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This blog collects news, announcements or other information which could be of interest to our ISCB members. We are a group ISCB members who volunteer to populate this blog on a regular basis. In case you want to become an "ISCB-News Reporter" yourself, let us know: contact ISCB
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Monday, April 23, 2012

TWO DAYS LEFT - Abstract Deadline for INB2012

Integrative Network Biology 2012: Network Medicine

The Technical University of Denmark (DTU) is organizing a meeting of world-leaders in systems and network biology.

This symposium will take place in Helsingør, Denmark, on the 11th - 13th of May 2012.

The theme of this conference will be the use of novel experimental and computational approaches to study signalling networks, and how network models can be applied to the study and targeting of complex diseases such as cancer, diabetes and neurological disorders.

Final Poster abstract deadline: 25th April 2012.
-25 Travel fellowships available!
URL: http://www.networkbio.org

Contact Person: Rune Linding (networkbio@cbs.dtu.dk)

Tuesday, April 17, 2012

ISCB Congratulates Bonnie Berger on Being Elected to the American Academy of Arts and Sciences

Congratulations to ISCB member and ISMB 2012 Proceedings Chair Bonnie Berger on being elected as a new member of the American Academy of Arts and Sciences. Dr. Berger, professor of applied math and computer science at the Massachusetts Institute of Technology, is among 220 leaders from academia, business, public affairs, the humanities and the arts elected as new members, the Academy announced on April 17.

One of the most prestigious honorary societies in the United States, the Academy is also a leading center for independent policy research. Members contribute to Academy publications and studies of science and technology policy, energy and global security, social policy and American institutions, the humanities and culture, and education. See full announcement at http://www.amacad.org/news/pressReleaseContent.aspx?i=167.


Contact Person: Stacy Slagor (stacy.slagor@iscb.org)

Monday, April 16, 2012

Applications invited for the role of Bioinformatics Executive Editor

Following a successful eight year term, Alex Bateman will be stepping down from his role of co-Executive Editor of Bioinformatics at the end of 2012. The journal is therefore seeking applications for the role of Executive Editor to lead the journal alongside Alfonso Valencia.

This role is central to Bioinformatics' success and involves working closely with the editorial team, the publisher Oxford University Press, and representatives of the International Society for Computational Biology, of which Bioinformatics is an official journal.

The position is expected to take ~5 hours per week (although variable).

If you would like to express your interest please send your CV to Claire Bird (claire.bird@oup.com) by 14th May 2012. All applications will be acknowledged.

Those who have expressed an interest may subsequently be asked to submit a précis of Bioinformatics and an editorial vision for the journal.

The initial term of office is planned for January 2013 to December 2015, subject to agreement.
URL: http://bioinformatics.oxfordjournals.org/

Contact Person: Claire Bird (claire.bird@oup.com)

Tuesday, April 10, 2012

Meet the Scientists Behind PLoS Computational Biology Meets Wikipedia and Contribute Your Ideas

Meet the Scientists Behind PLoS Computational Biology Meets Wikipedia and Contribute Your Ideas

For the first time, an article published in PLoS Computational Biology, an official journal of ISCB, is also posted on Wikipedia.

During ISMB 2011 last summer, Robert Russell, Professor of Protein Evolution at the University of Heidelberg, discussed the the idea with Philip Bourne, Editor-in-Chief of PLoS Computational Biology and Professor of Pharmacology at UC San Diego. Eight months later, the debut Topic Page was published in the March 2012 issue, "Circular Permuations in Proteins" by ISCB members Spencer Bliven and Andreas Prlić. Topic Pages follow both the journal's and Wikipedia's guidelines and are indexed in PubMed while leading a dual life as evolving documents of record in the wiki community.

"PLoS and Wikipedia are an excellent match," stated Robert Russell. "Open access makes the transfer to Wikipedia relatively simple. We all use Wikipedia, and it will be better as it becomes a reliable starting point by accurately reflecting the technical side of science. This will make it easier to get on with new discoveries if we do not have to linger on scientific facts."

Since Wikipedia's launch in 2001, many have doubted its accuracy. This view is changing as Wikipedia grows to include over 21 million articles in 284 languages. Wikidata, a new project announced by the Wikimedia Foundation and Wikimedia Deutschland, is expected to enhance consistency and quality within Wikipedia articles. Wikidata will be a collaboratively edited database of the world's knowledge. The project is funded by donations from the Allen Institute for Artificial Intelligence, the Gordon and Betty Moore Foundation, and Google.

"I check Wikipedia for all kinds of things, it has good headings and citations, and the information is easy to find," said Spencer Bliven, co-author of the first PLoS Computational Biology Topic Page and a UC San Diego bioinformatics graduate student in Philip Bourne's lab. This is precisely what Spencer and co-author Andreas Prlić, Senior Scientist at the UC San Diego Protein Data Bank, had in mind while writing a computational biology Topic Page. Their goal is to increase public awareness of the field and benefit the scientific community by providing a new reference. They have seen a number of edits to their Topic Page from the nonscientific community. Andreas remarked, "I was surprised by how active Wikipedia members are. They have strong safeguards for accuracy, including both content and form standards."

Before the pair could create their Wikipedia entry, they had to solve the licensing issue. Wikipedia is more restrictive than PLoS. One can transfer an article from PLoS to Wikipedia, but not from Wikipedia to PLoS. By publishing the Topic Page in PLoS, they were then able to move their article to Wikipedia.

Andreas and Spencer noted that there have been few scientists that contribute to Wikipedia. They believe that the PLoS Computational Biology Topic Pages will help change this by rewarding scientists and rewarding Wikipedia. A Topic Page offers important career benefits. Wikipedia's open editing offers the ability to reflect rapid scientific advances and the article is exposed to more readers. The author may add publication in both PLoS Computational Biology and Wikipedia to their curriculum vitae, demonstrating scientific rigor and a commitment to educating the public, which are key to obtaining grant support. In turn, Wikipedia's knowledge base grows, attracting more readers and participants by adding authoritative reference resources in computational biology, one of science's most dynamic fields.

Ensure that computational biology is appropriately represented on Wikipedia, the world's most widely used knowledge source. Please send your ideas for Topic Pages to ploscompbiol@plos.org. The editors of PLoS Computational Biology are looking for topics in computational biology that are of interest to the readership, the broader scientific community, and the public at large, and that are not yet covered, or only poorly so (i.e., exists as a "stub"), in Wikipedia: http://en.wikipedia.org/wiki/Wikipedia:WikiProject_Computational_Biology. The guidelines for Topic Pages are available here: http://www.ploscompbiol.org/attachments/topicpages.pdf.

For more information read the full article at PLoS or take a look at the latest version of the article at Wikipedia. Also read the PLoS Computational Biology editorial announcing the Topic Pages, and check out blog posts by Spencer and Andreas. Come and meet Andreas and Spencer, and engage in more exciting discussions at the 13th Annual Bioinformatics Open Source Conference (BOSC 2012), a Special Interest Group (SIG) of ISMB 2012.

ISMB 2012 Dates:
July 13-14, 2012 BOSC 2012/Special Interest Groups & Tutorials

July 15-17, 2012 Conference

Location: Long Beach, California
Web sites:

URL: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002446

Contact Person: Stacy Slagor (stacy.slagor@iscb.org)

Tuesday, April 3, 2012

Call for Papers: Machine Learning in Genetics and Genomics

Workshop on Machine Learning in Genetics and Genomics [MLGG] co-located with ICML 2012

Location: Edinburgh, Scotland

Important Dates:

Deadline for paper submission: May 7, 2012
Author notification: May 21,2012
Workshop date: July 1,2012

Motivation: The field of computational biology has seen a dramatic growth over the past few years—not only in terms of new available data, but also in new scientific questions, and new challenges for learning and inference. For instance, multiple types of large-scale (often genome-wide) datasets, such as gene expression, genotyping data, whole-genome sequences, protein-protein interactions, and protein abundance measurements, are widely available for multiple model organisms and across multiple conditions, and some of these data types are also available for large patient cohorts. Computational approaches for analyzing and learning from these data are faced with major challenges including scalability, data heterogeneity, missing data and confounding factors to name a few. The goal of this workshop is to present emerging genomics research questions and machine learning techniques that can address some of the challenges on the way to answering fundamental biological questions and refining our understanding of the genesis and progression of diseases.

Topics of Interest: We encourage both contributions describing new research areas and work on established problems using methods that are different from standard approaches. Probabilistic models, sparse regression and classification, semi-supervised approaches, feature selection and other techniques applied to relevant bioinformatics problems would all be appropriate for the workshop. All submissions will be anonymously peer reviewed and will be evaluated on the basis of their technical content. The workshop allows submissions of papers that are under review or have been recently published in a conference or a journal. This is done to encourage presentation of mature research projects that are interesting to the community. The authors should clearly state any overlapping published work at time of submission.

Paper Format: Authors are encouraged to use ICML style file (http://icml.cc/2012/author-instructions/), but are also free to use other styles as long as they use standard font size (11 pt) and margins (1 in). All submissions have to be submitted in PDF format.

Reviewing will be double-blind where each paper will be evaluated on the basis of their technical content and general interest to the audience.

Submission Procedure: Papers should be submitted online: https://www.easychair.org/account/signin.cgi?conf=mlgg2012

Workshop Organizers

Anna Goldenberg, University of Toronto
Pierre Baldi, University of California, Irvine
Sara Mostafavi, Stanford University
Michal Rosen-Zvi, IBM Research, Haifa
URL: http://ai.stanford.edu/~saram/MLGG/MLGG.html

Contact Person: Anna Goldenberg (anna.goldenberg@utoronto.ca)