Welcome to the ISCB Community News Blog

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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Wednesday, December 18, 2013

OMICtools: An informative directory for HTS and array analysis

Dear All,

Current software and database resources for high-throughput sequencing (HTS) and microarray informatics are extremely fragmented. OMICtools (http://omictools.com) is a manually curated central directory that provides an overview of more than 1800 web-accessible tools related to HTS and microarrays.

Regards,

Arnaud

URL: http://omictools.com

Contact Person: Arnaud Desfeux (arnaud.desfeux@gmail.com)

ISCB Congratulates Philip Bourne on Recent NIH Appointment

The International Society for Computational Biology (ISCB) congratulates past president and Fellow, Philip E. Bourne, Ph.D., on being selected as the first permanent Associate Director for Data Science (ADDS) at the National Institutes of Health (NIH). Dr. Bourne will start his new role at NIH in early 2014.

Dr. Bourne received his training as a physical chemist and his Ph.D. in chemistry from The Flinders University in South Australia, taking him to his current position at the University of California, San Diego, where he is the Associate Vice Chancellor for Innovation and Industry Alliances and a Professor in the Department of Pharmacology and Skaggs School of Pharmacy and Pharmaceutical Sciences. In addition, he currently holds the positions of Associate Director of the Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank and Adjunct Professor at the Sanford Burnham Institute.
"The creation of the ADDS position represents the commitment of NIH Director Francis S. Collins to a trans-NIH investment in advancing computational efforts and support in this age of biomedical research as an information science," said Jill P. Mesirov, Associate Director and Chief Informatics Officer at the Broad Institute of MIT and Harvard and member of the ISCB Board of Directors, who served on the NIH Advisory Committee to the Director's Data and Informatics Working Group. "Phil Bourne has long been involved in community efforts around this same goal. We all look forward to working with him and lending him our support as he takes on this critical role."
Dr. Bourne brings to NIH a professional focus on relevant biological and educational outcomes derived from computation and scholarly communication entailing algorithms, text mining, machine learning, metalanguages, biological databases, and visualization applied to problems in systems pharmacology, evolution, cell signaling, apoptosis, immunology and scientific dissemination.

As a founding board member of ISCB and president from 2002 – 2004, Dr. Bourne's vision and leadership has helped establish the Society which has greatly contributed to advancing the worldwide awareness and understanding of the science of computational biology. Dr. Bourne was named to the prestigious group of ISCB Fellows in 2011. Dr. Bourne is the co-founder and founding Editor-in-Chief of the open access journal PLOS Computational Biology. He has published over 300 papers and 5 books, selling over 150,000 copies. Dr. Bourne's professional focus has lended itself to a commitment to furthering the free dissemination of science through new models of publishing and better integration and subsequent dissemination of data and results which as far as possible should be freely available to all.

"ISCB is honored to have Phil's participation over the years," said Burkhard Rost, ISCB President. "We look forward to his future contributions to our fields as the Associate Director for Data Science at NIH."

About ISCB:
The International Society for Computational Biology (ISCB) - www.iscb.org - has been the first and continues to be the only society representing computational biology and bioinformatics on a worldwide scale. ISCB serves a global community of over 3,000 scientists dedicated to advancing the scientific understanding of living systems through computation. We convene the world's experts and future leaders in top conferences, we host the Intelligent Systems in Molecular Biology (ISMB) Conference, and we partner with publications that promote discovery and expand access to computational biology and bioinformatics. We deliver valuable information about training, education, employment, and relevant news. ISCB also provides an influential voice on government and scientific policies that are important to our members and benefit the public.

URL: http://www.iscb.org

Contact Person: Nadine Costello (ncostello@iscb.org)

Tuesday, December 17, 2013

Virtual Workshop on Bioinforma​tics from Bioclues (January 6-11, 2014)

The virtual workshop is aimed at research staff and those in the research community who fall under broader disciplines of Biotechnology.  Bioinformatics and systems biology will be catered to the inte....
URL: http://www.bioclues.org/joomla3/index.php/2-bioclues/11-courses-and-workshops
Contact Person: Prash Suravajhala  (news@bioclues.org)

The virtual workshop is aimed at research staff and those in the research community who fall under broader disciplines of Biotechnology.  Bioinformatics and systems biology will be catered to the interest of researchers. Hands-on sessions, a group discussion and a mini project at the end of the workshop will be done in the form of a group assignment. At the end of the workshop, the scientists are also invited to submit abstracts for presentation on the areas of their interest as talks in concurrent sessions, or as posters. Ample time will be set aside for discussion during the presentation of participants. The topics are then discussed with them for any collaboration for future virtual projects in Bioclues.org and also from the various collaborators of Bioclues across different countries.  This is a 20 hour taught programme interceded by 20 hours of home work plus mini project.

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Networking points:

* Where is the NGS heading towards  bioinformatics research?

* Have we 'coded'  the genome?

* Ten simple steps to do bioinformatics research

* Whither programming?

* How's Modern Biology applied today?

* Does Bioinformatics really help us save time for wet-lab experiments?

More at events page of www.Bioclues.org

Thursday, December 12, 2013

FASEB Urges Congress to Support the Budget Deal Negotiated by Representative Paul Ryan and Senator Patty Murray

Bethesda, MD – The Federation of American Societies for Experimental Biology (FASEB) congratulates Representative Paul Ryan (R-WI) and Senator Patty Murray (D-WA) for reaching a bipartisan budget agreement for fiscal years (FY) 2014 and 2015. "The Ryan-Murray budget agreement represents a breakthrough in the Capitol Hill gridlock, recognizes the importance of providing additional funding for discretionary programs, and provides partial relief from sequestration. We are very grateful to Chairman Ryan and Chairwoman Murray for their hard work and willingness to compromise so that order can be restored to the budget process. We urge Congress to pass the agreement without any additional delay," said FASEB President Margaret K. Offermann, MD, PhD.

Passage of the Ryan-Murray agreement will also allow the Appropriations Committees to complete action on the unfinished FY 2014 spending bills. Failure to approve budgets for the federal research agencies in a timely manner impedes long term planning, disrupts research underway, and creates inefficiencies for institutions and individual scientists. "We sincerely hope that Congress will use the momentum created by the Ryan-Murray agreement to finally address the nation's long-term fiscal problems and adopt a plan that permanently replaces the indiscriminate cuts necessary under sequestration," stated Dr. Offermann. Over the next few weeks FASEB will be engaging the scientific community in reminding Congress about the benefits of providing sustained, predictable funding for the National Institutes of Health, the National Science Foundation, the Department of Energy Office of Science and competitive agricultural research supported by the U.S Department of Agriculture.

FASEB is composed of 27 societies with more than 110,000 members, making it the largest coalition of biomedical research associations in the United States. Our mission is to advance health and welfare by promoting progress and education in biological and biomedical sciences through service to our member societies and collaborative advocacy.


URL: http://www.faseb.org

Contact Person: Lawrence Green (lgreen@faseb.org)

NIH Names Dr. Philip E. Bourne First Associate Director for Data Science

National Institutes of Health Director Francis S. Collins, M.D., Ph.D, announced today the selection of Philip E. Bourne, Ph.D., as the first permanent Associate Director for Data Science (ADDS). Dr. Bourne is expected to join the NIH in early 2014.

"Phil will lead an NIH-wide priority initiative to take better advantage of the exponential growth of biomedical research datasets, which is an area of critical importance to biomedical research. The era of 'Big Data' has arrived, and it is vital that the NIH play a major role in coordinating access to and analysis of many different data types that make up this revolution in biological information," said Collins.

Dr. Bourne comes to the NIH from the University of California San Diego, where he is the Associate Vice Chancellor for Innovation and Industry Alliances of the Office of Research Affairs and a Professor in the Department of Pharmacology and the Skaggs School of Pharmacy and Pharmaceutical Sciences. He also is the Associate Director of the Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank. Dr. Bourne was trained as a physical chemist and obtained his Ph.D. from The Flinders University in South Australia.

Dr. Bourne's professional interests focus on relevant biological and educational outcomes derived from computation and scholarly communication. This work involves the use of algorithms, text mining, machine learning, metalanguages, biological databases, and visualization applied to problems in systems pharmacology, evolution, cell signaling, apoptosis, immunology, and scientific dissemination. He has published over 300 papers and five books. One area to which he is extremely committed is to furthering the free dissemination of science through new models of publishing and better integration and subsequent dissemination of data and results.

Collins added, "I also must recognize and thank Dr. Eric Green, who served as the Acting ADDS since I announced the search to fill this new position. His willingness to take on this challenging role in its inception, and to get the ball rolling on the enormous tasks that accompany this high-priority initiative, is sincerely appreciated. Eric is certain to remain a tremendous source of knowledge and support as Phil continues the NIH's effort to manage 'Big Data'."

About the National Institutes of Health (NIH): NIH, the nation\\\'s medical research agency, includes 27 Institutes and Centers and is a component of the U.S. Department of Health and Human Services. NIH is the primary federal agency conducting and supporting basic, clinical, and translational medical research, and is investigating the causes, treatments, and cures for both common and rare diseases. For more information about NIH and its programs, visit www.nih.gov.

URL: http://www.nih.gov

Contact Person: NIH Office of Communications (nihnmb@mail.nih.gov)

Tuesday, December 10, 2013

DREAM and Sage Bionetworks: Call for Challenge Participation

DREAM8.5 CHALLENGES: The 81/2th DIALOGUE ON REVERSE ENGINEERING ASSESSMENT AND METHODS

Dear Colleague,

The DREAM8.5 Challenges are now open:
https://www.synapse.org/#!Challenges:DREAM8.5

1.The Alzheimer's Disease (AD) Big Data DREAM Challenge #1: Predict the best biomarkers for early AD-related cognitive decline, and the mismatch between high amyloid levels and cognitive decline. Open for registration.

2.The ICGC-TCGA DREAM Somatic Mutation Calling Challenge: Predict cancer-associated mutations from whole-genome sequencing data. Open for participation.

3.The Rheumatoid Arthritis Responder Challenge: Predict which patients will not respond to anti-TNF therapy. Open for registration.

Our DREAM8.5 Challenges, opening here at the tail end of DREAM8, respond to the shared mission that both DREAM and Sage Bionetworks have of using Challenges to accelerate the solutions to problems that matter to patients. The DREAM8.5 Challenges tackle important questions related to cancer, rheumatoid arthritis and Alzheimer's Disease. The traditional DREAM schedule of three-month long Challenges opening in the spring and completing in the fall seems insufficient to process the massive amount of data being generated in different disease areas that can be used in translational research. Help us journey forward as we strive to maintain DREAM's high level of excellence in systems biology while also welcoming new DREAMers to help us innovate and extend the wisdom of the crowds into new arenas of human health.

The 8.5 "Challenge season" has started and will wrap up in early Summer, 2014. Best performers from the 8.5 Challenges will be invited to co-author a Challenge-specific paper for submission to a scientific journal and to present their winning Challenge model at the 2014 DREAM conference (date and location to be determined).

To register for a Challenge, read details and get started, please go to https://www.synapse.org/#!Challenges:DREAM8.5

Sincerely,

Gustavo Stolovitzky and Stephen Friend (co-chairs)
On Behalf of the DREAM8.5 Challenge Organizers

URL: https://www.synapse.org/#!Challenges:DREAM8.5

Contact Person: Gustavo Stolovitzky and Stephen Friend (dream8.5challenges@sagebase.org)