NBIC research news http://www.nbic.nl/ In the list below you'll find the latest research news from NBIC. en TYPO3 - get.content.right http://blogs.law.harvard.edu/tech/rss Wed, 05 Nov 2014 11:36:00 +0100 Python for Life Sciences http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/python-for-life-sciences/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/python-for-life-sciences/ Fri, 30 Aug 2013 11:03:00 +0200 In the beginning of August Martijn Vermaat (LUMC) and colleague teachers* organized a course week aimed at his human genetics colleagues in Leiden.... participants from other LUMC-departments and by people from other organisations including a company. The course was successful and surely will be repeated. Probably as a national course open for all participants working in the field of Life Science as part of the Training & Education Programme of DTL. For those of you who can’t wait: slides of the course are available at the course website: https://humgenprojects.lumc.nl/trac/programming-course/ 

*) The course teachers are (see photo; from left to right): Zuotian Tatum (Human Genetics, LUMC), Wibowo Arindrarto (SASC, LUMC), Jeroen Laros (Human Genetics, LUMC) and Martijn Vermaat (Human Genetics, LUMC).]]>
Venture Challenge & Pre-Seed Grant open for submissions http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/venture-challenge-pre-seed-grant-open-for-submissions/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/venture-challenge-pre-seed-grant-open-for-submissions/ Thu, 01 Aug 2013 10:45:00 +0200 Are you thinking about starting a company based on your research results? Then you do not want to miss out on this opportunity to participate in the... Then you do not want to miss out on this opportunity to participate in the
NGI Venture Challenge and Life Sciences Pre-Seed Grant. Venture Challenge
The Venture Challenge is a ‘must-do’ opportunity for all aspiring Life Sciences entrepreneurs, it is the way to receive coaching and advice on essential elements of setting up a business, thereby paving the way for your future success. It is also superb preparation for the next stage: acquiring financing, such as the Life Sciences Pre-Seed Grant. Apply for the Venture Challenge!
Submission Deadline: 10 September 2013, 12:00 hrs
Read more on the Venture Challenge Website. Life Sciences Pre-Seed Grant
The Life Sciences Pre-Seed Grant offers a great opportunity for applied researchers associated with a Dutch university or research institution. Worth up to € 250,000, it offers superb prospects for those looking to exploit your fundamental research commercially by starting up a new business. Apply for the Pre-Seed Grant!
Submission Deadline: 10 September 2013, 15:00 hrs
Read more on the Pre-Seed Grant website.]]>
Just pick a card http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/just-pick-a-card/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/just-pick-a-card/ Mon, 29 Jul 2013 15:45:00 +0200 Researchers interested in metabolism have a wealth of information resources at their disposal in the form of metabolic pathway databases. For an... http://www.molgenis.org/c2cards) to test their concept on the information presented by five different human metabolic pathway databases. According to the authors, a concept like C2Cards will not only facilitate researchers in extracting information in a concise manner, it will particularly support database curators in their ongoing efforts to reconcile pathway databases and it will hopefully lower the threshold for domain expert to contribute their specific knowledge to these databases.

Stobbe MD, Swertz MA, Thiele I, Rengaw T, van Kampen AH, Moerland PD
Consensus and conflict cards for metabolic pathway databases.
BMC Syst Biol. 2013 Jun 26;7(1):50]]>
CTMM & NBIC present technology for the whole family! http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/ctmm-nbic-presented-technology-for-the-whole-family/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/ctmm-nbic-presented-technology-for-the-whole-family/ Mon, 17 Jun 2013 13:44:00 +0200 How large is DNA in my body? Is that why I look a bit like my father and my mother? This are some examples of questions that were answered during 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 life science technology inventions in a stand in the High Tech Discovery Route. Visitors could make a journey from their own DNA to proteins. Starting by isolating their own DNA from saliva and concluding by watching proteins in 3D. "Many visitors were interested in DNA and came to us with questions like How can you identify a specific gene in DNA? or Does every protein look different?", says Gitte Bunthof, NBIC. "And the youngest visitors could build molecules from candy and toothpicks.”]]> iAnn: community-driven platform for life science events http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/iann-community-driven-platform-for-life-science-events/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/iann-community-driven-platform-for-life-science-events/ Mon, 17 Jun 2013 10:31:00 +0200 iAnn is presented in the Oxford Journal Bioinformatics as an open source community-driven platform for dissemination of life science events, such as... Bioinformatics as an open source community-driven platform for dissemination of life science events, such as courses, conferences and workshops. Marc van Driel and Celia van Gelder, both NBIC team members, are co-authors of this publication. iAnn allows automatic visualisation and integration of customised event reports. A central repository lies at the core of the platform: curators add submitted events, and these are subsequently accessed via Web services. Thus, once an iAnn widget is incorporated into a website, it permanently shows timely, relevant information as if it were native to the remote site. At the same time, announcements submitted to the repository are automatically disseminated to all portals that query the system. To facilitate the visualisation of announcements, iAnn provides powerful filtering options and views, integrated in Google Maps and Google Calendar. For more information you can read the full article in Bioinformatics. All iAnn widgets are freely available: http://iann.pro/node/18.  ]]> Sampling the Dutch http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/sampling-the-dutch/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/sampling-the-dutch/ Tue, 11 Jun 2013 09:23:00 +0200 With the worldwide take-off of genome-wide association studies (GWAS), thousands of genetic variants have been uncovered that are associated with a... Genome of the Netherlands (GoNL) project, part of BBMRI-NL, researchers based in the Netherlands are zooming in on this aspect by sequencing the genomes of 250 trio-families (two parents, one offspring) from the different provinces of the Netherlands. In a paper in the European Journal of Human Genetics, Dorret Boomsma (VU University Amsterdam) and colleagues describe the global characteristics of the project, which will not only provide a detailed contribution to the overall catalogue of human genetic variation, but also acts as a starting point to enrich GWAS samples with more functional DNA variation as part of the BBMRI-NL programme.

Boomsma DI, Wijmenga C, Slagboom EP, Swetz MA et al.,
The Genome of the Netherlands: design and project goals
EJHG (2013), 1-7. doi:10.1038/ejhg.2013.118]]>
ODoSE: Analysing adaptations http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/odose-analysing-adaptations/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/odose-analysing-adaptations/ Thu, 06 Jun 2013 12:53:00 +0200 In evolutionary and comparative genomics, one of the objectives is to distinguish patterns in genetic variation and link those patterns to phenotypic... Mark van Passel (Wageningen University). "Species formation is a fascinating phenomenon, but especially in prokaryotes the definition of a species is tricky. A few years back, Michiel Vos of the University of Exeter presented his work on using the MK test to analyse patterns of selection, which in turn could potentially be used to build a model of classification of bacterial species." Over a beer, Vos and van Passel further discussed the potential of this new approach.

Van Passel: "Michiel previously used the MK test on only a limited number of genes. We wanted to give it a more comprehensive scope and study adaptation on a genome-wide scale. Those are the interesting genetic changes, because they have become a defining element of any 'species’. I already worked with the NBIC Bioinformatics Research Support team before, so I approached them to help us with scripting this new application. And then they suggested to take it to the next level and create a webserver." Tim te Beek of BRS took up the work and the result is ODoSE - Ortholog Direction of Selection Engine, which enables researchers to compare large groups of genes of different species or complete genomes. Also on the team was Adam Eyre-Walker from (University of Sussex) whose refinements of the MK test have been implemented in ODoSE. Van Passel: "You can use ODoSE for a whole range of genomics analyses, for instance to find the genes that are shared between a selection of strains or species, which is often referred to as the 'core genome'. The possibilities are many and the webserver is designed in such a way that it is accessible to non-genomics experts.  Even simple microbiologists like myself can use it."

ODoSE runs in a Galaxy environment and is freely available through: http://www.odose.nl Vos M, te Beek TAM, van Driel MA, Huynen MA, Eyre-Walker A, van Passel MWJ
ODoSE: A Webserver for Genome-Wide Calculation of Adaptive Divergence in Prokaryotes
PLoS ONE 2013, 8(5):e62447. doi:10.1371/journal.pone.0062447

Text by: Esther Thole.]]>
Public release of OpenPHACTS API in London http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/public-release-of-openphacts-api-in-london/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/public-release-of-openphacts-api-in-london/ Tue, 04 Jun 2013 11:28:00 +0200 On April 22 and 23, the Open PHACTS consortium held a Community Workshop at Burlington House in London to feature the public release of the Open... Open PHACTS consortium and is involved in many of the technical developments of the Open PHACTS platform. The first day’s talks described the data accessible via the Open PHACTS Discovery Platform and technical aspects of the API of which NBIC's ConceptWiki module is a major contribution. The ConceptWiki provides the textual search capabilities for applications accessing the Open PHACTS semantic data. The soon to be released editing capabilities of the ConceptWiki will allow users to add synonyms to their concepts of interest to make the search capabilities more personalized and intuitive to individual users. The use of the ConceptWiki text search was demonstrated by the example application ChemBioNavigator and PharmaTrek. The second day involved discussion of Open PHACTS sustainability and plans for the successor organisation, the Open PHACTS Foundation. The afternoon was attended by those keen to further discuss the potential of the Open PHACTS API and the future of Open PHACTS.  Among the participants were publishers (Elsevier, Thomson Reuters and Nature Publishing Group), software providers (Accelrys, ChemAxon, Dotmatics, and IBM), North American attendees from the NIH and Carleton University and European technology startups Digital Science and Ontoforce. During talks, especially those detailing the Open PHACTS API, a steady stream of signup requests to the API via http://dev.openphacts.org were received. The hashtag #opslaunch was used to follow reactions to the workshop on Twitter, and showed the response amongst attendees to be overwhelmingly positive. A publicly available workshop summary can be found online: http://www.openphacts.org/4th-open-phacts-community-workshop-held-

Different backgrounds, common benefits http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/different-backgrounds-common-benefits/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/different-backgrounds-common-benefits/ Fri, 24 May 2013 13:18:00 +0200 Interdisciplinary research fields like bioinformatics and systems biology require a broad range of skills and a thorough understanding of diverse...
In a paper in Briefings in Bioinformatics, Sanne Abeln (VU University Amsterdam) and colleagues describe their experiences and learning points from the Bioinformatics and Systems Biology MSc programme, a joint effort between the two Amsterdam-based universities. Instead of tailoring the curriculum to the specific needs of the various subgroups in the student population (e.g. offering more programming courses to biology BSc's and vice versa), they have opted for early mixing of students with different backgrounds in intensive group projects, with specialized conversion classes to bridge gaps in knowledge and skills. To the students, this mixed environment is very stimulating, offers them insight in their own gaps in knowledge and is a good preparation for their future fields of employment.

Abeln S, Molenaar D, Feenstra KA, Hoefsloot HC, Teusink B, Heringa J
Bioinformatics and Systems Biology: bridging the gap between heterogeneous student backgrounds
Brief Bioinform. 2013 Apr 19 Text by Esther Thole.]]>
The Power of RNA seq http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/the-power-of-rna-seq/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/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... 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@removethis.nbic.nl)]]>
Still some seats left for Variant Detection and Interpretation http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/still-some-seats-left-for-variant-detection-and-interpretation/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/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... 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@removethis.nbic.nl)]]>
Enlighten Your Research Global competition - Call for Proposals http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/enlighten-your-research-global-competition-call-for-proposals/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/enlighten-your-research-global-competition-call-for-proposals/ Thu, 23 May 2013 10:50:00 +0200 deadline draft proposals extended to July 1st! The competition for researchers “Enlighten Your Research” - successful in the Netherlands - now becomes International! The Enlighten Your Research Global (EYR-Global) program is an international competition that invites researchers and their collaborators to submit proposals that highlight how access to world-class research networks would significantly improve their research and discovery process.
Modern science is generating large amounts of data and timely data transfers are a crucial aspect for the emerging international scientific  collaborations. High-speed networks are an important enabler for the sharing of these large amounts of data. In many cases, researchers are unaware of the possibilities of such high-speed networks, offered by their National Research and Education Networks (NREN’s). In order to help researchers with their international collaborations and to further promote the benefits of international-scale networking to researchers, five leading NRENs are working together to create an exciting opportunity for the research communities.

Researchers from any discipline are invited to submit a proposal with challenging research questions. The program is open to a wide range of research teams - ranging from novice to expert in the use of information technology - to support their research projects to participate in the competition.

The competition winners will have access to:
  • World-class network infrastructure operated by the NRENs and their partners.
  • Support and advice on end-to-end network connectivity.
  • NREN commitment to an agreed level of network resource provisioning and support during the competition period.
Visit http://www.enlightenyourresearch.net to find details of the competition, its timeline and the procedure for submitting a draft proposal.

Important dates
  • Monday July 1, 2013: (Extended) Submission deadline draft proposal
  • Friday August 2, 2013: Notification 1st round winners:
  • July 30 - September 30, 2013 Consultation round for fine-tuning proposal and technical feasibility
  • Monday October 14, 2013: Submission deadline final proposal
  • December 2013: Announcement of the winners                      
  • Early 2014: Award ceremony and Implementation of services awarded
Global Partners Please email info@removethis.enlightenyourresearch.net if you have any questions.]]>
NBIC Research School for Bioinformatics & Computational Biology http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/nbic-research-school-for-bioinformatics-computational-biology/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/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... 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 http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/ebi-roadshow-on-his-way-from-amsterdam-to-maastricht/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/ebi-roadshow-on-his-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... 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. NBIC is sponsoring some seats in this course. Take a look at the course webpage for full details! ]]> Journal of Web Semantics on Life Science and e-Science http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/journal-of-web-semantics-on-life-science-and-e-science/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/journal-of-web-semantics-on-life-science-and-e-science/ Thu, 16 May 2013 11:55:00 +0200 Special issue Journal of Web Semantics of interest to bioinformatics community Important dates
Paper submission deadline: July 31, 2013
Initial notification of acceptance (approximate): November 2013
Publication in early 2014

Full details http://www.journals.elsevier.com/journal-of-web-semantics/call-for-papers/web-semantics-on-life-science-and-e-science/ 

Bioinformatics in Berlin http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/bioinformatics-in-berlin/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/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... 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 http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/an-inspiring-place/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/an-inspiring-place/ Mon, 29 Apr 2013 12:01:00 +0200 David van Dijk (group Peter Sloot, Amsterdam) visited the Weizmann Institute in Israel in 2010 using a NBIC Travel Grant.The result: a wet lab debut,... 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.]]>
Chris Lauber wins NBIC Young Investigator Award http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/chris-lauber-wins-nbic-young-investigator-award/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/chris-lauber-wins-nbic-young-investigator-award/ Thu, 11 Apr 2013 16:31:00 +0200 Chris Lauber (LUMC) is the winner of the NBIC Young Investigator Award. NBIC yearly presents this award for a young researcher who has significantly... NBIC Young Investigator Award Committee. Chris will be awarded with a cash prize of 2.500 Euro funded by NBIC.  The award ceremony is planned on April 16th at the Netherlands Bioinformatics Conference NBIC2013 in De Werelt in Lunteren (Ede). The ceremony will be followed by an honorary lecture of 20 minutes by Chris Lauber “On the Evolution of Genetic Diversity in RNA virus species”. During his lecture he will summarize the work in his PhD thesis which is devoted to studying the evolution and genetic diversity of several RNA virus families.

Panter released http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/panter-released/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/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... 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 http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/misty-and-inspiring-winter-school/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/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... NBIC PhD school aimed at training and education of bioinformatics and life science researchers.

Congratulations to SIB http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/nbic-congratulates-sib-with-its-15th-anniversary/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/nbic-congratulates-sib-with-its-15th-anniversary/ Fri, 05 Apr 2013 14:49:00 +0200 On March 30, the SIB Swiss Institute of Bioinformatics celebrated its 15th anniversary. NBIC congratulates its colleagues in Switzerland. Since its...
You will find more details in the press release online on the SIB website.

Netherlands hosts first ELIXIR nodes workshop http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/nbic-hosted-elixir-workshop/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/nbic-hosted-elixir-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... 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 http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/nbic-ngs-course-portfolio-complete/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/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.... 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: 
  1. RNAseq Data Analysis, co-organised with LUMC and AMC
  2. Genomic Resequencing: Variant Detection and Interpretation in a Diagnostic Context, co-organised with the Centre for Genome Diagnostics (CGD) and UMC Radboud
  3. De novo assembly from NGS data, co-organised with WUR
  4. Metagenomics Approaches and Data Analysis, co-organised with LUMCUMC 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 http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/recon-2-metabolic-reconstruction-by-consensus/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/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...
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 http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/nbic-young-investigator-award-2013-is-looking-for-nominees/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/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...
  • 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.]]>
    Knowledge is like Love http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/knowledge-is-like-love/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/knowledge-is-like-love/ Tue, 26 Feb 2013 09:32:00 +0100 ..... it multiplies when shared his inaugural speech with the title “Knowledge is like Love..... it multiplies when shared“. In his lecture he described the new field of Biosemantics, and more specifically the methodology of nanopublications. Professor Mons: “Biosemantics is indispensable to understand the complexity of biology. Not because biology is so much more complex than in the past, but simply because we uncover layer after layer of the complexity that was always invisibly there. With the advent of high-throughput technologies in the life sciences we have had a crisis in scientific communication evolving in stealth mode, which is now hitting with full force: an unmanageable amount of relevant data.” With the explosion of information in the biomolecular field, there is a dire need for tools that assist biologists in retrieving, extracting, and relating information and knowledge in the literature and in molecular databases. This will be done in the new field of Biosemantics. Barend Mons was appointed Professor of Biosemantics at the Leiden University Medical Centre, a chair established by NBIC. The Biosemantics group is a structural collaboration between two research groups in Leiden (LUMC) and Rotterdam (EMC) with a focus on in silico knowledge discovery in the life sciences. You can read more in the full text of inaugural lecture Barend Mons.]]> CIMP, BRAF, FOX http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/cimp-braf-fox/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/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... 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<br />]]>
    NBIC2013: Call for Abstracts http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/nbic2013-call-for-abstracts/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/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... 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@removethis.nbic.nl ]]>
    Call for proposals - NWO TOP Grant http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/call-for-proposals-nwo-top-grant/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/call-for-proposals-nwo-top-grant/ Thu, 31 Jan 2013 11:06:00 +0100 The Board of NWO Physical Sciences (GB-EW) invites researchers with an interest in astronomy, computer science and mathematics to submit proposals... NWO website.]]> Bioinformatics in the movies http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/bioinformatics-in-the-movies/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/bioinformatics-in-the-movies/ Fri, 25 Jan 2013 14:29:00 +0100 Bessensap, the yearly “science and press” event organized by NWO offers the opportunity to make a video about your research results, method or... the website of Bessensap (in Dutch).

    SARA & NBIC collaborate in the cloud http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/sara-nbic-collaborate-in-the-cloud/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/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... 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 http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/nbics-flying-course-circus/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/nbics-flying-course-circus/ Mon, 21 Jan 2013 11:31:00 +0100 On January 8th-9th, the first NBIC course of this year was held in Wageningen. 42 (!) participants from the Netherlands and some neighbouring... th-9th, 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 21st till 25th, 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 6th-8th, 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 http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/metagenomics-popular-amongst-high-school-teachers/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/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... 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 http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/biocafe-and-course/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/biocafe-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... 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 http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/changed-acces-to-national-e-infrastructure/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/changed-acces-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... 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 http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/metagenomics-research-of-skin-bacteria-in-public-media/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/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... 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! http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/apply-now-for-funding-for-pcdi-postdoc-retreat-2013/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/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’... the annual Postdoc Retreat, will be held for the 9th 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@removethis.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!]]>
    Inken Wohlers (CWI) defended thesis on protein structure comparison http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/inken-wohlers-cwi-defended-thesis-on-protein-structure-comparison/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/inken-wohlers-cwi-defended-thesis-on-protein-structure-comparison/ Thu, 13 Dec 2012 16:17:00 +0100 CWI researcher Inken Wohlers from the group of Gunnar Klau has developed mathematical models and computer algorithms to compare two protein... the group of Gunnar Klau has developed mathematical models and computer algorithms to compare two protein structures optimally according to given criteria. Because of their complex structure, comparing proteins accurately is difficult. There are many criteria that can be used to compare proteins, leading to a myriad of different computer algorithms and methods that are currently in use. The general frameworks presented in Wohlers' thesis incorporate existing criteria as well as novel criteria and calculate an optimal solution based on that. Exact algorithms for pairwise protein structure alignment
    Inke Wohlers


    Groningen and Chromosome 5 http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/groningen-and-chromosome-5/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/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 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. ]]> Pig genome reveals genes that made domesticated pigs longer http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/pig-genome-reveals-genes-that-made-domesticated-pigs-longer/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/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,... 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 15th 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]]>
    Galaxy on cloud http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/galaxy-on-cloud/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/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... 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@removethis.trac.nbic.nl ]]>
    VarioML: lightweight option for variation data http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/varioml-lightweight-option-for-variation-data/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/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.... 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) http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/duplicates-are-not-the-same-anymore/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/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...
    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 http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/tool-cli-mate/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/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... 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.]]> TNO and Sanquin in NBIC consortium http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/tno-and-sanquin-in-nbic-consortium/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/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... 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 http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/the-power-of-combining/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/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... 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<br />
    Biobank Life Lines in 8 o’clock news http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/biobank-life-lines-in-8-oclock-news/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/biobank-life-lines-in-8-oclock-news/ Fri, 05 Oct 2012 16:04:00 +0200 LifeLines, the biobank and multidimensional cohort study developed by UMC Groningen, got the attention of the 8 o’clock news (NOS journal). Morris... LifeLines, the biobank and multidimensional cohort study developed by UMC Groningen, got the attention of the 8 o’clock news (NOS journal). Morris Swertz, NBIC Faculty and PI of the BioAssist Biobanking taskforce, is involved in this project. LifeLines has become one of the most valuable public, multidimensional cohort studies and biobanks in the world. LifeLines offers a unique data resource to study a broad scope of (epi)genetic, biomedical, environmental and psychosocial  factors in relation to healthy ageing, disease development, and general well-being.]]> 3rd NBIC Pattern Recognition Course: Registration open now! http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/registration-open-for-nbic-phd-course-pattern-recognition-3rd-edition/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/registration-open-for-nbic-phd-course-pattern-recognition-3rd-edition/ Fri, 05 Oct 2012 15:26:00 +0200 On January 21-25 2013, the 3rd edition of the Pattern Recognition course of the NBIC PhD school will take place in Amsterdam. Perry Moerland has... 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 1st and 2nd 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.

    SIB Fellowship program: Call for applications http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/sib-fellowship-program-call-for-applications/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/sib-fellowship-program-call-for-applications/ Tue, 02 Oct 2012 09:47:00 +0200 The SIB Fellowship program aims to train outstanding bioinformatics PhD students as well as promote bioinformatics research for the life sciences.The...
    The SIB Swiss Institute of Bioinformatics, thanks to the generous support and trust of its partners*, is offering the opportunity to a selection of the best students worldwide to carry out their PhD research in one of its groups, all of which are located across Switzerland. The laureates will receive a financial grant for 3 years (extendible for 1 year) and:
    • Become a member of SIB, the leading network of Swiss bioinformatics
    • Have access to professional training courses
    • Be part of the Swiss PhD Training Network in bioinformatics
    • Be introduced to industrial partners during specific events
    • Participate in SIB events such as the yearly SIB Days (scientific conference)
    • Attend the Summer School and Students’ Retreat
    • When in collaboration with industry, have direct hands-on experience within that company
    SIB provides core databases, software and support for the worldwide life science research community. It leads and coordinates the field of bioinformatics in Switzerland by federating bioinformatics research groups from Swiss schools of higher education and research institutes. Currently, SIB consists in 38 research and service groups located in the country’s seven main cities. SIB creates, maintains and distributes world-renowned bioinformatics resources, mainly free of charge, to the national and international life science research community. A few examples include UniProtKB/Swiss-Prot, STRING, SWISS-MODEL, SwissDock and neXtProt.

    Key dates of the SIB Fellowship program:
    • Closing date for applications:15 November 2012
    • Shortlist selection announcement:10 December 2012
    • Interviews: January/February 2013
    • Start of PhD: September 2013
    Further information and application forms for the SIB Fellowship program are available at www.isb-sib.ch/fellowship.

    *) SIB Partners: King Abdullah International Medical Research Center, the Leenaards Foundation, the Swiss Foundation for Excellence and Talents in Biomedical Research, SystemsX.ch and the University of Lausanne.]]>
    Maastricht UMC+ partner in NBIC consortium http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/maastricht-umc-partner-in-nbic-consortium/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/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... 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 http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/dairy-details/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/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...
    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 http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/propseg-determining-copy-number-alternations/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/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... 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]]>
    New tool: PhenoLink http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/new-tool-phenolink/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/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... 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 http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/distiguished-scientist-siezen-visits-usdavis/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/distiguished-scientist-siezen-visits-usdavis/ 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... 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 http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/gunnar-klau-extraordinary-professor-at-vu-university/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/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... 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.

    New tool: GO-Elite http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/new-tool-go-elite/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/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... 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 http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/tight-leash-on-ammonia/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/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...
    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 http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/disagreeing-databases/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/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...
    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 ]]>
    Veni and Vidi http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/veni-and-vidi/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/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...
  • The press release about the Veni grant  
  • The complete list of Veni researchers
  • The press release about the Vidi grant
  • The complete list of Vidi researchers
  • ]]>
    Pump your career http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/pump-your-career/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/pump-your-career/ Mon, 06 Aug 2012 14:27:00 +0200 Talent day for female scientists
    During Pump Your Career female scientists can follow workshops, make acquaintance with role models, obtain information about applying for grants and, of course, network with each other. NWO and LNVH hope to welcome about 500 women. For who?
    • Women working in science (postdocs, and assistant/associate/full professors)
    • (University) policy officers who are involved in policy on women
    When and where?

    11 October 2012 in the Beurs van Berlage, Amsterdam

    On the NWO-website you can find more information and a link to the registration form (in Dutch).]]>
    Individual pathways, similar response http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/individual-pathways-similar-response/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/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,...
    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

    Barend Mons appointed as professor at LUMC on behalf of NBIC http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/barend-mons-appointed-as-professor-at-lumc-on-behalf-of-nbic/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/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...  
    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 http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/insight-into-leukemia-and-bloodtransfusion/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/insight-into-leukemia-and-bloodtransfusion/ Mon, 09 Jul 2012 13:22:00 +0200 NWO Open Competition grant awarded to Anton Feenstra 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.]]>
    A yeast top-model sequenced http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/a-yeast-top-model-sequenced/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/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... 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]]>
    A warm winter with NBICs advanced NGS courses - presenting our LS course overview for 2012 http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/a-warm-winter-with-nbics-advanced-ngs-courses-presenting-our-ls-course-overview-for-2012/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/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... 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): 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@removethis.nbic.nl.]]> Workshop on cross technology http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/workshop-on-cross-technology/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/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 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.]]> What you need to know about licensing http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/what-you-need-to-know-about-licensing/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/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... 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:

    Participants interested in contributing to the programme, please contact Rob Hooft at: rob.hooft@removethis.nbic.nl ]]>
    Prize winners at NBIC 2012 http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/prize-winners-at-nbic-2012/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/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... 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!]]> NBIC is first virtual organisation in SURFconext http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/nbic-is-first-virtual-organisation-in-surfconext/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/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... Surf-website. More information about SURFconext:
    http://www.surfnet.nl/en/Thema/coin/Pages/default.aspx ]]>
    OntoCAT: easy ontology search http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/ontocat-easy-ontology-search/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/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...
    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  

    Dutch Techcentre for Life sciences (DTL) http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/dutch-techcentre-for-life-sciences-dtl/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/dutch-techcentre-for-life-sciences-dtl/ Fri, 18 Nov 2011 11:24:00 +0100 Framework of top-level expertise centres in life science technologies 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.” ]]>
    Online demonstration of OpenPHACTS http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/online-demonstration-of-openphacts/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/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... 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. ]]>
    NBIC Biobank Taskforce develops software for BBRMRI-NL Biobank Catalogue http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/nbic-biobank-taskforce-develops-software-for-bbrmri-nl-biobank-catalogue/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/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.... 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

    Galaxy Community Conference 2011 hosted by NBIC http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/galaxy-community-conference-2011-hosted-by-nbic/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/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... 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 http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/launch-of-open-phacts-consortium/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/launch-of-open-phacts-consortium/ Fri, 27 May 2011 11:49:00 +0200 An information framework to drive drug discovery. NBIC Faculty members from the Leiden University Medical Centre, VU Amsterdam and Maastricht University are in leading positions in this consortium. ]]> Prize winners at NBIC conference http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/prize-winners-at-nbic-conference/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/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... 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 http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/6th-edition-of-the-nbic-conference-attracted-over-200-participants/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/6th-edition-of-the-nbic-conference-attracted-over-200-participants/ Thu, 28 Apr 2011 16:11:00 +0200 More than 200 people visited the sixth edition of the NBIC conference, April 19-20. The plenary programme included keynote lectures, workshops... 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 http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/nbic-young-investigator-award-2011/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/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... Generalized Genetical Genomics -Advanced methods and applications. ]]> Protein structure bioinformaticians unite http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/protein-structure-bioinformaticians-unite/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/protein-structure-bioinformaticians-unite/ Mon, 12 Apr 2010 16:37:00 +0200 Providing a platform for researchers active in protein structure bioinformatics in the Netherlands - that is in short the goal of the brand new... Lude Franke wins NBIC Young Bioinformatician Award 2010 http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/lude-franke-wins-nbic-young-bioinformatician-award-2010/ http://www.nbic.nl/nl/about-nbic/news-press/bioinformatics-news/detail/article/lude-franke-wins-nbic-young-bioinformatician-award-2010/ Mon, 22 Mar 2010 13:32:00 +0100 Dr. Lude Franke of the University of Groningen has won the first edition of the NBIC Young Bioinformatician Award. NBIC yearly presents this award... NBIC conference on March 30th in Lunteren followed by a lecture by the winner.]]>