharmaceutical companies. NBIC will be represented as part of the Open PHACTS consortium at ICBO 2012: 3rd International Conference on Biomedical Ontology, July 21- 25 at the Medical University of Graz, Austria. A demo entitled, “The Pharmacology Workspace: A Platform for Drug Discovery” will present the current state of the Open PHACTS project, which uses NBIC’s ConceptWiki software as an integral part of the system.

Press release by Open PHACTS.

A yeast top-model sequenced

Fri, 29 Jun 2012 09:10:00 +0200

In the 1990's, an isogenic family of yeast strains, the Saccharomyces cerevisiae CEN.PK strains, was developed by crossing different laboratory strains. Since then, this family and especially the CEN.PK113-7D strain, has become widely used in systems biology studies, as well as in metabolic and evolutionary engineering studies. Because of the relevance of S. cerevisiae CEN.PK113-7D as a model strain, a large group of academic and industrial researchers set out to perform a de novo sequencing, assembly and annotation of the genome of this strain. The group identified almost 3000 indels (insertion/deletions) compared to the reference genome of S. cerevisiae S288C. A number of genes relating to maltose metabolism and biotin biosynthesis were identified in CEN.PK133-7D that is absent in S288C. It appears that CEN.PK133-7D is not only related to laboratory strains, such as S288C, but also to industrial strains. This may explain the robust physiological performance of CEN.PK113-7D in industrial settings. The annotated genome of S. cerevisiae CEN.PK113-7D is available through http://cenpk.tudelft.nl Nijkamp JF, van den Broek M, Datema E, de Kok S, Bosman L, Luttik MA, Daran-Lapujade P, Vongsangnak W, Nielsen J, Heijne WH, Klaassen P, Paddon CJ, Platt D, Kotter P, van Ham RC, Reinders MJ, Pronk JT, Ridder DD, Daran JM
De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology.
Microb Cell Fact 2012, 11:36, doi:10.1186/1475-2859-11-36

Get your data out there

Thu, 28 Jun 2012 16:13:00 +0200

The strong growth in sequencing capacity and application in a clinical setting is often heralded as an important step towards better diagnosis and better care. This is true only if we find a way to ensure that researchers and physicians around the world have easy access to data on gene variants generated by clinical laboratories, argues a group of researchers, including NBIC Faculty member Johan den Dunnen, in a commentary in The Clinical Biochemist Reviews. They offer a concise overview of why holders of gene variant information should submit their data to public database and what information is required. Plazzer J-P, den Dunnen JT, Smith T, Macrae F and Cotton RG
Reporting of genetic variants by diagnostic laboratories and other centres
Clin. Biochem. Rev. 2012, Vol 33(1):21-24

Polar interactions drive drug absorption

Tue, 26 Jun 2012 17:19:00 +0200

Being able to predict the absorption of drugs is highly relevant to drug discovery and drug development. In this respect, the concept of the polar surface area (PSA) has been successful. The PSA is defined as the combined surface area of oxygen and nitrogen atoms and the hydrogen atoms bound to these. To contribute to improving the correlation between PSA and absorbed drug fraction, Gijs Schaftenaar and Jacob de Vlieg (CMBI, Nijmegen) approached the problem from a quantum mechanical perspective. They focused on the role of the quantum mechanical electrostatic potential in drug absorption and were able to establish a correlation between the absorbed fraction and the so-called Quantum Mechanical Polar Surface Area (QMPSA) for structures where the carboxyl groups are deprotonated. Calculations on neutral gas phase optimized structures resulted in a much weaker correlation. According to the authors, this suggests that the polar interactions of the drug molecules in solution strongly determine the absorption process. Schaftenaar G and de Vlieg J
Quantum Mechanical Polar Surface Area
J. Comput. Aided Mol. Des. 2012, 26(3):311-318, doi:10.1007/s10822-012-9557-y

Plasmid-free LAB

Mon, 25 Jun 2012 15:31:00 +0200

Lactobacillus plantarum is one of the most versatile species of lactic acid bacteria (LAB), which are widely used in food fermentation processes, but also inhabit the gastrointestinal tract. So far, four L. plantarum genomes have been sequenced. A group of Norwegian and Dutch researchers, including NBIC Faculty member Sacha van Hijum and Roland Siezen, has added the genome of a fifth strain, L. plantarum NC8 (CCUG 61730). A remarkable feature of this strain is that it is naturally plasmid free, which distinguishes it from other L. plantarum strains. NC8 has been used as a model strain in the development of genetic tools, as well as in general fermentation and metabolic engineering studies. Axelsson L, Rud I, Naterstad K, Blom H, Renckens B, Boekhorst J, Kleerebezem M, van Hijum S and Siezen RJ
Genome Sequence of the Naturally Plasmid-Free Lactobacillus plantarum Strain NC8 (CCUG 61730)
J. Bacteriol. 2012, Vol.194(9):2391-2392, doi:10.1128/JB.00141-12

Where the genome breaks

Mon, 25 Jun 2012 15:24:00 +0200

Human genetic variation is not only caused by mutations that alter the sequence. Structural variation, in which regions of the genome are for example duplicated or deleted, is also an important source of genetic diversity between individuals. One, by now well-known form of structural variation is the so-called copy-number variation (CNV). Here, the variation does not relate to the sequence of a particular gene, but lies in the number of copies present. One of the reasons for CNV to gain a lot of attention lately is that de novo CNVs have been linked to a number of disorders and diseases. To learn more about the fundamental mechanisms that underlie genome plasticity and genomic rearrangement processes, it is essential to determine the exact breakpoints within the genomic regions that are duplicated. Such repetitive regions, segmental duplications, are characterized by high sequence identity, which makes it very difficult to precisely localize the breakpoints. Furthermore, gaps in the human genome reference often occur precisely at the expected breakpoints. By combining somatic cell hybrids, array comparative genomic hybridization and next-generation sequencing, Andy Itsara (University of Washington) and colleagues (including NBIC faculty member Edwin Cuppen of the Hubrecht Institute) managed to determine CNV breakpoints with molecular resolution in three individuals diagnosed with the 17q21.31 microdeletion syndrome. Itsara A, Vissers LELM, Meltz Steinberg K, Meyer KJ, Zody MC, Koolen DA, de Ligt J, Cuppen E, Baker C, Lee C, Graves TA, Wilson RK, Jenkins RB, Veltman JA and Eichler EE
Resolving the Breakpoints of the 17q21.31 Microdeletion Syndrome with Next-Generation Sequencing
Am. J. Hum. Gen 2012, Vol 90(4):599-613

A warm winter with NBICs advanced NGS courses - presenting our LS course overview for 2012

Mon, 25 Jun 2012 15:10:00 +0200

In recent years NBIC has set up the successful PhD school for bioinformaticians and is now filling the Life Sciences (LS) programme. Following up on the “Next Generation Sequencing (NGS) data analysis” course co-organized with LUMC, NBIC presents a set of four advanced NGS courses to offer a solid foundation to Life Sciences researchers in this field. All NBIC NGS courses are co-developed and co-organised by experts in the field and in close collaboration with leading research groups throughout the Netherlands. The first two courses had a first run in the past year and were well received or as one of the participants of the Genomics Resequencing course stated: “I would certainly recommend this course to anybody that deals with NGS…”. All courses are open for national and international participants from both public and private parties. NBIC NGS Course overview (2012-2013):

Next Generation Sequencing (NGS) data analysis, 6th edition (September 11-13th, 2012, Rotterdam).
Advanced NGS course: RNA-seq data analysis (2nd edition, October 2012). See also the programme of the first edition of this course.
Advanced NGS course: Metagenomics approaches and data analysis (November 2012)
Advanced NGS course: de novo assembly from NGS data (end of 2012)
Advanced NGS course: Genomic resequencing - Variant detection and interpretation in a diagnostic context (2nd edition, early 2013). See also the programme of the first edition of this course.

As soon as course dates have been set or when course programmes are available, these will be published on the NBIC website and on-line registration forms will be made available. As you can see, NBIC is expanding its activities and domains. We are open for your ideas about new topics and additional courses you would like us to organise or you would like to organise with us. For more information about the BioWise LS programme, please look at www.nbic.nl/education/biowise or send an e-mail to Patrick Koks or Celia van Gelder at education@nbic.nl.

Workshop on cross technology

Thu, 21 Jun 2012 11:27:00 +0200

Friday June 1st, the Dutch Tech Centre for Life Sciences (DTL) organized a workshop with representatives from key Life Sciences technologies: sequencing, proteomics, metabolomics, bioimaging, data integration and stewardship (bioinformatics, systems biology and e-science). It was a real WORK shop where the invited participants discussed what infrastructure, expertise, organisation and funding are required to successfully run cross technology projects. The discussions were centred on case studies, such as an integrated biology approach for cancer treatment and an enabling technology platform for plants. The case studies and the “slow-dating” lunch offered ample opportunities for “cross-technology encounters”. That way, the workshop was also a first event to meet each other and build on the DTL community. If you also want participate in DTL, you can visit the DTL website, join the group on LinkedIn or follow DTL on Twitter (#DTL_nl). A photo impression of the workshop is available on de DTL website.

Phenotype Database Jamboree

Thu, 14 Jun 2012 10:00:00 +0200

NBIC is co-organizing a 3-day jamboree around Phenotype Database, one of the NBIC showcase software products. A dedicated group of participants from academic partners, such as University of Bologna, Maastricht University, Wageningen University, and industrial partners, such as TNO, Nestle and Thomson Reuters will get together to discuss the roadmap for the software. The (Nutritional) Phenotype Database (DbNP) helps biologists to interpret the results of biology studies which involve multiple 'omics' techniques. Initially, it was aimed at medium sized nutrigenomics intervention studies (hence the name), but it is now also used for storing studies from different biology areas, such as environmental plant studies. DbNP can be used to store detailed information about the design of your studies, to link those study designs to actual 'omics' data, and to interpret the measured data along the axes of your study design. At the Jamboree Scientists will perform a hands-on multi-study meta-analysis. They will try to find out how the Phenotype Database metadata mechanisms can be used to compare omics and clinical data across multiple heterogeneous studies. In parallel, software developers will facilitate this comparison: they will upgrade the various API's of Phenotype Database to connect public data repositories in order to interchange data. More information: http://phenotypefoundation.org/events/jamboree/

CTMM and NBIC gave insight into DNA at Technology Week

Fri, 08 Jun 2012 12:55:00 +0200

What is my genetic identity? What does my DNA look like? Can I find my DNA online? Answers to these questions were given during the Dutch Technology Week at the NBIC/CTMM-stand.

The Dutch Technology Week (DTW) is an initiative of the Eindhoven Brainport Region to show the public “how enjoyable and challenging it is to work on inventions which change the world”. The Centre for Translational Molecular Medicine (CTMM) and the bioinformatics@school project of NBIC demonstrated the life science technology inventions in a stand in the “High Tech Discovery Route”.

Visitors were guided throughout DNA-research, starting with isolating DNA from buccal and concluding in getting lost in online DNA-databases. Hienke Sminia, NBIC: “Many visitors came to us with questions like: “Tell me, is DNA a protein?” or “What is the difference between diagnostic testing and DNA-profiling used in forensic science?” For the youngest visitors we offered the possibility to build molecules from candy and toothpicks.”

Please take look at the photo impression.

Genalice has won ICT Innovation Award

Thu, 07 Jun 2012 13:41:00 +0200

Genalice, partner in the NBIC consortium, has won the ICT Office Innovation Award for its Biomarker Discovery Platform for Oncology. Summary of the jury report: “Genalice has shown that a small company in collaboration with other private parties, academia and medical centres can develop smart solutions. The BioMarker Discovery Platform will help the medical science to do faster and cheaper analyses in order to provide tailor-made treatment for cancer patients.” You can read the full Press Release (in Dutch) on the website of Genalice.

Visit DTL online

Fri, 01 Jun 2012 15:40:00 +0200

The Dutch Tech Centre for Life Sciences (DTL) is a collaborative public-private initiative to provide high-end and pioneer technology to enable ground-breaking research in molecular biosciences. In essence, DTL is a strongly intertwined network of expert centres among the Dutch universities, university medical hospitals as well as public and private research institutes. NBIC is one of these expert centres and founding partner of DTL. To support the development and branding of DTL, the Community and Outreach Team developed a logo and website for DTL. In addition, a LinkedIn group is opened for discussions. Please join!

Genalice BV became NBIC Partner

Thu, 31 May 2012 13:26:00 +0200

Genalice BV signed the partner agreement with NBIC and became partner in the NBIC consortium. Genalice aims to build scalable and cost-reducing solutions for large scale DNA correlation. They designed a set of new techniques in the area of data-presentation, data-processing, execution optimizations, data-storage and indexing. Genalice is the 9^th industrial partner in the NBIC consortium, in addition to 17 academic organisations and 6 research institutes. The consortium partners are listed on the NBIC website.

Many small improvements

Tue, 22 May 2012 16:38:00 +0200

First described in 1993, Nicolaides-Baraitser syndrome (NBS) is rare, severe disorder that causes a variety of symptoms. Most notable characteristics of NBS are sparse hair, typical facial morphology, distal-limb anomalies and intellectual disability. The lack of known familial cases of NBS suggests that the disorder is caused by de novo mutations. Employing exome sequencing in ten individuals with NBS and extended molecular screening in a larger group, Jeroen van Houdt (Catholic University Leuven) and a large group of colleagues from various institutes identified mutations in SMARCA2 as a cause of NBS. SMARCA2 is a member of the family of Snf2 helicase proteins. A nice study, according to Antoine van Kampen who, together with shared first author Barbera van Schaik (Academic Medical Centre, Amsterdam), performed the bioinformatics analysis. "For us, this was the first exome sequencing study. We identified SMARCA2 to be linked to NBS and we were able to start functional studies into this protein."

Genome of the Netherlands
The ever-increasing amount of sequencing data proved helpful, says van Kampen. "In one of the validation steps, we compared our data to those of more than 200 genomes sequenced as part of the Genome of the Netherlands-project. In contrast to the NBS exomes with common SMARCA2 mutations clustered in the ATPase region we found no mutations in this region in the genomes, which supports our findings about the role of SMARCA2 in causing NBS." Although this study did not result in radically new insights from a bioinformatics perspective, projects like these are worthwhile, Van Kampen feels. "Here, the biological question and the biological data are in the lead. We implement and apply a bioinformatics analysis pipeline, which to a large extent is similar to the pipelines used by other groups. Nevertheless, every exome study allows us to further extent and refine the methods used in our pipeline."

Filters
Crucial to accuracy and usability of the analysis results are the filter steps. Starting with filtering out low-quality sequencing data, every step in the pipeline comes down to choosing which data to remove. Van Kampen: "We try to generate a manageable, high quality dataset for the biologists to process further. For bioinformaticians, the challenge is to choose the best filters for each particular question and dataset. What you find depends on how you search. We deliver suggestions for candidate-genes, which the biologists try to validate. Depending on discussions with the biologists and/or the outcome of the validation, we have to adjust the filters and go through the data again. It sometime happens that your filters remove the crucial data."

Imperfections and unknowns
With the outcomes being so dependent on the selection method applied, how reliable is the information generated by such an analysis? Van Kampen: "The bioinformatics workflow is certainly not perfect yet. Chances are that when you apply a different workflow to the same dataset, you come up with different or partially different results. Studies that compare the effect of different components of the workflows could potentially help in identifying the best way to set up an analysis pipeline. However, such studies are scarce." He mentions the lack of a golden standard. "That is a major problem. Work in that direction is ongoing, but we are not there yet." Imperfections in bioinformatics are however not the only problem as sequencing data are also not perfect. Van Kampen: "We are dealing with many unknowns. You're looking for an unknown gene using experimental and analysis methods that are both still subject to continuous development."

Van Houdt JKJ, Nowakowska BA, Sousa SB, van Schaik BDC, et al.
Heterozygous missense mutations in SMARCA2 cause Nicolaides-Baraitser syndrome
Nature Genetics 44, 445-449 (2012); doi:10.1038/ng.1105

Lodewyk Wessels appointed as professor

Tue, 15 May 2012 14:55:00 +0200

NBIC Faculty member Lodewyk Wessels has been appointed as professor at the Delft University of Technology where he will hold a chair in computational cancer biology. Lodewyk will fulfill this chair while remaining group leader of the Bioinformatics and Statistics group at the Netherlands Cancer Institute. The Netherlands Bioinformatics Centre congratulates Lodewyk with his new position!

Call for contributions: Bioinformatics Training for Life Scientists

Fri, 11 May 2012 13:26:00 +0200

On September 9, 2012, as a satellite meeting of the ECCB, NBIC is co-organizing a Workshop entitled: Bioinformatics Training for Life Scientists: Showcases and Challenges from tutors’ perspectives.
Everyone involved in training life scientists in bioinformatics is invited to submit an abstract for oral presentation at the workshop.

This workshop 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. Topics will include:

Current state of the art and challenges in bioinformatics training for life scientists in the world.
Specific challenges for those delivering bioinformatics training – organizers and teachers - and how we can address these.
Successful showcases of teaching bioinformatics to life science researchers.
Exchange views on the future of Bioinformatics Training, going global: building and strengthening networks of trainers, possible collaborations, international developments, and getting recognition for training efforts.

Abstract Submission
Participants can submit their contributions on one of the following topics:

Successful showcases of face-to-face bioinformatics teaching to life science researchers
Successful showcases of e-learning solutions for teaching bioinformatics to life science researchers

The abstracts will be reviewed by the organisers and they will be selected for oral presentation according to the relevance to the sessions, innovation and country balance.

Instructions for the abstracts submission can be found in the workshop website: http://www.eccb12.org/WS4

Important dates
Submission Deadline: June 8, 2012
Author Notification: June 29, 2012

Organisers
Patricia Palagi (SIB Swiss Institute of Bioinformatics, Patricia.Palagi@isb-sib.ch)
Vicky Schneider (European Bioinformatics Institute, EBI, vicky@ebi.ac.uk)
Allegra Via (Dept of Physics, Sapienza University of Rome, allegra.via@uniroma1.it)
Celia van Gelder (Netherlands Bioinformatics Centre, NBIC, celia.van.gelder@nbic.nl)

What you need to know about licensing

Thu, 10 May 2012 10:19:00 +0200

On 25 May, NBIC and the Netherlands Metabolomics Centre host a workshop on 'Software licensing and valorisation'. Rob Hooft, chief technology officer at NBIC explains why licensing is an important topic for the bioinformatics community.

Too late
"NBIC aims for a broad usability of the software that is developed within the various projects. We think it is important to ensure that others can easily benefit from the tools and programs we develop here and that is why we support open source software", Hooft starts out. "The problem is that many software developers as well as their group leaders are unaware of what an open source license actually means and what the requirements and possibilities are." According to Hooft, too often people starting thinking too late about the use of their software by others. Will others be interested in their software? Under what terms do they want to share their software with others? Are these terms acceptable to potential users? Do the developers intend to commercialize their software in the future? "It is very important to think about these aspects early on in the process, because they determine the boundary conditions and restrictions the developer has to deal with. Each choice comes with certain consequences and in this workshop, we want to present those consequences to stimulate the participants to think about these matters. The longer you wait, the more difficult it becomes to make changes."

Real life issues
During the workshop, actual cases will be presented and discussed. Hooft emphasizes that participants are very welcome to contribute problems and choices they are currently facing or cases they have dealt with. "It would be nice if we could really help participants during the workshop to make the right choice. That is why we do not present theoretical cases, but real life issues and projects."

For more information and registration, check:
http://www.nbic.nl/about-nbic/events/registration-forms/ba-progrmtng-25052012/

Participants interested in contributing to the programme, please contact Rob Hooft at: rob.hooft@nbic.nl

New mutations, new database

Thu, 10 May 2012 10:12:00 +0200

The CHARGE syndrome is a rare genetic malformation disorder in which several organ systems, such as eye, ear and nose are affected. CHARGE is the leading cause of congenital deafblindness. The syndrome is caused by mutations in CHD7, a member of the CHD protein family that plays a role in transcription regulation. In a review in Human Mutation, Nicole Janssen, NBIC Faculty Swertz and colleagues from the University Medical Centre Groningen discuss all currently described CHD7 variants, including 183 new pathogenic mutations identified by the authors. They also present a dedicated, locus-specific database that lists all CHD7 variants. The database is accessible at: http://www.CHD7.org .

Janssen N, Bergman JE, Swertz MA, Tranebjaerg L, Lodahl M, Schoots J, Hofstra RM, van Ravenswaaij-Arts CM and Hoefsloot LH
Mutation update on the CHD7 gene involved in CHARGE syndrome
Hum Mut 2012, doi:10.1002/humu.22086

Metagenomics seminar attracted over 50 participants

Tue, 08 May 2012 11:46:00 +0200

On April 10th, NBIC organized a successful seminar on metagenomics. More than 50 participants from over 20 academic research groups and companies attended the seminar which featured several presentations by academic groups on their metagenomics projects in the field of healthcare, food and nutrition, and environmental science. We had active discussions through the whole seminar and ample time at the end of day to identify common interests and follow-up meetings and joint projects. This seminar was financially sponsored by NBIC and European AllBio project. Follow up
All presentations can be found at the seminar website.
A mailinglist and a wiki page are also set up to facilitate further discussions and projects.

Prize winners at NBIC 2012

Mon, 07 May 2012 16:46:00 +0200

Who is best at presenting their project and scientific results to a conference audience? According to the audience of the NBIC2012 conference Marlies v/d Wees gave the best poster presentation. Her poster collected the most “like stickers” of conference participants and therefore she received the NBIC Poster Award 2012. Patrick Deelen was awarded by the BioWise Student Poster Prize 2012 for the best BSc/MSc poster presentation, selected by a special poster committee. A jury of senior scientists selected Marnix Medema as winner of the Best Lecture Award for his presentation about “Computational Genomics and Synthetic Biology Implementation of Microbial Secondary Metabolite Biosynthesis Pathways”. And the Application Showcase was won by Kostas Karasavvas for showing his application to “Run Taverna workflows from the web”. Congratulations to all of you!

Ortho-Profile: Finding distant relatives

Thu, 26 Apr 2012 16:54:00 +0200

Predicting the function of proteins relies heavily on finding protein 'relatives' (orthologs) of known function in other organisms by comparing sequence data and other information. But when sequence similarity is lacking, for example due to large evolutionary distances or high rates of sequence evolution, potential orthologs could be overlooked. Radek Szklarczyk, Bas Wanschers (Radboud University Nijmegen Medical Centre) and colleagues introduce Ortho-Profile, an iterative prediction method that applies reciprocal best hits at three different levels to infer orthology. Next to sequence-to-sequence comparisons, this method also includes profile-to-sequence and profile-to-profile comparisons. The researchers applied Ortho-Profile in a large-scale prediction of human orthologs of mitochondrial proteins of two model species, the fungi Saccharomyces cerevisiae and Schizosaccharomyces pombe. The analysis resulted in an increase in ortholog detection by 20% compared to solely using sequence-to-sequence comparisons. Based on this analysis, the authors suggest 15 candidate proteins for inclusion in the human mitochondrial proteome.

Szklarczyk R, Wanschers BFJ, Cuypers TD, Esseling JJ, Riemersma M, van den Brand MAM, Gloerich J, Lasonder E, van den Heuvel LP, Nijtmans LG and Huynen MA
Iterative orthology prediction uncovers new mitochondrial proteins and identifies C12orf62 as the human ortholog of COX14, a protein involved in the assembly of cytochrome c oxidase
Genome Biology 2012, 13:R12

Review: R-spondin proteins

Thu, 26 Apr 2012 11:19:00 +0200

The canonical Wnt signalling pathway plays a central role in key biological processes like cellular proliferation, cell differentiation and stem cell maintenance. During embryonic development, Wnt signalling is involved in almost every crucial decision step. The four members of the relatively recently discovered R-spondin protein family act as agonists to the Wnt signalling pathway and are as such highly interesting study objects. However, also in their own right, R-spondins deserve attention as they control for example the sex phenotype (male or female) of an embryo and are crucial to the development of limbs, lungs and the placenta. In a review in Genome Biology, Wim de Lau, Berend Snel and Hans Clevers (Hubrecht Institute/University Medical Centre Utrecht) bring together current knowledge on the evolutionary history of R-spondins, structural features, roles in embryogenesis and operational mechanisms. The authors also present future opportunities and challenges in R-spondin research.

de Lau, WBM, Snel B, Clevers HC
The R-spondin protein family
Genome Biology 2012, 13:242

Splicing alternatives

Thu, 26 Apr 2012 11:10:00 +0200

Increasing protein diversity is one of the roles attributed to alternative splicing – the frequently occurring mechanism in which multiple transcript isoforms are produced from a single gene. Genome-wide studies in plants have shown that alternative splicing is responsible for increasing the transcriptome complexity, but it remains unclear whether this also results in function diversity on the protein level. That requires detailed analysis of the alternative splicing process relating to individual genes or gene families. Edouard Severing (Plant Research International/Wageningen University) and colleagues selected the well-studied MADS domain transcription factor family, for an in silico analysis of the potential impact of alternative splicing on protein-protein interactions of MADS domain proteins. Their results support the impact of alternative splicing on a subgroup of this family that followed earlier genome-wide studies. The authors state that their detailed approach has the power to reveal relevant alternative splicing events that are not distinguishable in global patterns.

Severing EI, van Dijk ADJ, Morabito G, Busscher-Lange J, Immink RGH and van Ham RCHJ
Predicting the impact of alternative splicing on plant MADS domain protein function
PLoS ONE 7(1):e30524. doi:10.1371/journal.pone.0030524

DNA-labs on International Conference for Young Scientists

Thu, 26 Apr 2012 10:39:00 +0200

High school students from Indonesia, South Korea, Russia, Brasil and many more countries came to Nijmegen for the International Conference for Young Scientists (ICYS) last week. The DNA-labs on the Road were invited to organize a DNA-practical for these excellent youngsters during the conference. All six DNA-labs were represented, and all 160 students were allowed to choose a practical of their choice. For example, one student choose for the Leiden-practical because: "... I've never experienced real cancer cells before." More pictures can be found here.

A selection of chickens

Thu, 19 Apr 2012 13:05:00 +0200

The domesticated chicken has been around for so long that we often forget that there are still 'wild' chickens out there. Domestication was initiated at different moments and in different regions, according to archaeological and molecular genetic studies. Selective breeding was already practised during Roman times, but in the 20th century commercial breeding really kicked off, when breeders started selecting specifically for meat production or egg-laying capacity. Domestication and selection must have impacted the variation in the chicken genome when comparing domesticated breeds to their ancestors. Selecting for desired traits has however also resulted in negative effects. Current commercial lines are for example more susceptible to infections, exhibit skeletal deformities and suffer from osteoporosis.

Pooling populations
To understand how these undesirable traits emerged, it is crucial to understand which genes and regions in the genome have been affected by selection. Martin Elferink (Wagening University) and colleagues performed a broad assessment of selection histories using 67 commercial and non-commercial chicken breeds. Of each breed, multiple populations were included to decrease the influence of, for example, genetic drift in just a single population. Based on shared history and breeding goals, 14 breed groups could be formed. Elferink et al identified 396 chromosomal regions that show signs of selection, with strong evidence found for 26 regions. Including many different populations helps to reduce stochastic effects caused by a single population, the authors state.

Elferink MG, Megens HJ, Vereijken A, Hu X, Crooijmans RPMA and Groenen MAM
Signatures of selection in the genomes of commercial and non-commercial chicken breeds
PLoS ONE 7(2): e32720. doi: 10.1371/journal.pone.0032720

New tool: xQTL workbench

Thu, 19 Apr 2012 11:38:00 +0200

With xQTL workbench, analysing large and complex datasets using QTL (quantitative trait loci) methods becomes easier than before. xQTL workbench allows QTL mapping at multiple levels, visualization of QTL profiles, addition of new algorithms, exploring underlying information and scalable data management. Using Molgenis software, xQTL workbench can be customized according to individual needs and preferences. xQTL workbench runs on all common platforms and is available through www.xqtl.org. Arends D., van der Velde KJ, Prins P, Broman KW, Möller S, Jansen RC and Swertz MA
xQTL workbench: a scalable web environment for multi-level QTL analysis
Bioinformatics 2012, 28(7):1042-1044.

NBIC and NMC organize a workshop about software licensing and valorization

Thu, 12 Apr 2012 11:42:00 +0200

Many software projects in the life sciences are written as "open source". But do we actually know what that means? 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 on May 25, in Utrecht.

Userfriendliness Peregrine Increased by Webbased Service

Thu, 12 Apr 2012 11:37:00 +0200

The NBIC's BioAssist Engineering Team announces the launch of a web-based Peregrine Indexing Service. This new API allows users/developers to easily include Peregrine indexing support in their program. It is a way to use Peregrine feature without installing anything locally (software, ontology database). Leon Mei, part of BioAssist Engineering Team: "This allows the potential user base of Peregrine to increase fast." The service is built on top of Peregrine software, an Open Source indexing engine originally developed in the department of Medical Informatics, Erasmus University Medical Center (EMC), Rotterdam. The BioAssist Engineering team worked with the EMC to improve the code quality, readability, and ease of maintenance. The release of this web service interface increases the user friendliness of Peregrine. Textual documents are easily uploaded, analyzed, and returned as a set of indexed concepts, formatted either as XML or JSON. Users can also take advantage of Peregrine's built-in disambiguation logic to get more accurate results. The present dictionary used for indexing is based on SwissProt and UMLS. The BioAssist Engineering team is currently preparing an update of the dictionary to ensure the service will deliver up-to-date comprehensive biomedical knowledge. The web service interface is available here: http://peregrine.nbiceng.net/

Bioinformaticians and clinicians work together in NGS course

Thu, 12 Apr 2012 09:38:00 +0200

Last week, an audience of 37 PhDs and researchers participated in the 2-day advanced NGS course "Genomic resequencing: variant detection and interpretation in a diagnostic context". NBIC organized this course together with Leiden UMC, UMC St Radboud and the Centre for Genome Diagnostics to cover a broad range of topics starting with technical issues around raw sequencing, through data analysis, data interpretation and ending "in the clinic". The course attracted NGS users both from the bioinformatics field and from clinical geneticists who participated all together in lectures, workshops, hands-on software demonstrations and in a lively discussion about the roles of- and communication between bioinformaticians and geneticists.

The course is part of the NBIC BioWise Life Sciences (LS) programme that offers bioinformatics courses for researchers in the life sciences. "Genomic resequencing and variant detection" is part of a set of advanced course topics covering the theme of Next Generation Sequencing. On top of the Next Generation Sequencing Data Analysis basic course, that will be organized in September for the 6th time by LUMC, NBIC is now developing a set of 4 advanced NGS application courses. The RNAseq course in Amsterdam in august 2011 was the 1st of this set and further advanced courses on Metagenomics and de novo assembly using NGS data are being developed right now. More information about the Biowise LS programme can be found at the NBIC PhD school.

BiG Grid, e-BioGrid, NBIC, SARA, Nikhef, EGI and NLeSC start e-infrastructure colloquia

Tue, 10 Apr 2012 16:47:00 +0200

The e-infrastructure colloquia are organized to show the opportunities and applications of e-infrastructure. The colloquia are once a month, admission is free, no registration needed and there will be drinks afterwards. e-science dictates e-publication
The first one is organized April 26 by NBIC with Barend Mons who will explain why e-ccience dictates e-publication in his talk about "Nanopublications as a Substrate for In-silico Knowledge Discovery". The following colloquia are planned as well:

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

Taming the Flood of Genomic Data

Mon, 26 Mar 2012 13:14:00 +0200

BGI (China), TTI GG, NLeSc and NBIC sign Memorandum of Understanding. BGI, the world’s largest genomics organisation, Technological Top Institute of Green Genetics (TTI GG), Netherlands eScience Centre (NLeSC), and Netherlands Institute of Bioinformatics (NBIC) signed a Memorandum of Understanding (MOU) to address the challenge of managing, transporting, integrating and analysing today’s tremendous flow of genomic data. The collaborating organisations advocate the adoption and application of Open Source and Open Access initiatives to genomic data to more easily and rapidly explore the mysteries of life science. Source: BGI website

International Chemical Design & Discovery Course: Registration open now!

Mon, 12 Mar 2012 15:30:00 +0100

June 18th-22nd, the Computational Drug Discovery Group of the Radboud University Nijmegen organizes a course about Chemical Design and Discovery, in cooperation with NBIC and the Netherlands eScience Center. The course covers the recent advances in discovery informatics, with a focus on the application of e-science to real life problems. Read more and register on the course website.

New NGS course: Genomic resequencing & variant calling

Thu, 08 Mar 2012 13:56:00 +0100

On April 4-5, a new BioWise LS course on ‘Genomic resequencing: variant detection and interpretation in a diagnostic context’ will be organised in Nijmegen by NBIC and the Centre for Genome Diagnostics (CGD). Patrick Koks, who joined the BioWise team earlier this year, explains why the time is right to put the spotlight on this particular topic. "It belongs to the broader area of Next Generating Sequencing, NGS. The latter has been the subject of a number of courses already. Participants in these courses are now ready to dive deeper into more specific topics within NGS. For 2012 we aim at a total of four advanced courses on specific NGS applications like RNAseq, metagenomics, de novo assembly and first on the list: exome sequencing in the upcoming course on genomic resequencing and variant calling", says Koks.

Into the clinic
Also the fact that exome sequencing is gaining ground in the clinical setting fuels the need for a targeted course. "The technique has rapidly become accessible over the past few years. It is now possible to sequence a patient's exome and although it is not routine practice yet, it is definitely moving in that direction." The course programme offers lectures to get the participants up to speed on basic aspects, latest developments and current methods. Next to the theory, the participants will be put to work to get hands-on experience with data analysis and will be offered demos on the commercially available tools and systems. "With the demos we aim to support the participants in choosing the packages that best serve their particular needs." The course exclusively deals with the clinical application of exome sequencing and target groups include researchers and technicians involved in sample preparation, sequencing, data collection, annotation etc. as well as clinical geneticists involved in data interpretation and communicating the results to physicians and patients.

Focus on users
'Genomic resequencing: variant detection and interpretation in a diagnostic context' is part of BioWise LS, the NBIC education programme geared towards life scientists – the 'users' of bioinformatics. Within the BioWise team, Patrick Koks will primarily focus on this target group. "We aim to offer an extensive and diverse course programme for biologists and other life scientists. To this end, we will expand the current course programme, but we will also further develop e-learning methods for this group. For over a year now, I have been working on the eBiomics project (www.ebiomics.org), a European project on e-learning in bioinformatics and this will stay part of my work within BioWise." More information about the course (programme). The course is planned to be organised again in the 2nd half of 2012.

NBIC is first virtual organisation in SURFconext

Mon, 05 Mar 2012 13:16:00 +0100

NBIC is the first virtual organisation connected to SURFconext as identity provider. Before, only institutions could connect to the collaboration infrastructure. NBIC is the first distributed (“virtual”) organisation that can serve as identity provider. SURFconext is a next generation collaboration infrastructure that creates new opportunities to collaborate online based on a combination of applications from different providers. Researchers, educators and students wish to select the tools that best fit their online collaboration needs. Organizations struggle with the integration of self-hosted services with commercial cloud services and service providers seek for ways to make their services easily accessible for users in higher research and education. SURFconext offers interesting clues to facilitate these needs. See also the news (in Dutch) on the Surf-website. More information about SURFconext:
http://www.surfnet.nl/en/Thema/coin/Pages/default.aspx

CWI and NBIC signed partner agreement

Mon, 05 Mar 2012 11:14:00 +0100

Last month CWI (Centrum Wiskunde & Informatica) signed the partner agreement with NBIC and became partner in the NBIC consortium. CWI (http://www.cwi.nl/) is a scientific research institute specialized in mathematics and computer science, and is located in Amsterdam. CWI is the 6th research institute in the NBIC consortium, in addition to 17 academic organisations and 6 partners from industry. The consortium partners are listed on the NBIC website.

Revealing deletions

Tue, 21 Feb 2012 13:07:00 +0100

NBIC Faculty Edwin Cuppen and colleagues performed multiplexed genomic enrichment and next-generation sequencing on deleted regions of patients suffering from mental retardation. Their approach is a targeted and highly sensitive method that can help in investigating missing heritability in genome-wide screening studies. Generally, it is believed that in sporadic patients suffering from mental retardation de novo deletions are pathogenic. However, in a similar inherited deletion the phenotypic effect of the genes present in the deleted region is compensated by the normal functioning genes supplied by the other healthy parent. Only when an inherited deletion happens to overlap with de novo or inherited damaging alleles on the other chromosome, the phenotypic effect of the genetic damage is revealed. This recessive mode of inheritance requires new diagnostic approaches as it may be overlooked by routine methods. To study whether this unmasking mechanism contributes to the phenotype of patients with mental retardation and/or multiple congenital abnormalities, Ron Hochstenbach, Martin Poot (both University Medical Centre Utrecht) and Isaac Nijman (Hubrecht Institute) and colleagues performed multiplexed genomic enrichment and next-generation sequencing on the deleted regions in the group of 20 patients. Although further functional validation is required to draw definite conclusions on the pathogenicity of the variants identified, the authors present their approach as a targeted and highly sensitive method that can help in investigating missing heritability in genome-wide screening studies.

Hochstenbach R, Poot M, Nijman IJ, Renkens I, Duran KJ, Van 't Slot R, van Binsbergen E, van der Zwaag B, Vogel MJ, Terhal PA, Ploos van Amstel HK, Kloosterman WP, Cuppen E
Discovery of variants unmasked by hemizygous deletions
Eur J Hum Genet. 2012

NBIC2012: Register now!

Tue, 21 Feb 2012 12:57:00 +0100

This year NBIC organizes the 7th edition of the Netherlands Bioinformatics Conference.
Please, register now!

First step towards synchronised catalogues

Tue, 21 Feb 2012 12:07:00 +0100

To stimulate information exchange and discussion between stakeholders, the NBIC Biobanking Taskforce and BBMRI-NL brought the participants of the various BBMRI-NL Rainbow project together in Utrecht on January 24. The meeting particularly focused on the work packages within the projects that deal with catalogues. Morris Swertz (NBIC/UMCG), Willem de Bruin and Annet Sollie (Project Mondriaan), Linda Mook ('Parelsnoer' Initiative) and Folkert van Kemenade (PALGA) presented examples of catalogues and zoomed in on aspects that are crucial to ensure optimal application of the systems.
One of the outcomes of the meeting was the initiation of a working group that will prepare an inventory of the catalogues within the Rainbow projects and will elaborate a number of user cases. In addition, it was agreed that the questionnaires employed by the various projects will be harmonised.

For more information (in Dutch) on the meeting and the presented examples, check:
http://www.bbmri.nl/nl-nl/nieuws/170-meeting-eerste-regenboogprojecten-bijeenkomst

Copy right transfer text mining tool Peregrine

Thu, 16 Feb 2012 11:57:00 +0100

On January 19^th Erasmus MC and the NBIC BioAssist Engineering Team signed the copy right papers for the software tool Peregrine. This way Erasmus MC is again the full 'owner' of the text mining tool. Jan Kors (EMC, Rotterdam) and his team developed the original tool, which was engineered by Rob Hooft and his BioAssist Engineering Team in order to improve the reach of the tool. The copy rights of the revised version of Peregrine were given (back) to Erasmus MC under the condition that the Peregrine tool would be available as an open source tool. After the open source release of the Peregrine text mining software at the end of 2011, it was therefore time for a festive copyright transfer session at the EMC in Rotterdam. Peregrine can be found at https://trac.nbic.nl/data-mining/ and downloaded under an AGPL license.

e-Pitch about high school innovation project

Thu, 16 Feb 2012 09:36:00 +0100

May last year, Hienke Sminia (NBIC, UMC St Radboud) was granted 10.000 Euro by the SURFnet/ Kennisnet Innovation Programme "Augmented Reality" for her project proposal about a 3D protein scanner for high school. Today, you can learn about the project outcome on ePtich.tv!

And yet another complicating matter

Fri, 10 Feb 2012 10:11:00 +0100

As if trying to understand how gene expression is regulated isn't complicated enough, new levels of complexity keep on emerging. Such as the tissue-dependency of cis-regulation – the phenomenon that single nucleotide polymorphisms (SNPs) can affect the expression of genes that are located nearby on the genome. Recently is has become clear that the effect of such an 'expression-affecting SNP' or eSNP on gene expression levels differs between different tissues. To assess the mechanisms by which genetic variants mediate gene expression, Jingyuan Fu (University Medical Centre Groningen) and colleagues compared the cis-effect of SNPs on gene expression levels in blood, liver, muscle and fat tissue. They propose four molecular models of tissue-dependent cis-regulation, of which opposite allelic direction is the most striking. Even though this model is probably the least common, its impact is huge as in different tissues the effect on gene expression is completely opposite. The authors therefore emphasize the need to use expression data from disease-relevant tissue when studying complex traits.

Fu J, Wolfs MGM, Deelen P, Westra HJ, Fehrmann RSN, te Meerman GJ, Buurman WA, Rensen SSM, Groen HJM, Weersma RK, van den Berg LH, Veldink J, Ophoff RA, Snieder H, van Heel D, Jansen RC, Hofker MH, Wijmenga C, Franke L
Unraveling the regulatory mechanisms underlying tissue-dependent genetic variation of gene expression
PLoS Genet 8(1):e1002431. doi:10.1371/journal.pgen.1002431

FAME: Modeling made easy

Thu, 09 Feb 2012 10:40:00 +0100

To facilitate systems biologists in their efforts to build genome-scale metabolic models, Joost Boele, Brett Olivier and Bas Teusink (VU Amsterdam) offer FAME - the Flux Analysis and Modeling Environment. FAME is a one-stop-shop as it combines the three key points in modeling, being model creation, result generation and interpretation, all into one open source, web-based tool. FAME, as well as a manual and a quick-start tutorial, can be accessed at: http://f-a-m-e.org/

Boele J, Olivier BG, Teusink B
FAME - the Flux Analysis and Modeling Environment
BMC Systems Biology 2012, 6:8, doi:10.1186/1752-0509-6-8

More than 25 students for “Algorithms for Biological Networks”

Mon, 06 Feb 2012 09:17:00 +0100

As part of the NBIC PhD School programme and the ASCI research school education programme, the one-week course “Algorithms for Biological Networks” was organized for the third time in Delft, January 16-20 2012.

This course introduces students to the most important aspects in representing molecular interactions as networks: distinguishing properties of biological networks, algorithms for network inference and enhancement by integrating additional knowledge, methods to execute and validate networks and finally ways of mining networks, to derive novel biological insights and hypotheses. The teaching staff of this course consisted of experts in these areas: Dick de Ridder and Marcel Reinders (Delft University of Technology), Anton Feenstra and Jaap Heringa (Vrije Universiteit Amsterdam), Aalt-Jan van Dijk (Wageningen University and Research Centre) and Gunnar Klau (Centrum Wiskunde en Informatica, Amsterdam).

Over 25 Dutch and Belgian PhD students and researchers attended the course, with various backgrounds, from computer science to the life sciences. This led to an interesting exchange of ideas, which students appreciated very much. An element of the course enjoyed as well as feared by participants was the paper discussion, in which small groups of participants read and discussed a recent scientific publication and prepared a short presentation on it, all within one hour.

Related information:

Alternative transporters

Thu, 02 Feb 2012 16:29:00 +0100

Microorganisms, especially those used in industrial production, are constantly under pressure to perform better. Generating microorganisms with improved characteristics is either done through direct engineering, which requires knowledge of the underlying genetic determinants, or through laboratory evolution, which opens the way for new mutations to occur in a more 'natural' process. Stefan de Kok (Delft University of Technology) and colleagues used laboratory evolution followed by transcriptome analysis and whole-genome resequencing to look for alternative lactate transporters in Saccharomyces cerevisiae (baker's yeast). So far, only one lactate transporter, Jen1p, has been documented in this yeast. The resequencing effort proved crucial and resulted in the discovery of single-nucleotide changes in ADY2, an acetate transporter gene. Introduction of these ADY2 alleles in a S. cerevisiae jen1∆ ady2∆ strain demonstrated that these alleles encode efficient lactate transporters.

de Kok S, Nijkamp JF, Oud B, Roque FC, de Ridder D, Daran JM, Pronk JT, van Maris AJ
Laboratory evolution of new lactate transporter genes in a jen1∆ mutant of Saccharomyces cerevisiae and their identification as ADY2 alleles by whole-genome resequencing and transcriptome analysis.
FEMS Yeast Research 2012 1-16. doi:10.1111/j.1567-1364.2012.00787.x

Cracking mitochondrial ribosome assembly

Thu, 02 Feb 2012 13:34:00 +0100

So far, already an extensive number of factors involved in the biogenesis of cytosolic ribosomes have been identified. However, when it comes to mitochondrial ribosomes, there is still a lot to be learned. For example on the proteins involved in the assembly process. In their search for novel human mitochondrial ribosome-associated proteins, Bas Wanschers (Radboud University Medical Centre Nijmegen) and colleagues performed a comparative genomics study leading to the identification of C7orf30 as the human homolog of the plant protein iojap. According to the authors, their data point to a role for C7orf30 in ribosomal large subunit function.

C7orf30 specifically associates with the large subunit of the mitochondrial ribosome and is involved in translation.
Wanschers BF, Szklarczyk R, Pajak A, van den Brand MA, Gloerich J. Rodenburg RJ, Lightowlers RN, Nijtmans LG, Huynen MA
Nucleic Acids Research, 2012, 1-12. doi: 10.1093/nar/gkr1271

Students visit BBC 2011 in Luxembourg

Thu, 02 Feb 2012 11:48:00 +0100

For several years, NBIC has sponsored students to attend scientific conferences, like the NBIC Annual Conference or the Benelux Bioinformatics Conference (BBC). Celia van Gelder, project leader education at NBIC, explains why. "Participating in a scientific conference is a great way for students to get a broader view of the bioinformatics field. They get updated on the currently leading scientific questions and the latest developments, but they also get a chance to talk to PhD students and researchers working in different areas. We hope this helps them to get an impression of their future professional environment and to establish contacts that might be useful later on."

In December 2011, the annual Benelux Bioinformatics Conference (BBC) took place in Luxembourg. The three Universities of Applied Sciences in The Netherlands that offer a dedicated bioinformatics programme could each select two students to attend the BBC, fully sponsored by NBIC. Maarten Hamberg and Stefanie Geisen, bioinformatics students at the Hanzehogeschool Groningen, were part of the 'Dutch delegation'. Through e-mail, they shared their experiences.

Q: "Why did you want to attend the BBC?"
A: "We were very curious to learn what is going in the bioinformatics field beyond our training. Of course, we learned a little about it already, but it remains limited."

Q: "Why were you selected?"
A: "We needed to submit a letter on our motivation for the conference and come up with a plan to communicate our experiences with students and others that were not attending. We decided to create a simple website where people could post questions that we would answer during or after the conference. We also used this site to share our experiences and some pictures."

Q: "What did you expect from the conference?"
A: "We had high expectations, because it is a international event so we expected high-level presentations and speakers."

Q: "And were these expectations met?"
A: "Yes and no. The keynote speakers generally delivered very interesting lectures that really captivated us. But there were also quite a lot of presentations by researchers who are without a doubt very knowledgeable on their own specific topic, but for 'outsiders' these sessions were really difficult or simply incomprehensible. So from a number of sessions, we learned less than we hoped."

Q: "Did the topics match your training or was it all new?"
A: "As said, with some presentations it was hard to keep up. Lately, we focused a lot on assembly and genome annotation in our training, but unfortunately there was only little attention paid to this topic. We expected more on this."

Q: "Are there topics or contacts that you will follow up, for example for a research project or an internship?"
A: "We talked about studying in Luxembourg, because the city is really beautiful. We already arranged our internship before going to the BBC, but we did learn about some impressive new techniques and tools. For example, a tool that visualizes the different cellular phases in different types of cancer was really interesting."

Q: "Is it worthwhile for students to visit a conference like the BBC?"
A: "Yes, it is certainly useful to participate in such an event, but it probably especially useful for people engaged in actual research, because they can get new ideas by discussing their research with others working in the same area."

Links:

Website of the students of the Hanzehogeschool Groningen about their visit to the BBC: http://bioinformatica42.wordpress.com/
Students of the Hogeschool Arnhem Nijmegen wrote a blog (in Dutch) about the BBC visit:http://blog.han.nl/studeertechniek/2012/01/12/bbc-luxemburg-congres-voor-bioinformatici/

From harmless to harmful

Tue, 31 Jan 2012 15:56:00 +0100

Stramenopiles are a major and diverse line of eukaryotic organisms, predominantly algae, but also including the generally pathogenic oomycetes. One of the most notorious oomycetes species is Phytophtora infestans, which causes late blight in potato. Oomycetes are known to have flexible genomes. To learn more about the evolutionary processes that shaped gene content and the origin of the oomycetes' pathogenicity (in contrast to the non-pathogenic nature of the algae they are related to), Michael Seidl (Utrecht University) and colleagues applied systemic tree reconciliation. They focused on ten Stramenopiles (algae and oomycetes) and were able to reconstruct a last common ancestor that contained appr. 10,000 genes. It appears that throughout evolution, the oomycetes genomes underwent a continuous flow of gene duplication and gene loss. According to Seidl et al., the branch leading to the notorious Phytophtora genus marks a major transition point in oomycetes evolution.

Seidl MF, van den Ackerveken G, Govers F, Snel B
Reconstruction of oomycete genome evolution identifies differences in evolutionary trajectories leading to present-day large gene families.
Genome Biol Evol. 2012 Jan 13

The Longevity Puzzle

Tue, 31 Jan 2012 14:35:00 +0100

The secret to a long life; who doesn't want to know? Performing gene expression profiling on a group of nonagenarians (people in their 90s), their middle-aged offspring and the offspring's partners as controls, Willemijn Passtoors (Leiden University Medical Centre) and colleagues, among which NBIC faculty member Judith Boer (LUMC), succeeded in coming up with a new small piece of the puzzle. Using by now standard bioinformatics tools, such as Limma for single gene analysis and Globaltest for pathway analysis, the group found an 'ageing-signature' of 21 genes. Reduced expression of two of these appears to mark familial longevity already at middle age.

Passtoors WM, Boer JM, Goeman JJ, van den Akker EB, Deelen J, Zwaan BJ, Scarborough A, van der Breggen R, Vossen RH, Houwing-Duistermaat JJ, van Ommen GJ, Westendorp RG, van Heemst D, de Craen AJ, White AJ, Gunn DA, Beekman M, Slagboom PE
Transcriptional profiling of human familial longevity indicates a role for ASF1A and IL7R.
PLoS One. 2012;7(1):e27759

Towards interoperable bioscience data

Mon, 30 Jan 2012 13:55:00 +0100

Fifty researchers representing 37 research groups from all over the world plead in Nature Genetics to use the ISA standard in order create data interoperability. Chris Evelo, group leader BiGCaT Maastricht University and NBIC Faculty, is one of the authors.

Shared, annotated research data and methods offer new discovery opportunities and prevent unnecessary repetition of work. Although funding agencies, journals and community initiatives encourage good data stewardship and sharing through the use of community reporting standards, data sharing remains challenging.

To make full use of research data, the bioscience community needs to adopt technologies and reward mechanisms that support interoperability and promote the growth of an open 'data commoning' culture. The Nature Genetics paper describes the prerequisites for data commoning and presents an established and growing ecosystem of solutions using the shared 'Investigation-Study-Assay' (ISA) framework to support that vision.

Chris Evelo explains: “ISA introduces new ways of analysing the enormous amounts of bioscience data. For instance: the possibility to compare all diabetes studies which describe diet changes”.

Nature Genetics 44, 121–126 (2012) doi:10.1038/ng.1054
http://www.nature.com/ng/journal/v44/n2/full/ng.1054.html

Crossing borders

Mon, 23 Jan 2012 14:20:00 +0100

The action of genes is regulated through interactions with other genes. Understanding gene regulatory networks is therefore crucial to gain insight into the molecular mechanisms that underlie health and disease. Building such networks that involve thousands of genes and millions of interactions requires large-scale experimental datasets that in practice are affected by all kinds of artifacts. In particular when studying rare diseases of which the underlying biology is still largely unknown, the limited number of available samples further complicates the issue. In a recent paper in PLoS Computational Biology, Seyed Yahya Anvar (Leiden University Medical Centre) and colleagues hypothesize that biologically relevant relationships between genes are often conserved across species and that interspecies gene networks should be more meaningful from a biological perspective. Working from this hypothesis, they develop the Dandelion algorithm to construct and train intraspecies Bayesian networks. They demonstrate their approach on a dataset comprising both animal model and human data on OPMD, a rare muscular disorder.

Anvar SY, Tucker A, Vinciotti V, Venema A, van Ommen GJB, van der Maarel SM, Raz V, 't Hoen PAC
Interspecies translation of disease networks increases robustness and predictive accuracy
PLoS Comput Biol 7(11):e1002258

Driven by design

Mon, 23 Jan 2012 12:14:00 +0100

Functional genomics experiments are increasingly determined by a predefined experimental design. The design drives data generation and determines how the resulting data sets are organised. Knowledge of the underlying experimental design is therefore important to ensure adequate data analysis. Several methods have become available that utilize the underlying experimental design. Age Smilde (University of Amsterdam) and colleagues compared these methods and developed a general framework that supports researchers in understanding the differences between the methods, how to deal with factor effects that stem from the design used and selecting an alternative analysis method that might offer a better fit with their particular biological question.

Smilde AK, Timmerman ME, Hendriks MMWB, Jansen JJ, Hoefsloot HCJ
Generic framework for high-dimensional fixed-effects ANOVA
Briefings in Bioinformatics 2011, doi:10.1093/bib/bbr071

NGI calls for proposals Venture Challenge

Thu, 19 Jan 2012 11:29:00 +0100

The Netherlands Genomics Initiative (NGI) calls for proposals for their Venture Challenge Spring 2012. Deadline for submission: March 6th. The Venture Challenge is one of NGI’s activities aimed at stimulating and supporting Life Sciences (including bioinformatics!) researchers in translating their inventions into viable business ideas. The Venture Challenge is an opportunity for all aspiring Life Sciences entrepreneurs, it is the way to receive coaching and advice on essential elements of setting up a business.It is also good preparation for the next stage: acquiring financing, such as the Life Sciences Pre-Seed Grant. In two 3-day workshops, the facilitators and other ‘competing’ teams will challenge you to focus your business idea to create optimal customer value, and you will learn to pitch your business case.

At the end of the Challenge, the team with the best venture plan and pitch is awarded €25,000. For more information and the proposal form visit the NGI Venture Challenge website.

Resequencing: important, but hardly rewarded

Tue, 17 Jan 2012 08:50:00 +0100

With the advances in sequencing technology and analysis, the sequencing of genomes has become a routine activity. Even so, re-doing the whole exercise to improve your original sequence and annotation is much less common. The lactic acid bacterium Lactobacillus plantarum WCFS1 is one of the few organisms that have been 'honoured' with a complete resequencing and gene re-annotation.

Legacy
In 2001, a group of researchers from TI Food and Nutrition, Centre for Molecular and Biomolecular Informatics, NBIC and NIZO food published a sequence of L. plantarum WCFS1. Recently, they published the results of a complete resequencing and annotation efforts. Why go through all the motions again? "First of all, it is very important that a sequence and the annotation are as accurate as possible, because they are the starting materials for all subsequent research and analyses", says Sacha van Hijum, one of the contributors. "L. plantarum is one of the workhorses of the fermentation industry and it is a popular model system for research. There are so many researchers working with this bacterium that over the years an enormous amount of new knowledge and data on L. plantarum has been generated. But only the original authors of a sequence are allowed to make adjustments in the sequence and the annotation in the popular NCBI database. We wanted to do justice to this community effort and we also see the sequence and annotation as a legacy, which allows incorporating new insights and correcting inconsistencies."

Publication
Now that sequencing has become a lot faster and cheaper, does that mean we can expect a lot of re-sequencing efforts? Van Hijum: "Yes, I do think so, but it remains to be seen to what extent the results will be made public. I foresee that many labs will resequence the genomes of their 'own' strains, but will keep the results in-house. Unless you're an original author, it is very difficult to get this type of work accepted for publication. And that is a real shame because it is a common interest to update and improve sequencing information. With no 'reward' for this type of work, I think that many researchers will not bother to communicate their results to the broader community."

Siezen RJ, Francke C, Renckens B, Boekhorst J, Wels M, Kleerebezem M, van Hijum SAFT
Complete resequencing and reannotation of the Lactobacillus plantarum WCFS1 genome
Journal of Bacteriology 2012 (194:1), 195-196

Typing tuberculosis

Thu, 12 Jan 2012 15:01:00 +0100

Tuberculosis (TB) is one of the world's major health problems. It is estimated that roughly one-third of the global population is infected with Mycobacterium tuberculosis, the TB-causing pathogen. Especially for people with weakened immune systems (due to e.g. HIV infection, malnutrition or generally poor living conditions), TB is life-threatening. The so-called Beijing strains of M. tuberculosis have the dubious honour of being the most successful genotype of the pathogen, responsible for approximately 50% of the TB cases in Asia. The Beijing strains are also associated with the current multi-drug resistance TB epidemic in Eastern Europe and South Africa. To gain a more detailed understanding of the various strains within the Beijing genotype, Anita Schürch (National Institute for Public Health and the Environment, NL/Centre for Molecular and Biomolecular Informatics, Nijmegen, NL) and colleagues developed a typing scheme that uses SNPs and regions of difference (RDs) derived from whole-genome sequencing data of eight Beijing strains. Their analysis reveals that the Beijing strains' global spread was initiated on multiple occasions.

Schürch AC, Kremer K, Hendriks ACA, Freyee B, McEvoy CRE, van Crevel R, Boeree MJ, van Helden P, Warren RM, Siezen RJ, van Soolingen D
SNP/RD typing of Mycobacterium tuberculosis Beijing strains reveals local and worldwide disseminated clonal complexes
PLoS one, 2011, Vol 6, Issue 12

Interconnecting data

Thu, 05 Jan 2012 13:56:00 +0100

A major challenge of linked data is resolving the many different identifiers representing the same object. Interconnecting data requires mappings between the identifiers used in different data sets. To help with this issue, the NBIC BioAssist engineering team in conjunction NBIC Interoperability task force has developed a service that provides the conversion between two types of identifiers; the PubMed Identifier (PMID) which is a unique number assigned to PubMed citations of life science journal articles and the Digital Object Identifier™ (DOI) which is used for identifying digital content. DOI’s are used to provide current information, including where the content (or information about the content) can be found on the Internet. DOI’s are a very useful identifier as they often give a direct link back to the full text scientific article. The conversion service is available from SOAP and REST web services, and in addition, there is a SPARQL endpoint for querying the mappings.
These services can be found here: http://www.pmid2doi.org/

HPC Cloud available

Thu, 05 Jan 2012 10:39:00 +0100

Since the first week of January 2012, the HPC Cloud facility is available for users. With this infrastructure, BiG Grid and SARA offer self-service, dynamically scalable and fully configurable HPC systems. The HPC Cloud offers fast compute clusters to users for whom other HPC facilities are not an option. Read more on the SARA website.

Variation OK, but not in name

Tue, 20 Dec 2011 14:12:00 +0100

The boost in sequencing efforts provides a wealth of information on genetic variants. This information is highly valuable to clinical diagnosis of disease, but requires unambiguous descriptions of the variants to prevent mistakes. A standard nomenclature for sequence variants has been established, but due to additions and extensions the complexity of this nomenclature makes it increasingly difficult for non-experts to understand and use. To assist clinicians and researchers, as well as database curators, Jeroen Laros and colleagues at the Leiden University Medical Centre have worked out formal descriptions of the syntax in Extended Backus-Naur Form (EBNF) on the DNA-RNA level and on the protein level. These descriptions can be easily modified and extended and can be used to develop new tools for text mining and other programmes used in the handling of sequence variant descriptions.

JFJ Laros, A Blavier, JT den Dunnen, PEM Taschner
A formalized description of the standard human variant nomenclature in Extended Backus-Naur Form
BMC Bioinformatics 2011, 12(Suppl 4):S5

Intriguing repeats

Mon, 19 Dec 2011 14:28:00 +0100

In protein sequences, amino acid tandem repeats are among the most prevalent patterns. There are several types of repeats. Repetitions of a single amino acid (single amino acid repeats, SAAR) such as polyglutamine (polyQ) and polyalanine (polyA) have been linked to neurodegenerative diseases. Other SAARs are thought to play a role in various biological processes, including network evolution (proline repeats) and protein localization (histidine repeats). Repeats with more complex patterns have also been extensively studied. For example, the role of leucine rich repeats (LRR) as the structural framework in protein-protein interactions.

So far, most of the research has been limited to studying the role of certain repeats within a single organism, but due to the lack of repositories for large-scale investigation and comparison of repeats from a variety of proteomes, drawing more general conclusions on the functional and evolutionary roles of repeats has not yet been possible. With ProRepeat, Hong Luo and colleagues from the group of Jack Leunissen (Wageningen University) aim to provide an integrated, curated and updated repository and analysis platform for the study of amino acid tandem repeats. ProRepeat is available through http://prorepeat.bioinformatics.nl
H Luo, K Lin, A David, H Nijveen, JAM Leunissen
ProRepeat: an integrated repository for studying amino acid tandem repeats in proteins
Nucleic Acids Research 2011

Correlated variation

Tue, 13 Dec 2011 09:17:00 +0100

In predicting functional sites in proteins, conservation of amino acids in sequence alignments is a well-known indicator of functional properties. In addition, correlated variation among amino acid positions tells something about which residues are located close to each other in the 3D structure can be applied for the prediction of intra- or intermolecular contacts. Current methods are limited to the analysis of pairwise correlations, but this obscures the difference between direct and indirect correlations. Observed correlation therefore thus not necessarily indicate that residues are located close to each other. In a paper in BMC Bioinformatics, Sreekumar et al. present a new method for Regularized Multinomial Regression to obtain Correlated Mutations (RMRCM) from protein multiple sequence alignments. Using simulated and biological datasets, good performance of the method was shown.

RMRCM is available in R-code via www.ab.wur.nl/rmrcm
J Sreekumar, CJF ter Braak, RCHJ van Ham, ADJ van Dijk
Correlated mutations via regularized multinomial regression
BMC Bioinformatics 2011, 12:444

NBIC survey

Tue, 13 Dec 2011 08:59:00 +0100

We are continuously improving the activities organised by NBIC office and therefore are interested in your opinion. Please give your input about the NBIC newsletter, Interface, workshops and meetings by filling out this survey. Link to survey: http://www.nbic.nl/limesurvey/index.php?sid=55494&lang=en It will take no longer than 3 minutes of your time! Thank you!

OntoCAT: easy ontology search

Mon, 12 Dec 2011 13:04:00 +0100

In annotating life sciences data, ontologies are quickly gaining importance. Several ontology access resources are available, but these are not always easy to use and the differences in content and mode of operation makes integration with research data difficult. OntoCAT, developed by a team of bioinformaticians at the European Bioinformatics Institute and NBIC faculty member Morris Swertz (University of Groningen) offers a user-friendly interface to query heterogeneous ontology resources.

OntoCAT has been successfully applied in various use cases and is available through: www.ontocat.org
T Adamusiak, T Burdett, N Kurbatova, KJ van der Velde, N Abeygunawardena, D Antonakaki, M Kapushesky, H Parkinson, MA Swertz
OntoCAT - simple ontology search and integration in Java, R and REST/JavaScript
BMC Bioinformatics 2011, 12:218

N Kurbatova, T Adamusiak, P Kurnosov, MA Swertz, M Kapushesky
ontoCAT: an R package for ontology traversal and search
Bioinformatics 2011, 27:17

Jan Bot wins light path for Next Generation Sequencing

Mon, 12 Dec 2011 11:26:00 +0100

Jan Bot, e-BioGrid e-core member, wins the Enlighten Your Research (EYR) contest with the proposal 'Next generation networking for next generation sequencing'. The proposal aims to connect the institutes involved in next-generation sequence data analysis by developing five national and two international dynamic light paths including to Hong Kong where sequencing data are produced. Also extra storage is required to enable the transport of big datasets. The jury report says: 'Sound approach; impressive network both nationally and internationally' and 'genuinely next generation, with a major impact on both science and industry'.

The Enlighten Your Research contest is organised by SURFnet, SARA, BiG Grid and NWO to 'Take your e-Infrastructure to the next level'. E-Infrastructure refers to the combined use of central storage and computing capacity, grid-infrastructure and high level connectivity via light paths.

More information (in Dutch) can be found on the SURFnet website. In 2009, another Enlighten Your Research competition was organised. One of the winners then was Péter Horvatovich, University Groningen: a high speed lightpath network for the "Bioinformatics for Proteomics" Platform.
At our Vimeo-channel you can watch a video about the project.

Targeting the trainer

Thu, 08 Dec 2011 08:55:00 +0100

The demand for bioinformatics education aimed at life scientists, especially short focused courses, is rapidly increasing. To facilitate the sharing of teaching materials, expertise and experiences, a broad international community initiative – including Celia van Gelder, project leader education at NBIC – has launched the Bioinformatics Training Network (BTN).

The BTN website (www.biotnet.org) is a centralized resource where the bioinformatics community can share teaching materials. All materials listed on the site are freely available to everyone; the ability to upload materials requires prior registration. A distinguishing feature of the BTN website is that the teaching materials are rated and ranked by the community to stimulate constructive feedback.

MV Schneider et al.,
Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers
Briefings in Bioinformatics

Conserved yet flexible

Tue, 29 Nov 2011 11:58:00 +0100

In eukaryotic growth, a major regulatory role is played by the protein TOR (target of rapamycin). TOR is a kinase - a protein that phosphorylates other proteins - and is part of two protein complexes called TORC1 and TORC2. Both complexes are components of important pathways: TORC1 is activated by the insulin signalling pathway and TORC2 regulates cytoskeleton rearrangement in response to growth. Dysfunction of TOR or other components in TOR pathways is linked to cancer development. Although TOR has been characterised in animals, fungi and plants, not all of the TOR complex subunits or pathway components have been equally conserved. To study the evolution of the TOR pathway, John van Dam and colleagues at Utrecht University, performed phylogenetic analyses on the components of the TOR pathway. They found that TOR, the subunits of the two TOR complexes and a large part of the pathway components form an evolutionary core, while other regulatory inputs have been added to the pathway during evolution. According to van Dam et al., their results show that a highly conserved pathway can also be flexible. TJP van Dam, FJT Zwartkruis, JL Bos, B Snel
Evolution of the TOR pathway
Journal of Molecular Evolution, published online 5 November 2011 By: Esther Thole

Improving cancer gene identification

Tue, 29 Nov 2011 11:51:00 +0100

Actively causing mutations to disrupt cellular processes and thus, perhaps, cause cancer in mouse models is a widely used approach to find cancer genes and study affected regions in the genome. This process, called insertional mutagenesis, employs retroviruses and transposons that are integrated into the host DNA. Identifying which genes are affected by these insertions and are responsible for cancer development is not yet a straightforward task. To improve the analysis of large-scale insertional mutagenesis screens, Johann de Jong (Netherlands Cancer Institute) and colleagues developed Kernel Convolved Rule Based Mapping (KC-RBM), a computational method to map integration sites to target genes. When compared to existing methods, KC-RBM showed superior performance in identifying true positives. KC-RBM is available as R-package. J de Jong, J de Ridder, L van der Weyden, N Sun, M van Uitert, A Berns, M van Lohuizen, J Jonkers, DJ Adams, LFA Wessels
Computational identification of insertional mutagenesis targets for cancer gene discovery
Nucleic Acids Research 2011, (39), 15 published online 7 June 2011 By: Esther Thole

Peregrine released as open source

Tue, 29 Nov 2011 11:12:00 +0100

"Peregrine", a blazingly fast software package used to recognize interesting multi-word terms in human text, has recently been released as open source.

Peregrine was originally developed by Martijn Schuemie at the department of Medical Informatics of the Erasmus University Medical Center (EMC) in Rotterdam. The package was the first project in 2009 to be taken up by NBIC's BioAssist Engineering team, who have been preparing the open source release together with the EMC by making the program easy to use, and the code more easy to extend and maintain.

Peregrine can now be found at https://trac.nbic.nl/data-mining/ and downloaded under an AGPL license; the members of the BioAssist Engineering Team will be following the associated mailing lists in order to provide first-line support for users.

Information system for nuclear hormone receptors

Fri, 25 Nov 2011 15:56:00 +0100

This month, Bas Vroling (CMBI Nijmegen) published the NucleaRDB. NucleaRDB is a Molecular Class-Specific Information System that collects, combines, validates and disseminates large amounts of heterogeneous data on nuclear hormone receptors. It contains both experimental and computationally derived data.

The data and knowledge present in the NucleaRDB can be accessed using a number of different interactive and programmatic methods and query systems. A nuclear hormone receptor-specific PDF reader interface is available that can integrate the contents of the NucleaRDB with full-text scientific articles. NucleaRDB is freely available at http://www.receptors.org/nucleardb.

NucleaRDB: information system for nuclear receptors.
Vroling B, Thorne D, McDermott P, Joosten HJ, Attwood TK, Pettifer S, Vriend G.
Nucleic Acids Res. 2011 Nov 7

WikiPathways: new features for a growing community

Fri, 25 Nov 2011 15:11:00 +0100

New features of WikiPathways, a public wiki for pathway curation, are discussed in the November issue of Nucleic Acids Research. New features include a zoomable pathway viewer, support for pathway ontology annotations, the ability to mark pathways as private for a limited time and the availability of stable hyperlinks to pathways and the elements therein.

WikiPathways content is freely available in a variety of formats such as the BioPAX standard, and since it was first published in 2008 the content is increasingly adopted by external databases and tools, including Wikipedia. A recent development is the use of WikiPathways as a staging ground for centrally curated databases such as Reactome. WikiPathways is seeing steady growth in the number of users, page views and edits for each pathway. The novel use of pathway pages as supplementary material to publications, as well as the addition of tailored content for research domains, is expected to stimulate growth further.

http://www.wikipathways.org
WikiPathways: building research communities on biological pathways.
Kelder T, van Iersel MP, Hanspers K, Kutmon M, Conklin BR, Evelo CT, Pico AR
Nucleic Acids Res. 2011 Nov 16

Agilent Thought Leader Award for Chris Evelo

Fri, 25 Nov 2011 13:17:00 +0100

Agilent Technologies Inc. and the Agilent Technologies Foundation announced that Dr. Chris Evelo (Maastricht University, NBIC) receives the Agilent Thought Leader Award supporting development of software to integrate different types of biological data.

The goal of this award is to help accelerate breakthroughs in disease research by facilitating integrative systems biology approaches.

The Evelo Lab helped develop WikiPathways.org as a community-curated platform for structuring multi-omics data and the associated open-access pathway analysis tool PathVisio. The Agilent Thought Leader Award will fund development of tools for visualizing metabolite fluxes using PathVisio. The goal is to make modeling results much more accessible to biologists and easier for them to interpret.

You can read the full press release at the website of Maastricht University.

Bioinformatics Career Day very popular

Thu, 24 Nov 2011 14:34:00 +0100

The first ever NBIC-LOBIN career day for bachelor (HBO) bioinformatics students was extremely popular, as an overwhelming 130 participants came to Leiden on November 18^th. And all twenty stands where filled with companies and master tracks.

“If I could choose another education, it would be Bioinformatics,” declared Professor Johan Den Dunnen (LUMC) in his welcoming lecture. “You have chosen a field in full motion, where big things are happening right now. And with excellent job prospects: it’s been a while since I hired someone more able with pipette than keyboard.”
In several following lectures, the assembled 3^rd and 4^th year HBO students from Nijmegen, Groningen and Leiden saw their possible futures unfold. Alumni spoke of their choices: to start working right away, or participate in a master track first? The two directly accessible master tracks, at the VU University and Wageningen University, explained their expertise and mutual need to explore the systems biology field.

The afternoon was meant for mingling with employers in the bioinformatics field. There was a very mixed set, multinationals like Keygene stood side to side with start-ups and universities. For a select set of participants there was a guided tour in the Leiden Genome Technology Centre and its multitudes of sequencing machines of all ages. Keynote speaker Jaap Heringa (VU, scientific director NBIC) concluded the day with his vision of the field in the next 15 years, after which the mingling continued happily over drinks.

You can find more information in the programme of the Bioinformatics Career Day 2011. The next career day will be organized in 2013 by the Hogeschool Nijmegen and Arnhem, also together with NBIC.

Dutch Techcentre for Life sciences (DTL)

Fri, 18 Nov 2011 11:24:00 +0100

November 22^nd, at Life Sciences Momentum, six top expertise centres together presented the Dutch Techcentre for Life sciences (DTL). DTL is their answer to the rapidly growing need for high-end technologies in biomedical and biotechnological research. Mission of DTL is to give Dutch investigators in academia and industry access to up-to-date and high level expertise and equipment in the fields of next generation sequencing, proteomics, metabolomics, microscopy and data integration and stewardship.

DTL builds on centres of excellence, several of which have been established under the umbrella of the Netherlands Genomics Initiative (NGI). These are:

•   Netherlands Bioinformatics Centre (NBIC), www.nbic.nl
•   Netherlands Consortium of Systems Biology, (NCSB), www.ncsb.nl
•   Netherlands Metabolomics Centre (NMC), www.metabolomicscentre.nl
•   Netherlands Proteomics Centre (NPC), www.netherlandsproteomicscentre.nl
•   Centre for Genome Diagnostics (CGD)
•   Netherlands Society for Advanced Light Microscopy

Ruben Kok, managing director of the Netherlands Bioinformatics Centre (NBIC), explains: “No single research group, institute, university, or company will be able to maintain all key big life science technologies at a sufficiently high level. To secure the frontline position of Dutch R&D a new approach is needed to make these technologies available in a more efficient and cost-effective way. DTL offers dedicated technology expertise and collaborative research facilities that are coordinated at the national and international level.”

A growing urgency to change

Thu, 17 Nov 2011 09:53:00 +0100

According to Johan den Dunnen there are no valid reasons for not publishing all data on gene variants in a public database. "We urgently need access to this information, otherwise it is useless to perform whole genome analysis."

For a long time already, multiple efforts are ongoing to make all discovered gene variants accessible through public databases. So far, progress has been very limited and there is still no easily accessible, internationally accepted database that brings all the information (gene variants, phenotype descriptions, clinical information) together. "Currently, the vast majority of gene variants are not published at all. Academic and commercial diagnostic labs, as well as most researchers don't bother to make their findings available to the community", says den Dunnen, professor of Medical Genome Technology at the Leiden University Medical Centre. Discussions on the need for a standardized, curated and publicly accessible database have been going on for a long time, but the advent of whole genome sequencing in routine clinical practice is creating a sense of urgency. Den Dunnen: "The extent of the problem is dawning quickly. You can deal with three variants in the conventional manner of analysis, but confronted with a list of 10,000 variants or more, you are nowhere if you don't have access to a central resource for retrieval of relevant information. Using modern sequencing technology, clinical geneticists and diagnostic labs are confronted with such lists. The urgency is high and will only increase because physicians and patients will want the results on short notice."

MutaDATABASE
One of the initiatives that aim to come to a manageable and sustainable solution is MutaDATABASE (www.mutadatabase.org), in which den Dunnen is a participant. A correspondence by the MutaDATABASE consortium in Nature Biotechnology earlier this year (Feb 2011) led to a discussion with other initiatives in the field, including the Human Variome project and the Gen2Phen consortium. Den Dunnen emphasizes that he also participates in those initiatives and remains neutral on the back-and-forth comments that have been published in Nature Biotechnology (links listed below). "I am basically part of both sides in this discussion. This type of quarrelling usually comes up when an opportunity for funding is appearing. To me, the most important thing is that we are going to act. These discussions have been going on far too long already. We could have prevented this whole situation if we would have started acting ten years ago. It was clear that the technology was developing in this direction."

Compulsory
What is the crucial factor for this to become a success? How can you ensure that researchers will submit their data? Den Dunnen: "After many years I see only one solution, which is that it should be compulsory for anyone who performs such an analysis to submit the result and the accompanying clinical information in a public database and it should be obligatory to consult this database to interpret your results and formulate conclusions for the patient and physician." He does not share the much-heard concerns on privacy issues relating to such sensitive information. "Physicians are bound to act in the best interest of their patients and to me it is clear that having access to this information and thus sharing information is in the best interest of the patient. When nobody shares we can stop using DNA diagnostics because we have nothing to refer to. Many researchers and physicians use the need to be careful as an excuse, but this is really stalling the process. With the right software, all these concerns can easily be addressed." He has been around long enough that it will take a lot of time and effort to establish a new routine. But he stresses that there is no alternative. "If we don't make this work, the progress in sequencing technology has been in vain. Performing whole genome analysis is useless without access to this type of information. On the upside, if we have the funds and the will to change, we can make it happen in less than a year."

For the discussion in Nature Biotechnology, check

Bale et al.
MutaDATABASE: a centralized and standardized DNA variation database
Nature Biotechnology 29 117-118 (2011) (original correspondence)

Dalgleish et al.
Clarity and claims in variation/mutation databasing
Nature Biotechnology 29 790-792 (2011) (comment)

Bale et al.,
Reply to clarity and claims in variation/mutation databasing
Nature Biotechnology 29 792-794 (2011) (reply)

For related correspondence by members of the International Scientific Advisory Committee of the Human Variome Project (including Johan den Dunnen)
Mutation (variation) databases and registries: a rationale for coordination of efforts
Nature Reviews Genetics, doi:10.1038/nrg3011-c1 (published online 25 October 2011)

Pathway databases differ considerably

Thu, 17 Nov 2011 09:29:00 +0100

Studying and mapping the human metabolic network is an essential element in improving our understanding of human health and disease. A number of high-quality databases that contain data on human metabolic pathways have been constructed and have become an important and routinely used tool in biomedical research. Each database however contains part of the puzzle and the overall field would greatly benefit from an integration of all available data. To aid such integration, Miranda Stobbe (Academic Medical Centre, Amsterdam) and colleagues have performed the first, systematic comparison of five frequently used human metabolic pathway databases: BiGG, EHMN, HumanCyc, KEGG and Reactome. Their results show the overlap between the databases to be surprisingly low.

Stobbe MD, Houten SM, Jansen GA, Van Kampen AHC, Moerland PD
Critical assessment of human metabolic pathways: a stepping-stone for future integration
BMC Systems Biology 2011, 5:165

Genome of the Netherlands ready for the next level

Thu, 10 Nov 2011 10:27:00 +0100

The BBMRI-NL Rainbow Project Genome of the Netherlands project (GoNL) is ready for the next level. It has completed the alignment of all the DNA reads of the 750 individuals, producing a total of 350 billion reads. Based on these data, further analyses can be performed, enabling the development of new treatments and diagnostic techniques.

The GoNL project offers unique opportunities for science as it gives a close-up look at the DNA of 750 Dutch people—250 trio’s of two parents and an adult child—plus a global genetic profile of large numbers of Dutch people. This information will disclose a wealth of new insights and possible applications. A reusable pipeline has been assembled based on best practices in the field. Processing 250 trios represents a major computational challenge and required the assistance from SARA, CIT, Target, NBIC and BigGrid. Using both the national Grid infrastructure and cluster resources at the participating institutes, the GoNL project has already produced more than 300 TB of data. With the GoNL project BBMRI-NL expects to increase knowledge about the genetic variation in the Netherlands and complement international resources like the 1000 Genomes and HapMap Projects. The Genome of the Netherlands is an open national consortium of the UMCG, LUMC, Erasmus MC, VUMC, Hubrecht, AMC, RUNMC and UMCU led by Professor Cisca Wijmenga (GoNL) and Paul de Bakker & Morris Swertz (eBiobank). The sequencing work is done by BGI Hong Kong. More information about the project can be found on http://www.nlgenome.nl/ (GoNL) and http://www.bbmriwiki.nl/ (Bioinformatics) On our website you can find more information about the involved BioBanking Task Force and Genomics Task Force of NBIC.

All cells are not equal

Thu, 10 Nov 2011 10:17:00 +0100

Transcriptomics, i.e. studying gene expression levels in an organism, has become a routine activity in molecular biology. RNA is isolated from millions of cells and analysed using standard microarray technology. The resulting gene expression levels represent an average calculated from all those cells, which is very suitable to compare different individuals or populations, but obscures differences between individual cells.

However, it is also known that cellular heterogeneity is a widespread phenomenon. To gain insight into the extent of this heterogeneity in the filamentous fungus Aspergillus niger (a workhorse of the fermentation industry), Charissa de Bekker and Han Wösten (Utrecht University) performed the first-ever single cell transcriptomics measurements on microbial cells. They isolated RNA from five individual hyphae (the 'arms' of the fungus) of an A. niger colony, but their standard analysis methods were insufficient to deal with these absolute tiny amounts of material. "We basically did not have enough material to ensure proper hybridisation. Furthermore, as we were interested in individual cells, we had five unique datasets to deal with, without the duplicates you normally include. Clearly, we needed help", Wösten explains.

Through the Kluyver Centre, he became aware of the support offered by NBIC and contacted the group of Timo Breit (University of Amsterdam). "They really helped us out by applying advanced statistics to our datasets, so that we could generate reliable results. Without their contribution, we would never have been able to analyse the data." This would have been a shame, as their findings pave the way to a whole new area to be explored. Wösten: "We have shown that the general assumption that cells in a microbe are simply copies of each other is not true. Each cell is unique." Charissa de Bekker, Oskar Bruning, Martijs J Jonker, Timo M Breit and Han AB Wösten
Single cell transcriptomics of neighbouring hyphae of Aspergillus niger
Genome Biology 2011, 12:R71

Bioinformatics Research Support Team

To the rescue!

Mon, 07 Nov 2011 10:59:00 +0100

Good news for those of you working on the family of G protein-coupled receptors (GPCR). Keeping up with the massive amount of literature and data has become a lot easier thanks to work by Bas Vroling (CMBI, Nijmegen) and colleagues. In a paper in BMC Bioinformatics, they describe the GPCR-specific PDF reader, a new tool that is now part of the GPCR database (GPCRDB, www.gpcr.org/7tm/). When using the tool to read a paper, annotated concepts are immediately visible, which provides the researchers with quick access to related publications and relevant data sources.

"Our main goal was to develop a reader that allows researchers to easily review, find and analyse data and relevant literature. When a user opens a paper, the system immediately provides feedback by highlighting the annotated concepts, such as proteins, residues and mutations. Importantly, this information is also stored by the system to keep the information flow up to date", Vroling explains. According to him, what makes their tool stand out from other tools that target the same problems is that they can validate their tools using the GPCRDB. "This validation step makes our work unique. It is essential to have access to a reliable data source. That is what we hope to show with our work as well. Developing text mining tools is only worthwhile when you can check your results against a well-maintained, curated database."

A particularly sympathetic feature of GPCR-specific PDF reader is that it can help to rescue old data from oblivion. Vroling: "Because past interpretations have turned out to be wrong, the raw data can still be very useful. Our tool can track this data down so it can be interpreted again using current insights."

Bas Vroling, David Thorne, Philip McDermott, Teresa K Attwood, Gert Vriend and Steve Pettifer
Integrating GPCR-specific information with full text articles
BMC Bioinformatics 2011 12:362

Your personal guide to modelling

Thu, 03 Nov 2011 16:36:00 +0100

When asked to contribute a paper on genome-scale metabolic reconstruction and models to Methods in Enzymology, authors Filipe Santos, Joost Boele and Bas Teusink (VU University Amsterdam) decided to take their personal experiences in this field as the guideline. "We all have hands-on experience in making these models and we all have faced similar obstacles and bottlenecks along the way", says Santos. With their 'practical guide', Santos and colleagues aim to help others who are starting out in this field or who want to refine their own efforts. He admits: "It is actually the kind of guide we would have liked to have had when we started out making our own models."

Filipe Santos, Joost Boele and Bas Teusink
A practical guide to genome-scale metabolic models and their analysis
Methods in Enzymology, Vol 500, 2011, pp. 509-532

Data fusion at high level

Wed, 02 Nov 2011 08:46:00 +0100

In the omics field, combining data from different sources – i.e. data fusion – is becoming more and more important. In so-called high-level data fusion, model predictions from two or more models are combined to produce a 'fused' response. High-level data fusion is amongst others applied in classification, but little is known about the possibilities for improving classification after data fusion. Timo Doeswijk (Wageningen University) and colleagues have analysed to potential increase in predictive performance of fusing two classifiers. They checked their models against a real data set generated by metabolomics studies on different types of tomato, which showed the applicability of their simulation results. T.G. Doeswijk, A.K. Smilde, J.A. Hageman, J.A. Westerhuis, F.A. van Eeuwijk
On the increase of predictive performance with high-level data fusion
Analytica Chimica Acta 705 (2011) 41-47

RSG Netherlands visits GeneTwister

Mon, 31 Oct 2011 11:18:00 +0100

On September the 16th RSG Netherlands (the Regional Student Group) organised their second company visit. They visited GeneTwister in Wageningen, a biotechnology company, specialized in genomic breeding and green biotechnology of agri- and horticultural crops. The visit started off with a general talk on the growing role of bioinformatics within GeneTwister. This was followed by multiple talks on specific bioinformatics applications GeneTwister is working on. The talks were followed by a small excursion through the wet-labs. Altogether, this visit gave the participants a great opportunity to get an inside look at this specialized biotechnology company and their applications of bioinformatics. RSG Netherlands brings together PhD students in bioinformatics and computation biology in the Netherlands and company visits are part of their activity programme for junior researchers.

A superficial analysis?

Tue, 25 Oct 2011 14:10:00 +0200

The interactions at the interface between the biomaterial used in a medical device, such as stents or implants, and surrounding tissue cells are crucial in determining the body's response to the device. To counter potential complications, the surface of the implant is treated with specific coatings or modified using physical techniques like 'sanding'. Although effective, these techniques provide little control of surface characteristics. Such control is offered by micro- and nanotechnologies. However, determining the distinct surface characteristics to elicit a wanted response remains a big challenge. In a PNAS publication, a group of tissue engineers and bioinformaticians, including NBIC-faculty member Marcel Reinders, describe how they constructed a library of more than 2,000 distinct, randomly designed surface topographies and how such libraries can help to unravel the still elusive interplay between cells and biomaterial surfaces.

Unadkat HV, Hulsman M, Cornelissen K, Papenburg BJ, Truckenmüller RK, Post GF, Uetz M, Reinders MJ, Stamatialis D, van Blitterswijk CA, de Boer J
"An algorithm-based topographical biomaterials library to instruct cell fate"
PNAS 2011 Oct 4; 108(40):16565-70

MADMAX: Advanced analysis, easy to use

Fri, 21 Oct 2011 09:19:00 +0200

The MADMAX database is specifically designed to store, manage and analyse data from a variety of ~omics sources. To demonstrate the features and powers of MADMAX, Ke Lin of Wageningen University and colleagues performed a pilot study using different types of ~omics data from Brassica rapa. Their findings were published in the Journal of Integrative Bioinformatics on July 21, 2011. A major feature of MADMAX is its ease of use; no programming is required to employ the system. The advanced analysis pipelines incorporated in MADMAX are based on R/Bioconductor and thus offer state-of-the-art analysis methods for multiple microarray platforms. MADMAX has already been widely used by scientists around the world. "The user-friendliness is a recurring element in the user feedback", says Anand Gavai, bioinformatician in the group of NBIC Faculty member Jack Leunissen at Wageningen University and co-author of the JIB paper. "Users particularly appreciate the fact that advanced analyses and statistics are supplied simply at the click of a button." More information on MADMAX: http://madmax2.bioinformatics.nl

MADMAX - Management and analysis database for multiple ~omics experiments
Lin K, Kools H, de Groot P, Gavai A, Basnet RK, Cheng F, Wu J, Wang X, Lommen A, Hooiveld GJ, Bonnema G, Visser RG, Muller MR, Leunissen JA Journal of Integrative Bioinformatics, 8(2):160, 2011

Overcoming bias in phosphoproteomics

Fri, 21 Oct 2011 09:07:00 +0200

Phosphorylation, i.e. adding a phosphate group to proteins, is a key step in numerous biological processes and pathways. Insight into the functional dynamics of phosphorylation networks is essential to understand how a living cell operates. Studying the phosphoproteome - all proteins involved in phosphorylation - has recently gained an enormous boost. But comparing and integrating data on phosphoproteomes is complicated due to incomplete datasets and to biases caused by the use of different experimental workflows. Jos Boekhorst (Utrecht University) and colleagues have developed bioinformatics strategies to quantify the impact of different experimental workflows on measured phosphoproteomes by comparing datasets to a common reference. Their strategies also offer possibilities for extracting information through comparative analysis of available phosphorylation data from sources not specifically generated for phosphoproteome studies. Evaluating experimental bias and incompleteness in comparative phosphoproteomics analysis
Boekhorst J, Boersema PJ, Tops BB, van Breukelen B, Heck AJ and Snel B PLoS One 2011;6(8):e23276

Snooker: a tool to predict medicine binding sites on GPCRs

Fri, 14 Oct 2011 14:20:00 +0200

G-protein coupled receptors (GPCRs) are important drug targets for various diseases and of major interest to pharmaceutical companies. Bioinformatics researchers developed Snooker, a tool to predict possible drug binding sites on these receptors.

Snooker: A Structure-Based Pharmacophore Generation Tool Applied to Class A GPCRs.
Sanders MP, Verhoeven S, de Graaf C, Roumen L, Vroling B, Nabuurs SB, de Vlieg J, Klomp JP J Chem Inf Model. 2011 Sep 26;51(9):2277-92

Van Beek models Lance Armstrong climbing Alpe d'Huez

Fri, 14 Oct 2011 13:45:00 +0200

The human physiological system is stressed to its limits during endurance sports competition events. Hans van Beek (VUMC) and other NBIC Faculty described a whole body computational model for energy conversion during bicycle racing. They simulated a mountain time trial to Alpe d'Huez during the Tour de France and calculated the energy and heat transfer needed to approach the time realized by Lance Armstrong in 2004. The model showed that the leg temperature can approach 40 degrees Celsius.

Read more:
http://www.vumc.nl/onderzoek/nieuws/6343633/

Website VUMC (in Dutch)
Simulating the physiology of athletes during endurance sports events: modelling human energy conversion and metabolism.
Philos Transact A Math Phys Eng Sci. 2011 Nov 13;369(1954):4295-315.
van Beek JH, Supandi F, Gavai AK, de Graaf AA, Binsl TW, Hettling H.

Gene duplication leads to tissue specificity

Fri, 14 Oct 2011 12:15:00 +0200

Gene duplication is one of the main mechanisms by which genomes can acquire novel functions. The group of NBIC Faculty Martijn Huynen studied the levels of tissue specificity after gene duplication, combining phylogenetic analyses and expression data from human and mouse. Their results show that gene duplication leads to increased levels of tissue specificity and that this tends to occur promptly after the duplication event. Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication.
Brief Bioinform. 2011 Sep;12(5):442-8 Huerta-Cepas J, Dopazo J, Huynen MA, Gabaldón T

NBIC Education cited in Nature

Thu, 13 Oct 2011 13:59:00 +0200

The NBIC Education programme BioWise is worldwide noted. Education programme leader Jaap Heringa and education project leader Celia van Gelder are quoted in a Nature article about trainees in bioinformatics and computational biology. You can read the full text article online: Education: Inspiration for informatics

Online demonstration of OpenPHACTS

Fri, 07 Oct 2011 16:43:00 +0200

The knowledge management project Open PHACTS (Open Pharmacological Concepts Triple Store) demonstrates the results of the first 6 months of the project in a You Tube video. It shows pharmacological queries over a number of datasets using multiple user interfaces.

About OpenPhacts
Open PHACTS (Open Pharmacological Concepts Triple Store) is a knowledge management project of the Innovative Medicines Initiative (IMI), a unique partnership between the European Community and the European Federation of Pharmaceutical Industries and Associations (EFPIA). The Open PHACTS consortium is creating an open innovative platform, Open Pharmacological Space, which will be freely accessible for knowledge discovery and verification. NBIC researchers play a central role in the large-scale project, which focuses on data interoperability.

Vote for Leve DNA!

Wed, 05 Oct 2011 09:11:00 +0200

Leve DNA! is one of the finalists in the 'Academische jaarprijs'. They are in the running for winning an annual prize for the best public communication campaign of modern research. In short: the Leve DNA-plan wants to execute fun DNA-research that 'the public' can come up with. Together with high schools we will choose and elaborate twelve of such researches. We can, for example, compare the genome of the main Opera visitor with the genome of the main Lowlands-visitor. Or we can determine if chewing gum on the street near a hospital contains more pathogenic bacteria then the chewing gum near a high school. Hienke Sminia (NBIC) is part of the enthusiastic team (LUMC, LGTC, Naturalis and NBIC) and will help the team with the connection to high school education. But NBIC will of course also contribute in the bioinformatics support of these small scale researches. Part of the Academische jaarprijs is de public prize. This means that YOU can help us win! Vote for us via: http://www.wetenschap24.nl/programmas/labyrint/publieksprijs.html

Launch of IT infrastructure for translational research

Mon, 03 Oct 2011 00:00:00 +0200

A new 16 million Euro project called TraIT (Translational research IT) has been launched by CTMM (Center for Translational Molecular Medicine). The TraIT project will create an IT infrastructure that will help to accelerate the translational research in the Dutch Life Sciences and Health sector. A research environment will be created to expedite new discoveries and innovations to improve the medical care for patients.

Professor Gerrit Meijer, Chair of the Department of Pathology at the VU University Medical Center and Principal Investigator of the project: “TraIT specifically is user driven and process oriented, to make translational research work. In addition we want to avoid reinventing wheels built upon existing initiatives, while working in close collaboration with the NFU and capitalizing on the ICT infrastructure for biomedical research built by the Netherlands Bioinformatics Centre and the Parelsnoer initiative.”

Within TraIT, CTMM finds a strong collaboration partner in the Netherlands Bioinformatics Centre (NBIC) and the NBIC Consortium. NBIC and its consortium partners bring in crucial expertise in analysis, curation, standardization, integration and stewardship of CTMM data, all in a close link to the international bioinformatics field.

The TraIT project is a joint initiative between CTMM, Dutch Cancer Society, Dutch Heart Foundation, the Netherlands Federation of University Medical Centers (NFU), the String of Pearls Initiative (PSI), the Netherlands eScience Center (NLeSC) and the Netherlands Bioinformatics Centre (NBIC). Read more in the Press Release (below) and on the CTMM website.

NBIC Biobank Taskforce develops software for BBRMRI-NL Biobank Catalogue

Fri, 30 Sep 2011 13:38:00 +0200

In August, BBMRI-NL went online with its Biobank Catalogue. The NBIC Biobank Taskforce developed the software for the BBMRI-NL Biobank Catalogue. Based on the Molgenis framework developed in Groningen the Taskforce developed an online application where registered users can consult information on the 150+ Dutch biobanks associated with BBMRI-NL. All 150-plus Dutch biobanks currently associated with BBMRI-NL are in the catalogue, which is visible only for registered users and contains data on the type of tissue stored, GWAS- data, publications, etc. More information: http://www.bbmri.nl/nl-nl/biobanken-database

Course materials bioinformatics for life scientists available

Tue, 27 Sep 2011 09:27:00 +0200

In August this year NBIC and LUMC organised a course on RNA-seq data analysis, hosted by the AMC in Amsterdam. All course materials of the Advanced RNA-seq course are now available on the NBIC Wiki. NBIC is striving to make course materials open to the research community as much as possible.

The RNAseq course is part of the education package of NBIC aimed at researchers in the Life Sciences. More courses are planned for the near future on the following topics: variant calling/exome sequencing, de novo assembly and metagenomics.

FoldIt on Discovery festival

Mon, 26 Sep 2011 12:01:00 +0200

Together with Hannes Hettling and Punto Bawono, both bioinformatics researchers on the Vrije Universiteit Amsterdam, Hienke Sminia of the NBIC high school education programme demonstrated the Game FoldIt to the visitors of the discovery festival. Many youngsters have been playing the FoldIt game and thereby helped science in predicting better protein structures. Below you can find some pictures of the event. You might have noticed FoldIt in the news lately, because of their discovery of the protein structure of monomeric retroviral protease.

The Netherlands participates in ELIXIR

Mon, 19 Sep 2011 11:29:00 +0200

On September 14^th five countries plus EMBL have signed a Memorandum of Understanding to catalyse the implementation and construction of ELIXIR. The Netherlands is one of them. The other countries are Denmark, Finland, Sweden and the United Kingdom, and more countries are planning to join in the near future.

ELIXIR is a pan-European initiative to operate a sustainable infrastructure for managing and safeguarding biological information in Europe. It will secure public access to life science data and information. Consistent with the movement towards open access to data and publications, ELIXIR will make important information freely available to researchers throughout academia and industry.

The Memorandum is a first formal – yet non-binding – step towards the implementation and construction of ELIXIR. Countries signing the Memorandum and EMBL will be represented on the Interim Board, which will be the main body for negotiating the final legal and governance structure of ELIXIR. NWO will represent the Dutch Government in the ELIXIR board, while NBIC represents the DISC ELIXIR alliance. This alliance is preparing the Data Integration and Stewardship Centre ELIXIR (DISC ELIXIR) as the Dutch node of ELIXIR.

Subtyping makes sense

Tue, 13 Sep 2011 09:52:00 +0200

Predictive profiling, in which the gene expression profile of a tumour is used to predict for example the risk of metastasis (spreading of a tumour) in an individual cancer patient, is a hot topic among cancer researchers. Especially in breast cancer research, a lot of effort is dedicated towards developing reliable predictors for diagnosis and prognosis. A much-debated issue here is how to deal with the various subtypes of breast cancer. A novel protocol designed by PhD student Herman Sontrop and colleagues at Philips Research, Delft University of Technology and the Academic Medical Centre sheds a new light on this topic.

Unbalanced reference
"We now know that breast cancer is not one disease, but a collection of subtypes that show clear differences in terms of clinical outcomes, such as the risk of metastasis and survival rates. However, these differences are rarely taken into account in the development of predictors", says last author Perry Moerland, NBIC faculty member and assistant professor at the Academic Medical Centre, Amsterdam. This is due to two methodological drawbacks. Classification into subtypes reduces the sample size per subtype, which might impair the performance of a predictor. In addition, the complete non-subtyped dataset that is used as a reference is unbalanced with respect to the subtype distribution: the characteristics of the most prevalent subtype dominate the reference set, which impairs a realistic comparison for the less prevalent subtypes.

Strange behaviour
Convinced that using the characteristics of the breast cancer subtypes should lead to better predictors, Moerland and colleagues set out to find a way to circumvent the methodological obstacles. They took four breast cancer subtypes to work with: luminal A, luminal B, Her2 and basal, as these are generally accepted within the field. Moerland: "For each subtype, we built predictive models, as well as for all combinations of subtypes. Next, we compared the various models to see which performed best. An essential step was to come up with a good measure for the quality of our predictions. In many cases, the so-called balanced accuracy rate or bar is used in which both sensitivity and specificity are taken into account. However, when we combined the predictions of the four subtypes in one model, we noticed strange behaviour in the bar outcomes. It turned out that the bar of the combined model was higher than any of the individual bar scores of the subtypes."

Balancing the bar
Subsequent scrutiny of the bar itself revealed that the bar score is highly sensitive to the ratio between positive and negative outcomes. "And that ratio differs for each subtype. When combining all the subtyped models, this leads to a distorted overall score. In fact, the bar did not provide a true measure of the quality of the prediction", Moerland explains. They addressed this problem by constructing the models in two variants. In the balanced compendium, the volumes and ratios are controlled to prevent dominance of one single subtype and to control the ratio between positive and negative outcomes. This means leaving out data from the more prevalent subtypes in favour of the less prevalent ones. The unbalanced compendium in contrast contains all the available data. Furthermore models per subtype were paired with untyped models constructed on a mixture of subtypes with the latter being evaluated using the exact same samples that were used for evaluating the subtyped models. "That allows a realistic and fair comparison between the models. Our protocol offers a way to deal with the unbalance in datasets."

Controversial conclusions
"Comparing all our different models showed that predictors based on subtyped models outperform the untyped predictors. Subtyping clearly makes sense. And for each individual subtype, you should use all data available, because the more data you put in, the better your model." Moerland emphasizes that their work is not only of interest for bioinformaticians, but they came up with interesting biological results as well. "One of our results is that for predicting the risk of metastasis, there is no need to distinguish between the subtypes luminal A and luminal B. These subtypes can just as well be combined." Moerland realizes that the precise definition of relevant molecular subtypes is still a controversial subject. "It was the main reason that our work was rejected elsewhere. Clearly, those reviewers belong to the opposing side." The debate on predictive profiling continues.

Reference An evaluation protocol for subtype-specific breast cancer event prediction
Sontrop HMJ, Verhaegh WFJ, Reinders MJT, Moerland PD
PLoS One, 2011;6(7):e21681

NBIC and Ecogenomics consortium identify Genomic Islands

Fri, 09 Sep 2011 14:58:00 +0200

A cooperation between Mark van Passel (Ecogenomics Consortium) and Erik Roos from the Bioinformatics Research Support team led to the development of a new tool for automated analysis of large databases of genomic sequences and their genomic islands. The tool was used to identify the origin of genomics island in bacterial genomes, which resulted in the following publication: A quantitative account of genomic island acquisitions in prokaryotes.
Roos TE, van Passel MW.
BMC Genomics. 2011 Aug 24;12(1):427. [Epub ahead of print]

NBIC high school education programme received enthusiast response in Vienna

Mon, 05 Sep 2011 14:08:00 +0200

Hienke Sminia, project leader of the bioinformatics@school programme of NBIC, presented a technology track at the international bioinformatics conference ISMB/ECCB 2011 in Vienna. She showed the international community the work of NBIC in educating bioinformatics on a high school level in the Netherlands. More than 30 people visited Hienke's session and responded with enthusiastic reactions, helpful comments and requests for advice. As appears from the paid attention researchers are interested in education material at high school level to build the bridge to future students and junior researchers. Together with Burkhard Rost (chair ISCB) and Fran Lewitter (chair education committee ISCB) plans are being made to organize a workshop focused at the high school level at ISMB2012.

More information about the bioinformatics@school project of NBIC.

Using large scale computing facilities for Biobanks

Mon, 05 Sep 2011 13:16:00 +0200

The Netherlands have 150 biobanks with over 400,000 samples in total. To exploit these billions worth of material they are now embarking on large scale genetic profiling. An example is the highly visible Genome of the Netherlands project that will sequence the DNA of 750 Dutch individuals completely to elucidate the genetic diversity in the Dutch population, and to impute this new information onto existing more sparse genetic information of 100.000 Dutch individuals. However, the data handling and computational needs are enormous and Dutch Institutes are struggling to effectively use the hardware infrastructures available.

The e-BioGrid subproject on Biobanking will overcome this barrier by interfacing the data processing tools used in biobanking to the existing BiGGrid infrastructure and by supporting the Dutch biobanking community to deploy these tools for their large data and processing challenges.

Looking for an alternative

Mon, 22 Aug 2011 15:25:00 +0200

The genetic code is universal. No matter how different organisms are, the combination of three nucleic acids (C, A, T, G) that encodes a specific amino acids or a stop codon is always the same.

But that assumption is not universally true. Already quite some alternative genetic codes have been encountered in bacteria, organelles, viruses and even eukaryotic nuclei. "Of all the published genetic sequences so far, almost 1% contains an alternative genetic code, but most researchers in large scale sequencing projects simply assume that they are dealing with the standard code", says NBIC faculty member professor Martijn Huynen of the Centre for Molecular and Biomolecular Informatics (CMBI) at Radboud University Nijmegen. His group developed a new tool, FACIL, that allows for a fast and reliable check of raw data on the presence of an alternative genetic code (Dutilh et al, Bioinformatics, 2011, June 8).

Protein domains
"Our basic assumption is that the presence of proteins is much more universal than the genetic code. FACIL looks for homology in protein domains instead of comparing the sequence to all known proteins. That explains why FACIL is much faster than other methods", Huynen explains. "Next to being fast, FACIL also provides an indication on the reliability of its prediction, which is the other main characteristic of this new tool." FACIL is already available for use and does not require a lot of pre-processing of the raw data, Huynen points out. "FACIL can and should be employed in data analysis as early as possible." His personal main interest in FACIL is the potential to discover new alternative codes. "We are really interested in assessing how universal the genetic code is. Metagenomics data provides us with that opportunity for the first time and the tool is ready. All we need are the discoveries."

FACIL is available as a web-based service at http://www.cmbi.ru.nl/FACIL
or as a stand-alone program

FACIL: fast and accurate genetic code inference and logo
Duthilh BE, Jurgelenaite R, Szklarczyk R, van Hijum SA, Harhangi HR, Schmid M, de Wild B, Françoijs KJ, Stunnenberg HG, Strous M, Jetten MS, Op den Camp HJ, Huynen MA
Bioinformatics, 2011, June 8

MixupMapper checks your data

Mon, 22 Aug 2011 15:03:00 +0200

In spite of protocols, regulations and experienced staff, scientific research is as prone to human errors as are other professional fields. Sometimes, errors are clearly visible and can be easily corrected. But when confronted with large-scale, complex datasets, it is not immediately clear if, for example, samples have been mislabelled or swapped. Thanks to the work of PhD-student Harm-Jan Westra and colleagues at the University of Groningen, researchers can now employ the MixupMapper to check their results for any sample mix-ups (Westra et al., Bioinformatics, 2011 June 7).

Swaps in GWAS
The reason for developing the MixupMapper algorithm was a serious mistake made in their own lab during a genome-wide association study (GWAS) into gene expression levels, says joint last author Lude Franke. "That got us thinking about a way to track down sample swaps in datasets and correct them post hoc. Once we had established the MixupMapper, we wondered about the frequency of sample swaps in general and decided to test our algorithm on five publicly available genetical genomics datasets. We detected sample mix-ups in four of these datasets. In one dataset, we found that 23% of the samples were swapped!" Correcting mistakes is not only the right thing to do, it greatly improves the quality of your results, Franke explains. "Firstly, mix-ups create noise, so by removing them you enhance to overall signal-to-noise ratio. Secondly, by correcting mix-ups, true information is added which further boosts your findings." In their paper, the researchers state that correcting for mix-ups led to a significant increase in the number of cis-eQTLs (expression quantitative trait loci) identified and that it could substantially increase the explained heritability and power to detect genetic effects in GWAS on complex phenotypes.

Spell-checker
Simply put, MixupMapper checks whether a generated phenotype (in this case: a gene expression level is the phenotype) corresponds to what could be expected from the associated genotype. "A correlation between genotype and phenotype can be interpreted in two ways, which implies that you can also deduct a genotype from a phenotype to see if it corresponds to the actual genotype. That is the essence of the MixupMapper", explains first author Harm-Jan Westra. This also implies that some prior knowledge on genotype-phenotype relations is necessary to be able to perform this check. Franke adds: "The method only works for datasets that contain large numbers of phenotypes. The algorithm compares predicted outcomes based on SNPs to measured values and if these seriously diverge then a sample mix-up is a plausible explanation." He therefore urges researchers to include the MixupMapper in every data analysis involving both gene expression levels and genotype data. "It is like a spell-checker. The MixupMapper is really a quality control tool."

MixupMapper is available at: http://www.genenetwork.nl/mixupmapper

MixupMapper: correcting sample mix-ups in genome-wide datasets increases power to detect small genetic effects
Westra HJ, Jansen RC, Fehrmann RS, te Meerman GJ, van Heel D, Wijmenga C, Franke L
Bioinformatics, 2011, June 7

Meaningful variation

Thu, 11 Aug 2011 11:20:00 +0200

In the world of functional genomics (e.g. transcriptomics, proteomics, metabolomics), data analysis knows no shades of grey. Either you opt for univariate analysis – in which the focus is on a single gene or metabolite – or you look at all variables in one go, i.e. the multivariate approach. "Univariate analysis is attractive because there are many methods available and the interpretation is relatively easy, but correlation between different biological actors is left out. You loose a lot of valuable information that way", says NBIC faculty member professor Age Smilde of the Biosystems Data Analysis group at the Swammerdam Institute of Life Sciences (University of Amsterdam). "With multivariate analysis, all correlations are included, but here the drawback is that the interpretation becomes difficult. We have therefore come up with a middle course, the simplivariate models."

Fluttering
The leading idea behind the simplivariate approach is that a substantial part of the variation exhibited in the data does not offer any information on the biology of the system. Smilde explains: "Many variables are simply 'fluttering'. They vary, but their variation is not connected to an underlying biological phenomenon that is relevant to the biological research question. This type of variation is what we call non-informative. With our simplivariate approach, we can identify groups of variables that show coherent behaviour, which is an important clue to potentially underlying biological processes. Employing our algorithm is a first step towards tackling a complex dataset in a more efficient manner."

Coherence
To determine what type of behaviour should be considered 'coherent', close involvement of biologists is essential, according to Smilde. "You need continuous discussions with the biologist to learn for example how many biological phenomena they expect to see to get an idea of whether your analysis is making any sense. Also, they need to inform you on how strong a correlation needs to be to be considered relevant. Based on this information, the bioinformaticians can choose the right model to apply. There are several possibilities in our approach." The recently published algorithm (Saccenti et al., PLoS One, 2011) builds on earlier work into simplivariate models. "We have incorporated a new model and both the statistics and the algorithm itself have been improved", says Smilde. Right now, work is ongoing within the Data Support Platform of the Netherlands Metabolomics Centre in collaboration with NBIC, in which Smilde is also involved, to turn the simplivariate algorithm into a robust and user-friendly tool. Smilde expects this new tool to become available within 6 months - 1 year from now.

For those interested in the meantime, check the paper:
Simplivariate models: uncovering the underlying biology in functional genomics data
Saccenti E, Westerhuis JA, Smilde AK, van der Werf MJ, Hageman JA, Hendriks MM
PLoS One 2011;6(60):e20747

Peeling the potato

Thu, 11 Aug 2011 09:32:00 +0200

Started in 2006 and completed mid-2011 with a publication in leading science journal Nature: the sequencing of the potato genome. Roeland van Ham, currently vice-president Bioinformatics and Modeling with Dutch biotech firm Keygene N.V., has been involved in the international project right from the start. At the time, he was group leader bioinformatics and head of the sequencing facility at Wageningen University and Research Centre, one of the leading parties in the Potato Genome Sequencing Consortium. When asked about the role of bioinformatics in this undertaking, he doesn't hesitate. "Bioinformatics takes the key position in such a project. We ensure that the biologists can actually make sense of the data generated by the sequencers." This required however dealing with numerous technical challenges, not only caused by the sheer volume of the datasets generated, but also due to the specific characteristics of the potato genome itself.

Van Ham: "Especially the assembly phase of the project, in which the genome sequence is reconstructed from the smaller read-outs produced by the sequencers, proved really difficult and time-consuming due to the fact that potato is heterozygous. At the same time, these problems stimulated the development of new assembly tools. Within NBIC, I then headed the BioAssist Next Generation Sequencing taskforce and in the potato project, we could benefit from the taskforce's work on de novo assembly algorithms." In spite of the many hurdles they faced, no real breakthroughs were achieved (or required) from a bioinformatics perspective. But that does not imply that it was just a standard operation, Van Ham points out. "No, it was really cutting-edge bioinformatics work from start to finish. We came up with a lot of new tools and approaches, for example on assessing the quality of next generation sequencing data and on new ways to process raw data and genomes by k-mer analysis." Meanwhile, he has left academia, but food crops are still on his daily professional menu: a paper on the sequence of the tomato genome and a comparison to potato is about the be submitted, he reveals. Genome sequence and analysis of the tuber crop potato
The Potato Genome Sequencing Consortium
Nature, 2011 July 14;475(7355):189-95

New CytoscapeRPC plugin available

Thu, 11 Aug 2011 08:47:00 +0200

Cytoscape is widely used by biologist and bioinformaticians to visualize data in networks. Until recently, with each new or adjusted experiment, researchers had to create the visualization again from scratch. A tedious process that involved a lot of repetitive actions. Thanks to the new CytoscapeRPC plugin, developed by NBIC scientific programmer Jan Bot (research group of professor Marcel Reinders, Delft University of Technology), researchers no longer need to 'leave' their own work environment, but can create, modify and re-use scripts in their language of choice. This way, using Cytoscape has become much more efficient and user-friendly. The plugin was published June 27, 2011 in Bioinformatics.

Although the experiences within the Reinders-group were the driver behind developing the new plugin, it quickly became clear that others were looking for such a tool as well. "On the Cytoscape mailing list, people asked whether a tool was available that would allow them to do exactly what we were planning to deliver with our plugin", Bot says. "We started collaborating with these interested users and one of them, Paul Shannon, has meanwhile used our plugin as the basis for a completely new module in R. It is really nice to see that your tool is used by others in that way and that they create new possibilities that we didn't foresee." Exactly because of this collaboration with other users, the plugin boasts a very broad spectrum of functions within Cytoscape that are supported and can be queried. Bot: "Getting input from external users broadened our development work."

So far, the plugin has been downloaded over 200 times. Also interested? The plugin can be easily installed through the Cytoscape plugin manager. In addition, CytoscapeRPC is also available through the NBIC wiki.

BioAssist Engineering Team supports Pindel developers

Wed, 22 Jun 2011 10:33:00 +0200

Pindel is a tool widely used by major genome research groups. It detects breakpoints of large deletions and medium-sized insertions from paired-end short reads. It is developed largely by Dr. Kai Ye and Dr. Eric-Wubbo Lameijer at the LUMC with support from Chris Harris at the Genome Institute at Washington University (US) and Keiran Raine at the Sanger Institute (UK). Since September 2010, the Pindel developers have been working together with the BioAssist Engineering Team to improve the Pindel development process.

In May 2011 we collaborated in a refactoring project that focused on increasing the modularity of the code, adding tests and continuous integration, using code checkers, introducing dedicated logging functionality and various smaller code improvements. This has yielded a well structured and clearly documented version, an excellent starting point for further development. Dr. Ye and Dr. Lameijer appreciate the contribution of BioAssist Engineering Team as well as their expertise and advice on making Pindel easier to maintain and extend. They especially value the vastly increased ease in comparing Pindel versions due to the continuous integration and testing framework added. Also, the reduction of the number of global variables and code duplication by the BioAssist Engineering Team will be very helpful in supporting the further developments planned for Pindel.

Please visit trac.nbic.nl/pindel for more information on Pindel. To see what the BioAssist Engineering Team can do for you, please visit www.nbic.nl/support/bet.

Open PHACTS nanopublications published in Nature Genetics

Mon, 30 May 2011 14:10:00 +0200

Researchers from the Open PHACTS project have published a paper in Nature Genetics that proposes representing data and assertions in the form of nanopublications. The nanopublication is the smallest unit of publication and is essentially a single assertion and its associated data and material. According to the team, using nanopublications will make it easier to place a value on data, support research by tapping into vast, interoperable reserves of information, and also make it easier for scientists and others to follow up individual assertions or develop hypotheses. Open PHACTS will test the nanopublication concept to create an Open Pharmacological Space (OPS). In the OPS, a layer of data and text extraction methods is placed over existing data of different kinds (e.g. rough data, processed datasets and literature). The methods allow close to real time updates of nanopublications from these databases and make them publicly available via the OPS, but do not interfere with local database management. "The Open PHACTS consortium thus creates an extra, computer readable layer that works across previously isolated datasets," explains the lead author of the paper, Barend Mons of Leiden University Medical Center and the Netherlands Bioinformatics Centre.

Galaxy Community Conference 2011 hosted by NBIC

Mon, 30 May 2011 13:24:00 +0200

The 2011 Galaxy Community Conference was held 25-26 May, at the Conference Centre De Werelt in Lunteren, The Netherlands. The conference was co-organized and hosted by the Netherlands Bioinformatics Centre (NBIC). Advantages such as an open source license, simple user interface, easy extensibility, and abundant bioinformatics tools make Galaxy a good candidate to process the biological data that is being generated at an ever increasing speed. Galaxy has been used as the main integration platform in the NBIC BioAssist program to leverage the bioinformatics strength of various member groups. The conference featured 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 research. The event drew almost 150 participants from 19 countries on six continents. Among them, more than 30 people were from NBIC and NBIC affiliated Dutch institutions. A small number of participants did not make their trips due to the volcano ash cloud over several northern European countries. However, thanks to Skype and Twitter, they were able to present their talks remotely and follow the discussions real-time (with more than 600 tweets). Barend Mons (NBIC scientific director) opened the NBIC sponsored bar night on May 25th with a warm welcome speech. The pleasant atmosphere together with famous brands of Dutch beer created an unforgettable evening for all conference guests and apparently have paved ways for several future collaborations. Read the tweets (#usegalaxy ) on May 25-26 to get an impression by the participants of the conference. The videos of the conference are now available online at the NBIC video channel. Read also about the Galaxy Community Conference at Genomeweb.com.

NBIC Faculty in leading positions in Open PHACTS consortium

Fri, 27 May 2011 11:49:00 +0200

A new consortium of European organisations unite to support next generation drug discovery by providing a single view across data sources, bringing the semantic web to drug discovery. The Open PHACTS consortium, funded by the Innovative Medicines Initiative, will reduce the barriers to drug discovery by applying semantic technologies to available data resources, creating an Open Pharmacological Space.
NBIC Faculty members from the Leiden University Medical Centre, VU Amsterdam and Maastricht University are in leading positions in this consortium.

NBIC connects HBO Bioinformatics programmes

Thu, 19 May 2011 16:18:00 +0200

Teachers from the Dutch HBO schools offering a bioinformatics BSc programme gathered at the Hanzehogeschool Groningen for a teacher network meeting, organized by NBIC. During two days they shared their experiences and teaching material. Collaborative actions were planned, for instance for attracting more students and for starting a virtual teacher community. During the second day they followed lectures and practicals about Next Generation Sequencing (NGS), in this way learning about how to adapt their curriculum to the newest technologies. Read more

10.000 Euro awarded for 3D protein scanner in school

Tue, 03 May 2011 11:14:00 +0200

Hienke Sminia (NBIC, UMC St Radboud) is granted 10.000 Euro by the SURFnet/ Kennisnet Innovation Programme "Augmented Reality" for her project proposal about a 3D protein scanner for high school. The 3D protein scanner will be developed as a mobile phone application, which will help high school students to visualize and understand the proteins that are present in food. By scanning the QR tags on food products (butter, spaghetti) from the supermarket with their phone, the Augmented reality application will show the proteins inside. Hienke Sminia, coordinator of NBIC's bioinformatics-at-school project: "The 3D protein scanner combines two important themes in the biology and chemistry classes: food and proteins. The mobile phone application shows that proteins are part of daily life products and makes them tangible." More information:

SURFnet/Kennisnet Innovation programme: (in Dutch)
NBIC's bioinformatics at school project

Prize winners at NBIC conference

Thu, 28 Apr 2011 16:20:00 +0200

The NBIC conference programme included several competitions. A jury of the RSG Netherlands judged the oral presentations to choose the best lecture of the conference. Fiona Nielsen, PhD student at the Centre for Molecular and Biomolecular Informatics (CMBI, UMC St Radboud Nijmegen) won the prize with her lecture 'CATCHprofiles: Clustering and Alignment Tool for ChIP profiles'. Two prizes were available for the poster presentations. One prize was offered by the BioInformatics Industrial User Platform (BIUP), which organised a satellite meeting during the NBIC conference. They judged the posters from a industrial point of view. Patrick Koks (Wageningen UR) received the prize for his poster about 'eBiomics: an e-Learning environment on bioinformatics for life-scientists'. The other poster prize was given to the poster which was "liked" the most by the conference participants, who could show their appreciation by "Facebook like stickers". Wouter Meuleman (NKI/TUD) found the most stickers on his poster about 'Dynamics and evolution of genome – nuclear lamina interactions'. The third competition was the application showcase, where researchers could show the applications they developed. Three out of ten were selection for the final presentations on stage:

Bas Vroling (CMBI) presented GPCR-specific PDF reader
Miranda Stobbe (AMC) presented JamboreeCards
Kasper Dinkla (TU Eindhoven) presented BiotaViz

With 92 votes the audience selected the winner: Bas Vroling!

6th edition of the NBIC conference attracted over 200 participants

Thu, 28 Apr 2011 16:11:00 +0200

More than 200 people visited the six^th edition of the NBIC conference, April 19-20. The plenary programme included keynote lectures, workshops and several competitions. Satellite meetings were organised by the PhD students network RSG Netherlands, the BioInformatics Industrial User Platform (BIUP) and the Netherlands Society on Biomolecular Modelling (NSBM). All these groups together created a lively atmosphere, inside (and outside) the conference venue 'De Werelt' in Lunteren. For a first impression visit the NBIC page on facebook. A full photo impression by a professional photographer is also available on the conference website.

NBIC Young Investigator Award 2011

Thu, 28 Apr 2011 15:52:00 +0200

The winner of the NBIC Young Investigator Award 2011 is Dr. Yang Li, Groningen Bioinformatics Centre,University of Groningen. She is awarded with a cash prize of 2.500 Euro funded by NBIC BioRange and BioWise programmes. Yang Li has received the NBIC Young Investigator Award 2011 for her PhD research. Her PhD thesis shows a beautiful mix of bioinformatics method development and biological application, and as such the work is squarely positioned in mainstream bioinformatics, showing the essentiality of the field. The jury, chaired by Jaap Heringa, was further impressed by the novel methodological developments an innovation in Li's work, while her work is also highly interdisciplinary in that she has closely collaborated with biomedical experts. The award ceremony took place on the NBIC Conference (April 20th, 2011) and was followed by a honorary lecture by Yang Li about Generalized Genetical Genomics -Advanced methods and applications.

Many high school teachers visit national genomics conference

Wed, 30 Mar 2011 10:03:00 +0200

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. And that is exactly what we did during the 'DNA-labdag' on the 11th of March. This national conference on genomics was visited by 123 enthusiastic high school teachers and technical assistants. Lauke Ringens and Vera van Berlo, students fromd Radboud University, gave a workshop on NBIC's DNA-lab Bioinformatics: a bit of life. Hienke Sminia gave a workshop on NaviGene. Another bioinformatics workshop Confused Genome, was given by Wigard Kloosterman. Read more about the 'DNA-labdag' on www.dnalabdag.nl (Dutch).

NBIC BioAssist is establishing a new Interoperability Task Force (ITF)

Thu, 03 Feb 2011 13:46:00 +0100

The ITF will develop a variety of methods and infrastructure solutions necessary for effectively connecting disparate life sciences databases. Alignment and integration of data and information sources is a significant effort repeatedly undertaken by companies, institutes, and academic laboratories. The ITF held a kick off meeting on January 6, 2011. It generated significant interest from principal investigators within NBIC and beyond. Initially, the NBIC task force will focus on participating in the development of the Open PHACTS project. This project will focus on developing an open source and open access platform via a semantic web-based approach. The semantic integration hub, named the Open Pharmacological Space (OPS), will concentrate on the task of building coherent services guided by well-defined research questions assembled from the participating researchers. As the ITF gains momentum, facilitating data sharing between the different NBIC task forces such as Next Generation Sequencing and Biobanking will be a primary goal. More information

RSG Netherlands visits Agendia

Mon, 20 Dec 2010 09:51:00 +0100

RSG Netherlands – Regional Student Group – organised its first company visit on November 23 to innovative cancer diagnostics company Agendia in Amsterdam. RSG Netherlands brings together PhD students in bioinformatics and computation biology in the Netherlands and is part of the global network of the ISCB. Agendia is the developer of the MammaPrint, a prognostic test for breast cancer patients based on gene expression profiling. The visit, in which 19 students participated, was a success. RSG Netherlands, which was co-founded by NBIC in 2008, plans to organise more company visits in the near future. Read to the full report of the visit: http://www.iscbsc.org/rsg/rsg-netherlands/site-visit-agendia

Boolean modelling sheds light on regulatory circuits

Thu, 16 Dec 2010 15:35:00 +0100

Pairs of almost similar genes have long been thought to act as back up for each other. But in their paper published in Cell on December 10, shared first authors Patrick Kemmeren and Sake van Wageningen and their colleagues from the group of Frank Holstege (NBIC /UMC Utrecht) show that such gene pairs actually form regulatory circuits that influence different combinations of cellular processes. This way, an organism can efficiently couple or decouple processes, for example when dealing with altered environmental conditions. The ability to use genetic information in such an efficient way may also explain the high level of conservation of some of these gene pairs during evolution. The group analysed 150 deletion mutants of kinases and phosphatases in baker's yeast (Saccharomyces cerevisiae) using DNA microarrays to study relationships between phosphorylation-based signalling pathways. They particularly focused on genetic buffering relationships such as redundancy. To this end, they selected double mutants that exhibited a markedly different effect on growth compared to the effect of each single mutant. This resulted in the identification of three types of genetic buffering mechanisms: mixed epistasis, complete redundancy and quantitative redundancy.

Modelling the module
In mixed epistasis there is only partial overlap in function between the two genes and their coupling usually involved additional regulatory mechanisms such as repression of one by the other. This allows the gene pair to operate as a regulatory module that can control different processes under different circumstances. To unravel the mode of action of such a module, the researchers zoomed in on the FUS3-KSS1 kinase pair. "Our starting point was to define the regulatory module as a model consisting of four nodes: two regulators and two responses. We defined a number of boundary conditions, for example that each node was controlled by a maximum of two inputs and that there should always be at least one route to the responses, R1 and R2", Patrick Kemmeren explains. "This resulted in 794,176 possible models. Using Boolean modelling, Philip Lijnzaad reduced these to 106 models that would actually lead to the minimal mixed epistatic effect. Further pruning left us with 28 root models that all exhibit the experimentally observed mixed epistasis." Although the modelling concentrated on one particular gene pair, the approach revealed important information on how gene pairs with only partial overlap in function can operate as an effective regulatory module that has the ability to act as a multi-process control unit. In turn, this would explain their evolutionary conservation.

Sake van Wageningen, Patrick Kemmeren, et al., Functional Overlap and Regulatory Links Shape Genetic Interactions between Signaling Pathways, Cell, 143, 991-1004, December 10, 2010 http://www.cell.com/abstract/S0092-8674(10)01301-2

NBIC teacher training

Tue, 14 Dec 2010 13:25:00 +0100

Together with the Freudenthal Institute, NBIC organized its first-ever training for high school teachers on November 26^th. During the training, the teachers were challenged to use bioinformatics in their classes. In order to prepare appropriate lessons, they were supported by NAVIGENE, a scheme that helps in navigating through bioinformatics. Next to the teachers, also a number of high school students participated in the training. The participants, teachers as well as students, were all very enthusiastic about the training! The organisers plan to host a follow-up meeting in due course. Involved in this project are Hienke Sminia, Dirk Jan Boerwinkel and Lauke Ringens. Read more about the bioinformatics@school projects on teacher training and didactical research: http://www.nbic.nl/education/high-school-programmes/bioinformaticsschool/teacher-training/

Connecting Biobanks: Where generators and interpretators meet

Fri, 10 Dec 2010 15:46:00 +0100

On Monday November 22, over 200 participants gathered at the AMC in Amsterdam for the conference 'Connecting Biobanks'. The conference was an initiative of the Concept Web Alliance (CWA), NBIC and BBMRI-NL. Goal of the meeting: bringing together data generators and data interpretators to emphasize the importance of bioinformatics in connecting biobanks. "The conference underlined the importance of bioinformatics really well. Biobanks need bioinformatics to make their data available to the community at large", says Albert Mons, Executive Secretary of CWA. He points to the keynote lecture by Josh Sommer, a young American who was diagnosed with a rare type of bone cancer called Chordoma in 2006. He subsequently founded the Chordoma Foundation to stimulate the development of effective treatments. In his efforts to bring together academics that study Chordoma, it proved to be very difficult to locate clinical data on the disease even though he knew that Chordoma research was being performed at several sites. Mons: "His search for data clearly demonstrated the need for coupling biobanks. Important data is out there, but in many cases it is extremely difficult to find the datasets you need, let alone access and use them, because they are typically stored in locally distributed databases that all have their own format. It would help biomedical research tremendously if all datasets would be made interoperable."

Input from the biobanks field was secured through the involvement of BBMRI-NL in the conference. BBMRI-NL is the Dutch national 'hub' of the European Biobanking and BioMolecular Resources Research Infrastructure (BBMRI) and the conference marked the official start of BBMRI-NL. "The launch of BBMRI-NL provided a perfect opportunity to host this conference together", Mons explains. "From the CWA standpoint, we want to communicate our message of interoperability as broadly as possible. We are a supporting organisation and our work perfectly matches the needs and ambitions of BBMRI-NL and many other data generators."

The CWA parallel session in the afternoon programme focused on the practical side of connecting biobanks. Several prototypes were showcased and discussed. Topics included dealing with different languages, identifying and locating experts and performing data analyses within a database instead of transferring large amounts of data to your own environment. Part of the sessions were organised again the next day, November 23, during Life Sciences Momentum 2010 in Utrecht. At the same event, Barend Mons (NBIC/CWA) also presented CWA to the life sciences community in a '20-minute session'. The outgoing attitude of CWA will be sustained, according to Albert Mons. "Co-organising events with other organisations is a very good way for CWA to show what we have to offer and how we can help. I certainly foresee more of this type of activities in the near future."

More information: Presentations and pictures of the conference are available at
http://www.bbmri.nl/nl-nl/activiteiten/conference-connecting-biobanks

DNA-labs as motion picture

Mon, 06 Dec 2010 10:24:00 +0100

You can now watch the short movie of the educative high school program DNA-labs on the road: http://www.allesoverdna.nl/onderwijs/reizende-dna-labs/DNA-labs-on-the-road.html

Dutch bioinformatics community highly visible in IMI

Thu, 23 Sep 2010 12:08:00 +0200

The Open Pharmacological Space (OPS) project and the Drug Disease Modelling Resources (DDMoRe) consortium have been selected for funding by the European Innovative Medicine Initiative (IMI). NBIC researchers play a central role in these two large-scale projects, which focus on interoperability and modelling respectively.

Unique assertions
"The amount of information that is available in the life sciences field is overwhelming, but it is stored in numerous different databases that all employ different terminology", says Barend Mons (NBIC/LUMC), who is an initiator of the Open Pharmacological Space (OPS) project (total budget: €20 million) and a member its steering committee. "Also the data itself differs greatly, there is genomics data, transcriptomics, proteomics, etc. Our main challenge is interoperability, making sure that these different databases can 'talk' to each other. To this end, we will translate all the 'assertions' in the life science into unique concept triples, which we call 'nanopublications'. All the information amounts to roughly 10^14 triples right now, but we can bring that down to 200 billion unique assertions. That number makes it feasible to start in silico knowledge discovery."

Global standard
Next to the LUMC and NBIC, also Maastricht University and the University of Amsterdam are partners in the OPS project, creating a highly visible role for the Dutch bioinformatics community. That visibility is further enhanced by the involvement of the Leiden Institute of Advanced Computer Science (LIACS) and the Leiden Amsterdam Centre for Drug Research (LACDR) as key partners in the Drug Disease Modelling Resources (DDMoRe) consortium, which also boasts a total budget of €20 million. "Modelling plays a central role in clarifying the mode of action of a drug and models are an essential part of the filing dossier of newly developed drugs. With DDMoRe, we aim to set a global standard for the description of such models", Joost Kok (NBIC/LIACS/LUMC) explains. "Here in Leiden, we will primarily focus on designing a Model Description Language and the tools associated with such a design. This will involve the application of the technology behind programming languages. From an informatics point of view, it will be very interesting to apply text and data mining technology developed within NBIC to this type of biological models." Barend Mons agrees: "In fact, the evaluators of both projects and also the one selected for Electronic Medical Records, strongly advocated that the three projects operate on the ‘same ontological framework’ making modelling, in silico discovery and translation to patients one interoperable space."

Adoption by users
DDMoRe is in essence an infrastructure project and the success will ultimately be measured by the adoption of the Drug Disease Model Library Framework by pharmaceutical companies. "Translating our work to the end users is crucial", says Joost Kok. "After all, our ambition is to create a global standard in this field. It is good to mention here that valuable work on drug/disease modelling already has been done by the Top Institute Pharma in the Netherlands, which we can use as a basis for this project." There is a clear link with the OPS project, although both endeavours have completely different starting points. Joost Kok: "We start from the mathematical modelling side, more top down, whereas the OPS project is really data driven. But in the end, we will meet and it will be interesting to connect our models to the systems biology field."

Innovative Medicine Initiative
The Innovative Medicine Initiative (IMI) is a partnership between the European Commission and the European Federation of Pharmaceutical Industries and Associations (EFPIA). Main objective of the IMI is to support the overall drug discovery and development process by tackling pre-competitive bottlenecks in R&D that are too large and too complex for individual parties to take on. The European Commission has dedicated €1 billion to IMI, which will be matched by the pharmaceutical industry, bringing the total budget to €2 billion for the period 2007-2013.

More on IMI: www.imi-europe.org Interview on Open Pharmacological Space: http://www.youtube.com/watch?v=qB1ljMvGxXg

International Advisory Committee visits NBIC

Thu, 01 Jul 2010 16:35:00 +0200

On June 6 – 8 2010, the NBIC International Advisory Committee (IAC ) visited NBIC. The IAC, chaired by prof. Willem Stiekema (University of Amsterdam), further consists of prof. Carole Goble, (University of Manchester), prof. Ron Appel (SIB Swiss Institute of Bioinformatics), prof. Robert Glen (University of Cambridge), dr. Nick Goldman (EBI) and prof. Yves van de Peer (VIB, not present this meeting). The committee members received an update of the achievements within NBIC in a lively programme, involving over 30 NBIC participants. In the historic ambiance of the Royal Tropical Institute in Amsterdam, the IAC received a diverse mix of overview presentations, poster presentations during a dedicated “poster market”, and had separate meetings with young NBIC researchers, as well as group leaders and representatives of NBIC partner organizations. The IAC was updated on the achievements in the NBIC programmes in research (BioRange), education (BioWise) and support (BioAssist), and on the dissemination & “valorisation” activities (NBICommons). International embedding and future plans were important topics throughout the meeting. Overall, the committee was very pleased with the progress made within the Dutch bioinformatics field in general, and within NBIC in particular, which the IAC regards an essential part of the Dutch Life Science field. The IAC congratulates the NBIC partners with the scientific progress made in BioRange and the well structured and effective BioAssist support environment. The breadth of the NBIC education programme (from high school projects to the NBIC PhD School ) was also well received. Under the coordination of NBIC, the Netherlands has meanwhile reached a state of substantial critical mass in the international bioinformatics field, ranking it third behind EBI and SIB. The IAC strongly supports the strategy of the management team to plan for NBIC’s sustainability. The new board of directors will take up the recommendations made by the IAC towards further improving and strengthening NBIC in the coming years.

New Scientific Management at NBIC

Thu, 01 Jul 2010 16:10:00 +0200

Nijmegen, The Netherlands, June 28, 2010 The Netherlands Bioinformatics Centre (NBIC) presents its new scientific management staff: Jaap Heringa, Ph.D. (VU University Amsterdam), Barend Mons, Ph.D. (Erasmus MC Rotterdam/Leiden University Medical Centre) and Marcel Reinders, Ph.D. (Delft University of Technology). The three Scientific Directors together are responsible for the overall NBIC scientific programme, with each director managing an individual portfolio. Marcel Reinders heads the research programme (BioRange), Barend Mons manages the support programme (BioAssist) and is responsible for external relations and Jaap Heringa chairs the education programme (BioWise). The new team takes over from Antoine van Kampen, Ph.D. (Amsterdam University Medical Centre/University of Amsterdam) and Bob Hertzberger, Ph.D. (University of Amsterdam) who stepped down as scientific directors in March of this year. The composition of the new scientific management and the expansion to three members reflects the strong growth of the NBIC programme, both in number and different types of activities. The daily management of the NBIC Foundation will remain the responsibility of Managing Director Ruben Kok, Ph.D, who is also responsible for the valorisation programme NBICommons. Jaap Heringa (1957) is professor of Bioinformatics and director of the Centre for Integrative Bioinformatics at VU University Amsterdam. Next to his scientific work in the area of bioinformatics and computational biology, he has longstanding and broad advisory, management and education experience in both the Dutch and international arena. Barend Mons (1957) is associate professor of Biosemantics at Erasmus Medical Centre, Rotterdam and Leiden University Medical Centre. He bridges bioinformatics and biomedical research, has an extensive international network and is (co-)founder of a number of academic spin-offs. Mons is one of the initiators of the Concept Web Alliance (CWA). Marcel Reinders (1966) is professor of Bioinformatics and Pattern Recognition at Delft University of Technology. His research links bioinformatics, informatics and imaging. Reinders manages a large research group, which regularly publishes in leading international journals.

Article in 'Volkskrant' newspaper

Tue, 22 Jun 2010 13:14:00 +0200

On June 5, 2010 the Dutch article “Twitteren voor de wetenschap” (Twitter for science) was published in the Volkskrant newspaper. The article describes the new way of dealing with large amounts of data in science. It is based on an interview with Dr. Barend Mons, director of BioAssist. Unfortunately, the article is available in Dutch only. To read the article, please click here (PDF document, in Dutch only).

BioCatalogue: The 'Yellow Pages' of web services

Mon, 21 Jun 2010 17:10:00 +0200

The continuous flow of newly developed web services is of course great news for anyone working in bioinformatics and computational biology. But the overwhelming array of possibilities makes it also hard to identify the web service that suits your needs best. To assist researchers in their search for web services, the group of Carole Goble at the University of Manchester (UK) and the European Bioinformatics Institute have developed BioCatalogue – a common interface for registering, browsing and annotating web services.

One of the co-authors of the BioCatalogue-paper is Marco Roos (Leiden University Medical Centre/University of Amsterdam/NBIC), who acts as a liaison between NBIC and the Goble group. "BioCatalogue offers an overview of web services that are relevant to the life sciences community", Marco explains. "Right now, main sources for BioCatalogue are EMBRACE and Taverna, but as users start registering tools and web services themselves, the scope of BioCatalogue will expand. " He emphasises the role users play in making an interface like BioCatalogue work. "In the end, websites are made by the users. Social community mechanisms are driving the development and the relevance of a website. Your additions, feedback and annotations are important to other users and vice versa."

Feedback
He describes his own role in the project as that of a 'super-user'. "The developers of BioCatalogue are strongly user-oriented. They operate in short development cycles that immediately incorporate user feedback. Working with the different versions of BioCatalogue in my own research, I provided feedback that they used as input for the next development cycle. Pieter Neerincx of the NBIC proteomics platform also contributed feedback as one of the curators." This interactive approach is beneficial for both developers and users, says Marco. "They make the best software, so that we can get the best software."

Taverna plug-in
To increase easy of use, there is no shortage of plans for further development of BioCatalogue. Marco: "I am a Taverna user and we are currently testing a Taverna plug-in that enables you to use BioCatalogue as the search tool within Taverna. What I already like is that the search result presents you with a number of suggestions to explore further." Other plans include a combination of BioCatalogue and MyExperiment, monitoring web services to notify users when changes occur and the possibility to run services in BioCatalogue.

NBIC users test HPC Cloud

Mon, 14 Jun 2010 14:44:00 +0200

Following a successful pilot end of 2009, the beta-test phase of the HPC Cloud developed by SARA as part of a BiG Grid project is about to kick off. A call to recruit beta-testers got the project in the international limelight as it was picked up by 'HPC in the Cloud', an online newsletter that claims to have 30,000 readers. International groups immediately contacted SARA to require access to the HPC Cloud, but unfortunately for them, the new service is presently only available for Dutch users. Ideal environment
Selection of the 10 projects for the beta-phase is ongoing, but there will be a relatively high number of NBIC users Floris Sluiter of SARA expects. Together with colleague Tom Visser, he is responsible for the development of the HPC Cloud. The HPC Cloud project is funded and facilitated by BiG Grid – a collaboration between NCF, Nikhef and NBIC that provides access to grid infrastructure for the Dutch science and R&D communities. Floris: "Especially in bioinformatics, researchers work with a lot of different applications and tools. Because it is such dynamic field, these applications and tools quickly change as well. To this group of users, our HPC Cloud offers the ideal environment." 20-40 copies
In short, commercial cloud computing is about 'renting' unused external server capacity to run large jobs or to store data. Several commercial parties, such as Amazon, offer this type of cloud services. The development of virtualisation technology was the driver for SARA to develop a dedicated HPC (high performance computing) cloud system. "In essence, virtualisation technology offers you the possibility to 'copy' your own working environment to create a scale up in computing power", explains Floris. "You get your own 'Virtual Private HPC Cluster' based on the software environment you are used to. Your software can remain the same, you can run multiple copies and distribute the workload. For example, with the SARA HPC Cloud, you can clone your own laptop 20 to 40 times. If your software can run in parallel, for example with an MPI library, or if the workload consists of many similar tasks, it will not be difficult to run your software in the HPC Cloud on your Virtual Private HPC Cluster. On the traditional HPC systems, there is usually an incompatibility with the existing work environment of the user, making it necessary to adapt the application code. The ability to tailor the environment to the application code will greatly improve and shorten the time it takes to produce results." Faster and cheaper
Compared to the commercially available clouds, the HPC Cloud offers several important advantages. Floris: "We can guarantee the network speed, which is essential to the predictability of HPC jobs. And our networks are much faster than the commercial ones. Safety is well organised, you know your data are stored at a secure site in the Netherlands. Furthermore, our cloud is a dedicated HPC system, compared to the commercial parties where the cloud service is just a by-product. Last but not least, our services are a lot cheaper."
For more information: https://grid.sara.nl/wiki/index.php/Using_the_HPC_Cloud/betaevaluation

First NBIC Hackathon big success

Thu, 15 Apr 2010 09:24:00 +0200

Prior to the NBIC Conference 2010, the first NBIC Hackathon was organised to tackle a number of interesting problems.
Hackathon? A marathon for hackers? Basically, that is what it boils down to. In a Hackathon, enthousiastic programmers are 'locked up' together to work on challenges that require input from different areas of expertise. As such, it is perfectly suited to address 'dreams' - solutions or tools that many people would like to have, but fall outside the scope of the individual projects. Creating a dedicated environment to work with others on such tools is the hallmark of a Hackathon. For the first NBIC edition on March 26 and 27, approximately 15 participants gathered in Utrecht for two days of hard work. A rewarding enterprise, as concrete results could be communicated on the second day of the NBIC Conference 2010. The Hackathon delivered, for example, a new tool to add background information to PDF files using a special PDF viewer and information from the Concept Wiki. Prior to the Hackathon, this was only available for text on web pages. Another example is the use of context to decide the right meaning of terms that have multiple meanings and to use that decision to display only the relevant additional information in a pop-up. Judging from the response of the participants and the organisers, we can expect multiple editions of the Hackathon in the near future. Interested in participating? Contact Rob Hooft, rob.hooft@nbic.nl, to stay informed. For more information, pictures and videos: https://wiki.nbic.nl/index.php/March_2010_Hackathon

Latest issue of Interface

Fri, 11 Dec 2009 16:08:00 +0100

The latest issue of Interface (number 4) is published. In this issue the cover article describes how the complexitity of biological systems can be reduced. The interview with Professor Lars Juhl Jensen from the Novo Nordisk Foundation Centre for Protein Research shows that bioinformatics is a true science.

Innovation Award for DNA Labs on the Road

Mon, 23 Nov 2009 14:30:00 +0100

The 'DNA Labs on the Road', a collection of five hands-on workshops on 'omics' technologies aimed at high school pupils that includes the NBIC bioinformatics@school project, have been granted the Innovation Award of the Netherlands Association for Community Genetics and Public Health Genomics (NACGG). During the NACGG fall meeting on November 20, 2009, the award was presented to Dirk-Jan Boerwinkel, researcher at the Centre for Society and Genomics, on behalf of all the DNA Labs on the Road.

More information:
DNA Labs on the Road: www.dnalabs.eu (English) or www.dnalabs.nl (Dutch)
NACGG: www.nacgg.nl (Dutch)

NBIC PhD Course Algorithms for Biological Networks now open for registration

Fri, 13 Nov 2009 10:44:00 +0100

The PhD Course Algorithms for Biological Networks of the NBIC PhD School will take place on 11-15 January 2010 in Delft. More information about the content of the course can be found at the course website. Registration is now open.

NBIC@the museum

Tue, 10 Nov 2009 15:55:00 +0100

During 'Oktober Kennismaand' (October: Month of Knowledge), NBIC was present at Scientific, a science festival hosted by Science Centre NEMO in Amsterdam. The festival was themed 'Travelling into the unknown' and focused on the study of things that are for example very far away, happened in the past or are extremely small, such as DNA. NBIC and the Cancer Genomics Centre were invited by NEMO to demonstrate their respective 'DNA-labs on the road' (in Dutch: Reizende DNA Labs) to the audience, but with an additional request for NBIC to focus its bioinformatics@school material on the younger children aged 6-12. Candy molecules
NBIC presented three computer-based demo's that stimulate children to think about DNA in a very playful manner. "With the DNA Balance, you can calculate how many grams of DNA you have in your body based on characteristics like age, height and weight", explains Hienke Sminia, officer education at NBIC. "We also presented a game called DNA Inclusive, in which the children have to decide whether familiar products like apple juice or peanut butter contain DNA or not. And in the third demo, we used the Yasara programme to show the children very small molecules, which they had to build using candy and cocktail sticks." Expand audience
According to Hienke, the NBIC demo's were a big hit with the children. Not surprisingly, building molecules out of candy was especially popular. "Of course, at this young age they do not completely understand what they are doing, but they were already very good at the DNA Inclusive game. And they do realise that the world around them is made up out of tiny little particles." This type of spin-off from the bioinformatics@school project is definitely something that NBIC will actively pursue, says Hienke. "We are currently working out the best way to expand our audience and also include primary school pupils in our bioinformatics@school activities." Suited for adults
Next to presenting bioinformatics to children and teens, NBIC also readily springs to action when it comes to 'educating' adults. Recently, NBIC was present during a lecture on genetic descent organised by the Centre for Society and Genomics at the Boerhaave Museum in Leiden. The various demo's are definitely suitable for adults as well, says Hienke. "They are also curious to learn how much DNA they carry around in their body." All NBIC activities relating to education and public communication are regularly posted on the Events calendar.

PathVisio 2.0 released

Mon, 26 Oct 2009 13:12:00 +0100

An elegant new feature of PathVisio 2.0 (http://www.pathvisio.org/) is the ability to import experimental datasets and visualize them on top of biological pathways. Large microarray, proteomics or metabolomics datasets can be explored in a way that is more interesting and understandable than by using just a huge spreadsheet. Microarray reporters will be automatically converted to gene or protein identifiers. Visualization can be customized using gradients, boolean colour rules or coloured icons. Perform over-representation analysis to identify the pathway most affected by experimental conditions. A Visual Tour of new and existing features of PathVisio is available at http://www.pathvisio.org/wiki/VisualTour About PathVisio
PathVisio is a tool for creating and analysing biological pathway diagrams. Stay organized by using PathVisio as a notebook to collect the various bits of information related to a biological research subject. Create images suitable for presentation or publication. Draw pathways, export them to many image formats, annotate them with links to online biological databases such as Ensembl or Entrez gene, and add comments and literature references from Pubmed. PathVisio is fully compatible with WikiPathways (http://www.wikipathways.org/), a wiki where researchers can contribute pathway knowledge. Information for developers
PathVisio has a plug-in interface that allows customization by users to accommodate new analysis types, new visualization methods and new pathway formats. PathVisio is fully open source, and we are always looking for Java developers who are interested in contributing, either to new plug-ins or to the core of the program. Contact us through our mailing list: http://www.pathvisio.org/wiki/MailingLists PathVisio was developed by the BiGCaT Bioinformatics group at Maastricht University, the Netherlands, within the NBIC BioRange programme.

BioAssist reinforced by Engineering Team

Thu, 15 Oct 2009 11:11:00 +0200

As of September 2009, a dedicated, centrally managed, but distributed software engineering team has been added to the BioAssist programme. The engineering team supports the BioAssist platforms in their development activities relating to professional software and content services. The team consists of Barend Mons, who is also the new BioAssist programme leader; Rob Hooft, chief technology officer, who is responsible for 'code' and manages and supports the centrally located software engineers as well as those within the support platforms and Christine Chichester, who is responsible for all activities relating to 'content'. To learn more about the BioAssist support platforms and to get involved, please contact Barend Mons, programme leader BioAssist, or one of his colleagues.

New CLS projects awarded

Mon, 31 Aug 2009 16:41:00 +0200

The Netherlands Bioinformatics Centre (NBIC), the Netherlands Genomics Initiative (NGI) and the Netherlands Organisation for Scientific Research (NWO Physical Sciences) have launched a second round of the research programme Computational Life Sciences. Recently (June 2009) five new projects have been awarded: The evolution of stochastic heterogeneous networks as bet-hedging adaptations to fluctuating environments
Coordinator: P. Haccou, PhD (Leiden University)

Reverse physiology of the cortical microcircuit
Coordinator: A.R. Houweling, PhD (Erasmus Medical Centre, Rotterdam)

Multi-scale modelling of calcification in scleratinin corals
Coordinator: J.A. Kaandorp, PhD (University of Amsterdam)

The co-evolution of the receptor signalling network of natural killer cells with its ligands
Coordinator: Prof. R.J. de Boer (Utrecht University)

The regulatory network underlying malaria parasite-host interactions
Coordinator: T.M.H. Dijkstra, PhD (Radboud University Nijmegen)

Enlighten your research

Fri, 17 Jul 2009 14:07:00 +0200

Peter Horvatovich (BioRange researcher, University of Groningen) is one of three winners of the competition "Enlighten your research" on dynamics light paths, organised by SURFnet and NWO. Together with Bas van Breukelen (Netherlands Proteomics Centre, and participant in BioRange and BioAssist) he has described a high speed light path network for the Netherlands Bioinformatics for Proteomics Platform. The winners get free access to the light path network and 20.000 Euro to integrate light paths in their research. More information (in Dutch): http://www.surfnet.nl/nl/nieuws/Pages/SURFnetmaaktwinnaarslichtpadenwedstrijdbekend.aspx