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 12, 2012

In Silico Biology Relaunch and Call for Papers

We are pleased to announce that In Silico Biology is now a journal devoted exclusively to biological systems modeling and simulation, and we invite researchers working in this rapidly growing field to submit original research manuscripts for publication and proposals for reviews and special issues.

In Silico Biology has a new editorial team composed of internationally recognized, leading researchers in quantitative systems and synthetic biology, and aims to become one of the leading journals of research on modeling and simulation in these areas. We offer:

• Immediate online publication upon acceptance
• Rapid editorial decisions
• Traditional in-print publication
• No publication fee
• Low Open Access fee

Open Access fee will be waived for all manuscripts submitted in response to this call

About the Journal
In Silico Biology is a scientific research journal for the advancement of computational models and simulations in studies of complex biological phenomena. We publish peer-reviewed leading-edge biological, biomedical and biotechnological research in which computer-based (i.e., "in silico") modeling and analysis tools are developed and applied to generate new knowledge about biological systems dynamics, their design and control and their evolution.

Studies published in In Silico Biology generally use theoretical modelling and computational analysis to gain quantitative insights into molecular processes regulatory networks, cell physiology and morphology, tissue dynamics and organ systems. Specific areas of interest include signal transduction and information processing, gene expression and gene regulatory networks, metabolism, differentiation and morphogenesis, among others.

Submission of Papers
Authors are requested to submit their manuscript to isb_submissions@iospress.com. For detailed instructions to authors, check our website www.insilicobiologyjournal.com/submission-of-manuscript.

Advisory Board
* Dennis Bray, University of Cambridge, UK
* Roland Eils, University of Heidelberg, Germany
* Hiroaki Kitano, The Systems Biology Institute, Japan
* Michael Mackey, McGill University, Canada
* John Tyson, Virginia Tech, USA
* Hans Westerhoff, University of Manchester, UK

Editor-in-Chief
* Mads Kaern, University of Ottawa, Canada

Email: isb@iospress.com

For the complete Editorial Board, visit our website: www.insilicobiologyjournal.com/editorial-board.

URL: http://www.insilicobiologyjournal.com

Contact Person: Mads Kaern (mkaern@uottawa.ca)

Friday, November 30, 2012

PLOS Comp Bio Launches Software Collection

The PLOS Computational Biology Software collection launches today, 11/29/12 at 2pm PT, gathering together 7 Software articles and poised to publish more. These papers highlight and describe outstanding open source software of exceptional importance that has been proven to provide new biological insights. These papers are free to reuse, redistribute and modify. Another goal of the collection is to bring recognition to the developers of software. As Andreas Prlić and Hilmar Lapp state in the collection's Editorial, "software and those who develop it are generally underrated by the academic system. This is our effort to bring more recognition to them".

PLOS Computational Biology is a peer-reviewed, open-access journal featuring works of exceptional significance that further our understanding of living systems at all scales through the application of computational methods. It is an official journal of the International Society for Computational Biology.

URL: http://www.ploscollections.org/software

Contact Person: Mei Yan Leung (mleung@plos.org)

Thursday, November 29, 2012

20% off books in Computational and Systems Biology from Cambridge!

Click on the link below to get 20% off best-selling, new and forthcoming titles featured in our new catalogue! Just enter ISCB12 at the checkout!
URL: http://issuu.com/cambridge.org.uk/docs/computational_and_systems_biology_catalogue_2012-2

Contact Person: Cambridge University Press (information@cambridge.org)

Wednesday, November 28, 2012

U.S Dept. of Homeland Security Summer Research Team Program for MSIs - Up to $50,000 in Follow-on Funding

The U.S. Department of Homeland Security (DHS) is offering faculty and students at Minority Serving Institutions an opportunity to participate in a ten-week summer research team experience at university-based DHS Centers of Excellence as part of its DHS Summer Research Program for Minority Serving Institutions. At the end of the summer, faculty participants are encouraged to apply for up to $50,000 in follow-on funding to continue the research collaboration at their home academic institutions during the following academic year.

More information, including eligibility guidelines and applications forms, can be found at http://www.orau.gov/dhseducation/faculty/index.html

Faculty from all science, technology, engineering and math (STEM) disciplines are encouraged to apply, including faculty in agricultural sciences, biological/life sciences, computer and information sciences, engineering, mathematics, physical sciences, psychology, and social sciences.

While preference is shown to early career faculty, past participants have included both early and later career faculty. The program provides early career faculty with research and funding opportunities that can be advantageous when applying for tenure. The program also provides later career faculty with opportunities to apply their well-developed skill sets to homeland security research problems of vital interest to the nation.

Past faculty and student participants have enjoyed the summer research experience, conducted meaningful research, and made new professional connections, many of which have led to fruitful and ongoing research collaborations and additional funding opportunities. Below please find profiles of some of our former participants.

Please note the upcoming faculty application deadline of January 7, 2013. The faculty application solicits information about faculty research interests and is designed to take little time to complete.

Completed faculty applications and CVs are forwarded to DHS Centers of interest to the faculty to determine if there is a good fit between faculty research interests and those of the Center. If a good fit can be found, the faculty receives assistance from the Center in developing a research proposal. The faculty then selects one or two students to apply the program as part of the summer research team. Team applications are reviewed by DHS and the Centers, with award winners announced beginning in early March.

Please call or email Program Manager Patti Obenour with any questions about the application process, the summer research experience, the follow-on funding opportunity at the end of the summer, and/or any other aspect of the program. Patti can be reached at (865) 574-1447, DHSed@orau.org or patti.obenour@orau.org.
URL: http://www.orau.gov/dhseducation/faculty/index.html

Contact Person: Patti Obenour (patti.obenour@orau.org)

Wednesday, November 21, 2012

New Translational Medicine and Therapeutics Grants and Fellowships

The PhRMA Foundation is now offering Post Doctoral Fellowships and Research Starter Grants to support scientists in the field of Translational Medicine and Therapeutics (TMT). The purpose of the new PhRMA Foundation program is to promote the development and use of experimental and computational methods in an integrative approach towards clinical needs in diagnosis, treatment and prevention.
The application deadline is February 1, 2013 and funding will begin July 1, 2013. For detailed program information visit the website www.phrmafoundation.org.
URL: http://www.phrmafoundation.org/

Contact Person: Eileen Cannon (ecannon@phrmafoundation.org)

Friday, November 9, 2012

computational biology programs at the Simons Institute in Berkeley

The newly created Simons Institute for the Theory of Computing at UC Berkeley has recently posted the following announcements:

1. Details of programs for academic year 2013-14: http://simons.berkeley.edu
[See in particular the program on \\\"Evolutionary Biology and the Theory of Computing\\\" in Spring 2014: http://simons.berkeley.edu/program_evolution2014.html]

2. Research Fellow positions (application deadline Jan 15, 2013): http://simons.berkeley.edu/fellows.html
[Opportunities for outstanding junior scientists to spend one or two semesters at the Institute in academic year 2013-14, in connection with one of its programs.]

3. Call for program proposals (deadline Dec 15, 2012): http://simons.berkeley.edu/submit_proposal.html
[An invitation for groups of researchers to submit proposals for programs - typically one semester in length - to run at the Institute during Fall 2014, Spring 2015 or Fall 2015.]

Please follow the links above for details.
URL: http://simons.berkeley.edu

Contact Person: Alistair Sinclair (sinclair@eecs.berkeley.edu)

Thursday, November 8, 2012

Novel database PACT-F unifies the knowledge of 100 years of drug research

Novel database unifies the knowledge of 100 years of drug research

More than 5000 scientific publications on clinical trials in humans and preclinical animal trials concerning the bioavailability of drugs have been evaluated.

Emden, Germany (November. 7, 2012) – PharmaInformatic, a German biotech-company has developed a comprehensive knowledge base on bioavailability, which enables the targeted development of new drugs.

Several factors affect the oral bioavailability of drugs. For the first time, these can now be analysed in detail, thanks to a new resource. The new resource, called PACT-F (Preclinical And Clinical Trials Knowledge Base on Bioavailability) unifies the results and experiences of the last hundred years of drug research.

The development of the knowledge base began in 2005. Since then the detailed results and conditions of more than 5000 scientific publications concerning the bioavailability of drugs have been evaluated and integrated into the database.
Each of the 8296 records contains the chemical structure of the investigated drug and up to 17 additional fields, which describe in detail the experimental conditions of the trials (gender, age, health status and number of subjects, genetic differences, the species examined, route of administration, additional medication, method of measurement, drug formulation and further descriptions of the studies).

The knowledge base is a fundamental tool to develop computer models, which can predict the oral bioavailability of new drugs in humans, before clinical trials have to be conducted. This increases the prospects of new drugs and enhances the safety of clinical trials in humans.

Dr Wolfgang Boomgaarden, founder and CEO of PharmaInformatic, says, \\\'Our research is a huge step forward in the area of drug development and will improve the efficiency of clinical trials in humans. Fundamental new findings and conclusions can be derived from the knowledge base which will impact future drug discovery and development.\\\'

Oral bioavailability is one of the most important properties of a drug. If a new drug candidate has low or no oral bioavailability, further drug development will be stopped, because the candidate cannot be absorbed in the body.

Contact:
Dr. Wolfgang Boomgaarden
Email: presse@pharmainformatic.com, Tel: +49 (0)4921-99 33 60
PharmaInformatic Boomgaarden, Friesenstr. 36, 26721 Emden, Germany
http://www.pharmainformatic.com/index.html

http://www.pharmainformatic.com/index.html

Further detailed information:
http://www.pharmainformatic.com/html/pact-f.html

Press release as pdf:
http://www.pharmainformatic.com/html/press_releases.html

Twitter: https://twitter.com/PharmaInformati



URL: http://www.pharmainformatic.com/html/pact-f.html

Contact Person: Wolfgang Boomgaarden (presse@pharmainformatic.com)

Thursday, November 1, 2012

Petition to protect EU science budget

Dear colleagues,

The discussions at the next summit of the European Union heads of state or government, which is scheduled for 22 and 23 November, will be decisive in determining the EU research budget for the next seven years. Several Member States are demanding severe cuts on the total EU budget and research will have to compete with other policy priorities.

This is a time when we, the scientific community, should act together and make our case to protect research funding, including that of the European Research Council (ERC), from cuts. Decisions will be prepared in discussions among politicians at the national level. All of us must look for opportunities to affect these decisions and send a strong signal to the heads of state or government.

An open letter signed by European Nobel laureates has been published in top European newspapers this week. The impact of this letter will be increased if it is followed by a mobilization of the national scientific communities. To keep the momentum going, an online petition has been launched:

http://www.no-cuts-on-research.eu

I would like to ask you to sign it and to encourage all your colleagues to do likewise. Note that in the past, less than 30 000 scientists signed the largest petition for a European scientific cause compared to the hundreds of thousands of signatures on petitions from other groups of society. We must do better than that.

This action is coordinated by the Initiative for Science in Europe (ise@i-se.org; www.initiative-science-europe.org), of which EMBO is a member. Please contact Wolfgang Eppenschwandtner, Executive Coordinator of the ISE if you have any questions or suggestions.

URL: http://www.no-cuts-on-research.eu

Contact Person: Anna Tramontano (anna.tramontano@uniroma1.it)

Monday, October 15, 2012

Innovative Research Projects Aim to Prevent Preterm Birth

October 15, 2012, SEATTLE—Five innovative research projects aiming to prevent premature birth were announced today by the Global Alliance to Prevent Prematurity and Stillbirth (GAPPS), an initiative of Seattle Children's.

The projects are funded through the Preventing Preterm Birth initiative, part of the Bill & Melinda Gates Foundation's Grand Challenges in Global Health. The initiative seeks to discover biological mechanisms that lead to preterm birth and develop innovative strategies for prevention, with particular focus on solutions relevant to low- and middle-income countries, where 99% of the world's infant deaths occur.

More than 320 applications were received from 50 countries, with the top five applications awarded grants of up to $2 million to fund their projects for 2-4 years.

"The volume and quality of applications we received are indicative of the widespread impact of preterm birth and the number of excellent researchers who are ready to tackle this global crisis," said Craig Rubens, MD, PhD, executive director of GAPPS. "These projects will greatly increase our knowledge of what causes premature birth, and hopefully catalyze additional resources and commitments to help make every birth a healthy birth."

Of the 15 million babies born too soon every year, more than 1 million die in infancy, making prematurity the second-leading cause of death for children under 5 worldwide. The burden in low- and middle-income countries is even more concerning, where sophisticated medical care is often not available.

Throughout the world, many premature infants who survive face lifelong health complications such as asthma, cerebral palsy and developmental delays, making prevention paramount.

"Preterm birth is the leading cause of death for newborns, and the second leading cause of death in children before their fifth birthday, taking the lives of 1 million babies every year, affecting rich and poor countries alike," said Gary Darmstadt, Director of Family Health at the Bill & Melinda Gates Foundation. "We urgently need new tools and need to develop new solutions to give every baby a healthy start to life. These new projects are a critical step on the path to preventing preterm birth."

The causes of preterm birth are often unknown and strategies for prevention are limited. The projects funded by the Preventing Preterm Birth initiative will advance discovery of the underlying causes of preterm birth, particularly how infection, inflammation, and immune and hormonal responses disrupt healthy pregnancies. This innovative agenda spans the research spectrum from bench science to field research in low-and middle income countries, all with a focus on translating research to action.

The grant recipients include:

• Dr. David Aronoff of the University of Michigan, with an interdisciplinary team of experts in microbiology, immunology, reproductive biology, and vaccine development, will examine how infections of the female reproductive tract interact with and evade the immune system, resulting in infections of the uterus that cause preterm birth and stillbirth. This work will research potential targets for prevention of invasive infections of the female genital tract, including plans to investigate strains of group B Streptococcus (GBS) from low-income countries for vaccine and drug development.

• Dr. Margaret Hostetter from Cincinnati Children's Hospital Medical Center and her co-investigators will examine how disruption of the normal bacteria and other micro-organisms (the microbiome) of the lower female genital tract may increase risk of preterm birth. These investigations will focus on vaginal Candida infections in pregnancy, inflammation, and regulation of the immune response. Research will be conducted using animal models and laboratory investigations connected to studies of women in low-resource countries. Their goal is to investigate protective and pathogenic mechanisms of preterm birth and identify novel treatment strategies for vaginal fungal infections to prevent preterm birth.

• Dr. Kevin Kain of the University Health Network and the University of Toronto will be investigating malaria infections of the placenta to reveal specific roles of the immune response that lead to preterm birth, low birth weight, and stillbirth. This project will focus on discovering biomarkers to identify at-risk pregnancies as well as new interventions to prevent adverse pregnancy outcomes.

• Dr. Sam Mesiano from Case Western Reserve University School of Medicine and his team will investigate the body's receptors for progestin-based therapies in pregnancy to identify ways to enhance anti-inflammatory processes in all pregnant women and prevent preterm birth. The long-term goal of this project is to develop an inexpensive oral therapy that will reduce the prevalence of preterm birth worldwide.

• Dr. David Olson from the University of Alberta will be working to better understand how infections can cause preterm birth. Using animal models and in later studies of women in low-income countries, he and his team will investigate multiple mediators of inflammation in the uterus early in pregnancy, as well as test new diagnostics and therapeutics that can identify women at risk, modulate the inflammatory response, and prolong pregnancy.

More information about the Preventing Preterm Birth initiative can be found at www.gapps.org/healthybirth.

Grand Challenges in Global Health
Grand Challenges in Global Health is a global partnership first launched by the Gates Foundation and others in 2003 that seeks to engage the world's most creative minds to work on scientific and technological breakthroughs for the most pressing global health and development challenges.

Seattle Children's
Consistently ranked as one of the best children's hospitals in the country by U.S. News & World Report, Children's serves as the pediatric and adolescent academic medical referral center for the largest landmass of any children's hospital in the country (Washington, Alaska, Montana and Idaho). For more than 100 years, Children's has been delivering superior patient care and advancing new treatments through pediatric research. Children's serves as the primary teaching, clinical and research site for the Department of Pediatrics at the University of Washington School of Medicine. The hospital works in partnership with Seattle Children's Research Institute and Seattle Children's Hospital Foundation. Together they are Seattle Children's, known for setting new standards in superior patient care for more than 100 years. For more information visit http://www.seattlechildrens.org.

GAPPS
The Global Alliance to Prevent Prematurity and Stillbirth (GAPPS), an initiative of Seattle Children's, leads a collaborative, global effort to increase awareness and accelerate innovative research and interventions that will improve maternal, newborn and child health outcomes around the world.

URL: http://www.gapps.org/healthybirth

Contact Person: GAPPS (gapps@seattlechildrens.org)

Wednesday, October 10, 2012

miRandola: Extracellular Circulating microRNAs Database

MicroRNAs (miRNAs) are small (approximately 22 nt) noncoding RNAs that play an important role in the regulation of various biological processes through their interaction with cellular messenger RNAs. They are frequently dysregulated in cancer and have shown promise as tissue-based markers for cancer classification and prognostication. Extracellular miRNAs in serum, plasma, saliva, urine and other body fluids have recently been shown to be associated with various pathological conditions including cancer. miRNAs circulate in the bloodstream in a highly stable, extracellular form, thus they may be used as blood-based biomarkers for cancer and other diseases. Circulating miRNAs are protected by encapsulation in membrane-bound vesicles such as exosomes, but the majority of circulating miRNAs in human plasma and serum cofractionate with Argonaute2 (Ago2) protein, rather than with vesicles. In the present work, we performed a comprehensive classification of different extracellular c irculating miRNA types. A direct link to the knowledge base miRò together with the inclusion of datamining facilities allow users to infer possible biological functions of the circulating miRNAs and their connection with the phenotype. To our knowledge miRandola is the first database that provides information about all kind of extracellular miRNAs and we believe that it will constitute a very important resource for researchers.
miRandola is available online at:
http://atlas.dmi.unict.it/mirandola/index.html
URL: http://atlas.dmi.unict.it/mirandola/index.html

Contact Person: Francesco Russo (russo1945@libero.it)

Saturday, September 22, 2012

ENCODE Q&A

An interesting post from Ewan Birney on the ENCODE project.

5 September  2012 - Today sees the embargo lift on the second phase of the ENCODE project and the simultaneous publication of 30 coordinated, open-access papers in Nature, Genome Research andGenome Biology as well as publications in Science, Cell, JBC and others. The Nature publication has a number of firsts: cross-publication topic threads, a dedicated iPad/eBook App and web site and a virtual machine.

This ENCODE event represents five years of dedicated work from over 400 scientists, one of whom is myself, Ewan Birney. I was the lead analysis coordinator for ENCODE for the past five years (and before that had effectively the same role in the pilot project) and for the past 11 months have spent a lot of time working up to this moment. There were countless details to see to for the scientific publications and, later, to explain it all in editorials, commentary, general press features and other exotic things.

Read more...

Thursday, September 20, 2012

Bioclues Innovation, Research and Development (BIRD) Award for Outstanding Contributions in the area of Bioinformatics for the year 2012

Nominations are invited for the second BIRD annual award for outstanding contributions in the area of Functional Genomics and Bioinformatics. This award is meant not just for academicians but also for scientists who have shown exemplary excellence in the field of Bioinformatics. While scientists who have been working for not-for-profit organizations will be given importance, the ones who are working for commercial organizations are no less exception if the research they have carried out has been widely honored and have made longstanding contributions.The inaugural awards kicked off in 2011 with couple of awards given to Dr. Pugalenthi Ganesan and Sarwar Azam.



More details at http://www.bioclues.org
URL: http://www.bioclues.org

Contact Person: Prash Suravajhala (prash@bioclues.org)

Tuesday, September 18, 2012

Bioinformatics Forum for SMEs (Small-Medium sized companies), Barcelona 8-9, Spain, October 2012

SME Bioinformatics Forum, Barcelona, Spain, 8-9 October 2012

The workshop will introduce bioinformatics tools and data resources and will present opportunities for SMEs to use and integrate these resources in order to derive business benefit from the existing and developing infrastructure. There will be a combination of presentations and hands-on tutorials from EMBL-EBI staff and from several of the Spanish organisations and research institutes within INB. The meeting is subsidised by the sponsoring organisations and provides an excellent learning and networking opportunity for SMEs with an interest in publicly available resources in bioinformatics and cheminformatics.

The full list of topics covered are:

Genomic resources: the Ensembl genome browser and the European Nucleotide Archive (ENA)
Proteomics resources: UniProt and InterPro
Chemical resources: the ChEMBL database, ChEBI and MetaboLights
Functional genomics: ArrayExpress and the Gene Expression Atlas
Molecular interactions: the Protein Data Bank (PDB) and ligand information Integration services and EBI Search
EBI Web services

For a detailed agenda and registration information visit:
www.ebi.ac.uk/industry/SME/121008_SME.html

This meeting is co-sponsored by:

EMBL-EBI (www.ebi.ac.uk/industry/SME)
BioCat (www.biocat.cat)
INB (www.inab.org)
GRIB (grib.imim.es)
Psimex (www.psimex.org)


URL: http://www.ebi.ac.uk/industry/SME/121008_SME.html

Contact Person: Dominic Clark, Industry Programme Manager, EMBL-EBI (clark@ebi.ac.uk)

Friday, September 14, 2012

RECOMB2013 Call for Papers

RECOMB2013 Call for Papers:

The 17th International Conference on Research in Computational Molecular Biology (RECOMB 2013) will be held in Beijing, China on April 7-10, 2013. The RECOMB conference series was founded in 1997 to provide a scientific forum for advances in computational biology and applications in molecular biology and medicine. The conference aims at bridging the computational, mathematical, statistical, and biological sciences, and bringing together researchers, professionals, students and industrial practitioners from all over the world for interaction and exchange of new developments in all areas of bioinformatics and computational biology. The conference will feature keynote talks by leading scientists in life sciences in the world, presentations of peer-reviewed high-quality research papers, and poster sessions on latest research progress.


Key dates (Extended Abstract)
Submission opens: September 3, 2012
Submission deadline October 7, 2012
Acceptance notification December 9, 2012
Final version due January 9, 2013

For more details about the conference, please visit

http://bioinfo.au.tsinghua.edu.cn/recomb2013/
URL: http://bioinfo.au.tsinghua.edu.cn/recomb2013/

Contact Person: Fengzhu Sun (fsun@usc.edu)

Monday, September 3, 2012

BioVis 2012 early registration deadline approaching

BioVis 2012 (http://www.biovis.net) promises two full days of exciting talks on cutting-edge research in biological data visualization. The program includes sessions on systems biology and omics data, neurobiology, cellular data and molecular pathways as well as a poster and demo session. A keynote by Christof Koch (Caltech & Allen Brain Institute) and challenges talks by Inna Dubchak (LNBL) and Valerie Daggett (University of Washington) will be among the highlights of the symposium. BioVis 2012 will take place in Seattle, WA on October 14th and 15th as part of the IEEE VisWeek conference.

The early registration deadline is September 7th.
URL: http://www.biovis.net

Contact Person: Nils Gehlenborg (nils@hms.harvard.edu)

Saturday, July 28, 2012

First articles now live on F1000 Research

Faculty of 1000 (F1000) announces the publication of initial articles on F1000 Research, the innovative open access publishing program in biology and medicine. These articles also feature a novel inline data viewer, and a new method of article citation.

F1000 Research's revolutionary vision has been inspiring debate across the scientific community since the beginning of the year. Its informed contribution to the wider discussion about open access publishing has advanced to a new level this week with the publication of its first few articles (please see http://f1000research.com/articles). A call for papers has been issued and further articles will be published on the current consultation site while the publishing model and editorial systems are fine-tuned in preparation for a complete launch later this year.

F1000 Research challenges traditional models by defining new standards for speed, peer review, and the sharing of data. Features include:

* immediate publication
* rapid, formal, and completely open peer review process post-publication
* acceptance of null/negative and replication/refutation findings
* publication and refereeing of datasets as separate data articles

All submissions to F1000 Research will go through a fast initial review by the in-house editorial team who will check to ensure that articles are sensible, intelligible, and written in good English. Each article will then be published with the status 'awaiting peer review'.

On publication, the article will be sent to 3-5 expert referees who will be asked to state, firstly, whether the work seems scientifically sound. These responses will be displayed immediately alongside the article and its citation, and will be updated as new referee responses arrive. Subsequently, referees will be asked to provide more detailed comments and feedback, which will also be displayed with the article. Authors will be encouraged to revise their articles in response to referee comments and each article version will be citable with its own DOI. A novel article citation mechanism, developed with the assistance of the F1000 Research Advisory Panel and the leading indexers, will capture the article version number and referee status.

Once an article receives two positive referee responses, it will be indexed. Scopus, Embase and Google Scholar have agreed to index F1000 Research content immediately, and discussions aimed at putting in place similar arrangements with other major indexers are ongoing. Should an article receive no positive reviews it will not be indexed and will be removed from the default search on the site.

These first articles showcase a novel inline data viewer that has been developed in conjunction with figshare (http://figshare.com). It enables readers to preview data files without having to download them, and allows all readers, even those without suitable viewers for these files, to view the datasets in a 'friendly' format.

All publishing charges are waived for 2012. Moderate author processing charges will be introduced in 2013. More information can be found at: http://f1000research.com.

Commenting on this significant development, Dr Rebecca Lawrence, Publisher for F1000 Research, said: "We are very excited to announce the publication of our first articles on F1000 Research. We would like to thank everyone who has helped us get this far, not least our Advisory Panel and Editorial Board. The discussion continues on Twitter at @F1000Research, and we invite the research community to join us as the project takes shape."

More than 200 of the most eminent names in biology and medicine have joined the international Advisory Panel (see all members at: http://f1000research.com/advisory-panel), and more than 1000 global experts sit on the newly formed Editorial Board (see http://f1000research.com/editorial-board). The project has received great support from the wider scientific community, sparking extensive discussions about the future of scholarly publishing.

To find out more about F1000 Research, please contact Rebecca Lawrence at rebecca.lawrence@f1000.com. For more information, visit http://f1000research.com.

To find out more about Faculty of 1000, please contact Eleanor Howell on +44 (0)20 7631 9129 or email press@f1000.com. For more information, visit http://f1000.com.

*************************

About F1000
Faculty of 1000 is a unique online service that selects, rates, and evaluates important articles based on the opinions of global leaders in biology and medicine. The distinguished international Faculty identify articles that impact their research, providing a rapidly updated, authoritative guide to the life science literature. Find out more at http://f1000.com.

About F1000 Research
F1000 Research is a new fully Open Access publishing program across biology and medicine. It is addressing the major issues afflicting scientific publishing today: timely dissemination of research, peer review, and sharing of data. Diverging from traditional journal publishing, F1000 Research offers immediate publication; open, post-publication peer review; open revisioning of work including ongoing updates; and encourage raw data deposition and publication. In addition, F1000 Research is accepting a broad range of article formats and content types.

URL: http://f1000.com/resources/Announcing_the_start_of_publishing_on_F1000Research_WEB_FINAL.pdf

Contact Person: Eleanor Howell  (press@f1000.com)

Announcing BioGene - a Mobile Web Browser Application

This is to announce BioGene, a free application for mobile web browsers to quickly look up gene function.

The Computational Biology Center at MSKCC (cBio) has recently released BioGene, an application for mobile web browsers, with primary content from NCBI's (US National Center for Biotechnology Information) Entrez search engines.  BioGene allows you to quickly and easily access gene information from Entrez.  For example, should you see a reference to "NCOA3" in a lecture presentation, within moments you can have basic and reasonably up-to-date information about the function of this gene at your fingertips on your smartphone; including a list of references with abstracts (from GeneRIFs).

We are making BioGene available to the public free of charge to promote its use in scientific research and lecture rooms.

You can access BioGene from your iPhone, Android, or Blackberry OS device by visiting the following link: http://cbio.mskcc.org/biogene/
You can also continue to use BioGene for iOS which is available for download via the App Store:
http://bit.ly/14GtrQ

More information at: http://cbio.mskcc.org/tools/biogene/mobile.html

We would appreciate feedback including ideas for additional features to be incorporated in future versions.  To do so, please send email to biogene@cbio.mskcc.org.

BioGene has been fun to develop and has already had a positive impact on our research.

We invite you to explore the function of genes of interest instantly and from anywhere.

Thanks,

Benjamin Gross, Nathan Marks, and Chris Sander

Computational Biology Center
Memorial Sloan Kettering Cancer Center, New York City

Contact Person: Benjamin Gross (grossb@cbio.mskcc.org)

Thursday, July 12, 2012

Hop on the Ion Bus @ ISMB- NGS on wheels!

Join Ion Torrent aboard our mobile sequencing laboratory to see Ion NGS sequencers & Software in action!

See a 1976 Tour bus converted to a molecular biology laboratory- the Ion Bus will be parked atop the Grand Staircase by the Solar Flora at the Long Beach Convention Center.

Check out semiconductor sequencing data on iPads while learning about Torrent Browser plugins. Register for a spot between 12-3pm Sun & Mon http://ow.ly/ccYPI

URL: http://ow.ly/ccYPI

Contact Person: Eric Vennemeyer (eric.vennemeyer@lifetech.com)

Wednesday, July 11, 2012

Prize4Life Launches Prize Competition to Unlock Mysteries of Disease Progression in Amyotrophic Lateral Sclerosis (ALS) Patients

Prize4Life is proud to announce the launch of a computational challenge to predict the future progression of disease in Amyotrophic Lateral Sclerosis (ALS), also known as Lou Gehrig's disease. The DREAM-Phil Bowen ALS Prediction Prize4Life (or ALS Prediction Prize) is being run by Prize4Life in collaboration with The DREAM Project and carries a $25,000 prize for the winning prediction.

The new Prize4Life Challenge is based on the PRO-ACT database, which upon completion will contain clinical data for more than 7,500 ALS patients from completed clinical trials. The entire PRO-ACT database will be available for research purposes by year's end and the ALS Prediction Prize will use a subset of this data. Ultimately, it is expected that the solution resulting from this Challenge will improve disease prediction and lead to more accurate methods of forecasting progression earlier on in the course of the disease.

The ALS Prediction Prize challenge will be run on the InnoCentive prize platform (https://www.innocentive.com/ar/challenge/9933047). Use your computational expertise to win a Prize4Life, register now.

If you are interested in receiving more information as the challenge launches, please send us your name and e-mail at: Prediction@Prize4Life.org. To read more about the prize criteria, visit http://www.prize4life.org/page/prizes/predictionprize.

URL: http://www.prize4life.org/page/prizes/predictionprize

Contact Person: Neta Zach, Ph.D. (Prediction@Prize4Life.org)

Tuesday, July 10, 2012

Casual pizza'n'beer workshop introducing CLC bio'€™s SDK

Join us for a casual workshop introducing how to use our SDK to create plugins - and stay for pizza, beer, and a fun quiz with cool prizes!

Hope to see you this Sunday in Long Beach!
Don’t miss this workshop on Sunday the 15th of July, from 6 to 10 PM. You’ll find the workshop in rooms E-F on the 3rd level at the Hyatt Regency Long Beach. You don’t have to register, but there’s only 50 seats…

The program is centered around four external speakers from Convey (US), Bioformatix (US), NICTA (AUS), and Ablynx (BE), who all have used our API for different kinds of integrations, including examples of commercial plugin development. You can also learn how to distribute your own algorithms and workflows to our customer community through plugins for our platform.
URL: http://www.clcngs.com/2012/07/clc-bio-presents/

Contact Person: Lasse Goerlitz - CLC bio (lgoerlitz@clcbio.com)

Thursday, June 28, 2012

Abstract Deadline Approaching for Wellcome Trust/ CSHL Genome Informatics conference

The abstract deadline is approaching for the fifth CSHL/Wellcome Trust Scientific Conference on Genome Informatics, which will focus on large-scale genome informatics.

Abstract submission is strongly encouraged as several talks for each session will be selected from abstracts. Abstracts must be submitted by 12 July. Full details can be found on our website.

Scientific organisers
Inanc Birol (BC Cancer Agency, Canada)
Jennifer Harrow (Wellcome Trust Sanger Institute, UK)
James Taylor (Emory University, USA)

Scientific sessions
Population and Personal Genomics
Transcriptomics, Alternative Splicing and Gene Predictions
Epigenomics and Non-Coding Genome
Databases, Data Mining, Visualization and Curation
Sequencing Pipelines and Assembly
Comparative and Evolutionary Genomics

Keynote speakers
Pavel Pevzner (University of California, San Diego, USA)
Chris Ponting (Oxford University, UK)

Invited speakers
Mathieu Blanchette (McGill University, USA)
Martha Bulyk (Harvard University, UK)
Inna Dubchak (Genomics Division, DOE Joint Genome Institute, USA)
Anne Ferguson-Smith (University of Cambridge, UK)
Kelly Frazer (University of California, San Diego, USA)
William McCombie (Cold Spring Harbor Laboratory, USA)
Elaine Ostrander (National Institutes of Health, USA)
Benedict Paten (University of California, San Diego, USA)
Janna Saarela (University of Helsinki, Finland)
Andrew Smith (University of Southern California, USA)
Andrew Su (Scripps Research Institute, USA)
Thomas Wu (Genentech, Inc., USA)

For more information: https://registration.hinxton.wellcome.ac.uk/display_info.asp?id=296
URL: http://registration.hinxton.wellcome.ac.uk/display_info.asp?id=296

Contact Person: Treasa Creavin (treasa.creavin@hinxton.wellcome.ac.uk)

Wednesday, June 27, 2012

Report Addresses Challenges in Implementing New Diagnostic Tests Where They Are Needed Most

Easy-to-use, inexpensive tests to diagnose infectious diseases are urgently needed in resource-limited countries. A new report based on an American Academy of Microbiology colloquium, "Bringing the Lab to the Patient: Developing Point-of-Care Diagnostics for Resource Limited Settings," describes the challenges inherent in bringing new medical devices and technologies to the areas of the world where they are needed most.

A PDF of the free report can be found online at: http://bit.ly/Lgk8Zf

URL: http://bit.ly/Lgk8Zf

Contact Person: Leah Gibbons (lgibbons@asmusa.org)

Thursday, June 21, 2012

Call for Papers: PSB 2013 Epigenomics Session

Dear Colleague,

We would like to cordially invite you to submit a full-length paper to the Epigenomics Session at the eighteenth Pacific Symposium on Biocomputing (PSB). This session will focus on computational methods for the analysis and interpretation of various types of epigenomic data. The main conference will be held January 3-7, 2013 at the Fairmont Orchid on the Big Island of Hawaii.
Key dates

Paper submission deadline: July 31, 2012 midnight PDT
Notification of acceptance/rejection: September 10, 2012
Camera-ready final paper deadline: October 1, 2012 midnight PDT

Invited speakers

Michael Snyder, Ascherman Professor and Chair of Genetics and the Director of the Center of Genomics and Personalized Medicine at Stanford University, USA.
Frank Pugh, Willaman Chair in Molecular Biology in the department of Biochemistry and Molecular Biology at Penn State University, USA.

Scope
Scientists have known for a long time that the sequence of nucleotides that comprise the genome is not sufficient to explain the heritability of traits from one generation to the next, nor is that sequence sufficient to drive the myriad functions of a living cell. Recently, however, catalyzed by the rapid acquisition of a wide variety of genome-scale data sets from projects such as ENCODE, modENCODE, and the Epigenomics Roadmap, scientists have begun to recognize just how much information is encoded beyond the primary DNA sequence. Accordingly, many of the central questions facing biology today concern the interpretation and integration of epigenomic data with our existing knowledge of the molecular pathways within the cell, including DNA, RNA, proteins, and metabolites.
Topics

Computational methods for interpreting epigenomic data such as:
Histone modifications,
DNA methylation,
Nucleosome positioning,
Chromatin structure and accessibility,
DNA-DNA interactions
Computational models of chromatin structure on a genome-wide scale.
Methods for integrating heterogeneous epigenomic data.
Methods for relating genome structure and function.
Application of existing methods to novel epigenomic datasets.
Detailed analysis of well-studied loci with broader methodological or biological insights.

Organizing committee

Alexander J. Hartemink, Alexander F. Hehmeyer Associate Professor of Computer Science, Statistical Science, and Biology at Duke University
Manolis Kellis, Associate Professor, Department of Computer Science and Engineering, Massachusetts Institute of Technology
William Stafford Noble, Professor, Department of Genome Sciences and Department of Computer Science and Engineering, University of Washington
Zhiping Weng, Professor, Program in Bioinformatics and Integrative Biology and Department of Molecular Pharmacology, University of Massachusetts Medical School
Ferhat Ay, Postdoctoral Fellow, Department of Genome Sciences, University of Washington

Submission guidelines
The scientific core of the conference consists of rigorously peer-reviewed full-length papers reporting on original work. Accepted papers will be published in an archival proceedings volume (fully indexed in PubMed), and a number of the papers will be selected for presentation during the conference.
Please see the PSB paper format template and instructions at http://psb.stanford.edu/psb-online/psb-submit.

Further information is provided at the conference website:
http://noble.gs.washington.edu/proj/epigenomics2013/

URL: http://noble.gs.washington.edu/proj/epigenomics2013/

Contact Person: Ferhat Ay (ferhatay@uw.edu)

Monday, June 18, 2012

ISCB Congratulates Janet Thornton on being made a Dame Commander of the Order of the British Empire

The European Bioinformatics Institute (EMBL-EBI) announced late last week that EBI Director Janet Thornton was made a Dame Commander of the Order of the British Empire.

Professor Dame Thornton is a past winner of the ISCB Accomplishment by a Senior Scientist Award, and in 2009 was made an ISCB Fellow.

Please join ISCB in congratulating her on this great honor in being recognized for the significant contributions she has made to our field of computational biology and bioinformatics.
URL: http://bit.ly/KeUoYj

Contact Person: BJ Morrison McKay (bj@iscb.org)

Tuesday, May 29, 2012

New Biorepository Opens to Help Uncover Mysteries of Pregnancy and Childbirth

The Global Alliance to Prevent Prematurity and Stillbirth (GAPPS), an initiative of Seattle Children's, has launched an internationally accessible biorepository to advance innovative research of both normal and abnormal pregnancies, including how pregnancy affects maternal and child health after delivery. Named the GAPPS Repository, it is the only collection of specimens linked to detailed information from pregnant women that is available to a wide range of researchers.

High quality specimens such as maternal blood and urine, cervical vaginal swabs, placenta tissue, and cord blood, are collected from the first trimester through the postpartum period. The specimens are paired with information about the mothers' preconception, current pregnancy, environmental exposures, medical and reproductive history, mental health, nutritional intake, and behaviors.

"While pregnancy specimen biobanks have been developed before, this is the first time that specimens paired with information about mothers and their pregnancies have been made widely accessible," said Craig Rubens, MD, PhD, executive director of GAPPS. "The GAPPS Repository provides a critical resource for maternal and child health researchers to study multiple factors at different points throughout pregnancy."

The GAPPS Repository was created to:
• Help researchers discover biomarkers and create screening tools to identify women and babies at risk for preterm birth and stillbirth
• Translate scientific discoveries into promising diagnostic, treatment and prevention strategies
• Conduct studies focused on poor birth outcomes and the fetal origin of adult diseases, with the potential for determining causes and developing cures for both acute and chronic diseases

"Many adult health problems can be traced to fetal development," Dr. Rubens said. "With these specimens, researchers can begin to understand what causes adverse pregnancy outcomes, and develop novel interventions to prevent them.\\\\\\\"

The GAPPS Repository currently has more than 9,000 individual specimens available to scientists, with 800-900 specimens being added each month. The collection includes contributions from women representing a range of racial, ethnic, regional, and socioeconomic backgrounds.

GAPPS Repository lab scientists oversee each step in the sample collection and storage process in order to build and maintain the highest quality specimen bank. In addition, GAPPS upholds strict standards of privacy and confidentiality, with materials identified only by number and participant names kept in protected files at each collection site.

"My first pregnancy resulted in a premature birth, and when I heard about the GAPPS Repository during my second pregnancy, I wanted to help advance the pregnancy and childbirth research that is happening," said Leslie Tuomisto, a GAPPS Repository donor. "Donating took very little effort; it was just providing samples that were already being taken anyway."

To request specimens, scientists can visit http://www.gapps.org/repository or email gappsrepository@seattlechildrens.org.

URL: http://www.gapps.org/repository

Contact Person: Global Alliance to Prevent Prematurity and Stillbirth (gappsrepository@seattlechildrens.org)

Friday, May 11, 2012

ISCB Congratulates Rolf Apweiler and Ewan Birney on Their Election as EMBO Members

Congratulations to ISCB member Rolf Apweiler and 2005 Overton Prize winner Ewan Birney on being elected to membership of the European Molecular Biology Organization (EMBO). Apweiler and Birney, joint associate directors of the European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), are among 55 life scientists from Europe and around the world recognized by EMBO for their excellence in research, EMBO announced on May 9.

EMBO is an organization of more than 1500 leading life scientist members that fosters new generations of researchers to produce world-class scientific results. See full announcement at http://www.embo.org/news-a-media-centre/press-releases/embo-welcomes-55-leading-life-scientists-as-members.html

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

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.

URL:

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:
http://www.open-bio.org/wiki/BOSC_2012
http://www.iscb.org/ismb2012


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)

Saturday, March 31, 2012

CS2Bio'12 Final Call for Papers & Extended Deadline

=================================================================

Final Call for Papers & Extended Deadline (April 12)
=================================================================

CS2Bio'12
3rd International Workshop on Interactions
between Computer Science and Biology

Affiliated to DisCoTec'12

16th of June 2012
Stockholm, Sweden

http://cs2bio12.di.unipmn.it/

=================================================================

*** IMPORTANT DATES ***

- Submission deadline (EXTENDED) : April 12, 2012
- Notification to authors: May 16, 2012
- Workshop: June 16, 2012

=================================================================

The aim of this workshop is to gather researchers in formal methods
that are interested in the convergence of Computer Science, Biology
and life sciences. In particular, we solicit contribution of original
results that address both theoretical aspects of modeling and applied
work on the comprehension of biological behavior. We encourage
presentations of interdisciplinary work conducted by teams composed of
both life and computer scientists.

Papers selected for presentation at CS2Bio should either present the
modeling a specific biological phenomenon using formal techniques, or
a modeling, simulation, testing or verification approach in computer
science that leads to a novel and promising application to a range of
biological or medical systems. In the latter case, some emphasis on
the scope and scalability of the approach will be required. The
workshop intends to attract researchers interested in models,
verification, tools, and programming primitives concerning the complex
interactions encountered.

*** SCOPE ***

In general, topics of interest include, but are not limited to:

Formal Biological Modeling:
-- Formal methods for the representation of biological systems and
their dynamics (rewrite systems, process calculi, graph grammars,
hybrid systems, etc.);
-- Theoretical links and comparison between different formal
models for the modeling of biological processes;
-- Quantitative (probabilistic, timed, stochastic, etc.) languages
and calculi.
-- Spatial (geometrical, topological) languages and calculi.

Formal Testing and Validation of Biological Properties:
-- Prediction of biological behavior from incomplete information;
-- Model checking, abstract interpretation, type systems, etc.

Tools and Simulation
-- Modeling, analysis and simulation tools for systems biology;
-- Emergence of properties in complex biological and medical systems;
-- Tools for parallel, distributed, and multi-resolution simulation
methods;
-- Detailed biological case-studies.

*** DISSEMINATION***

Proceedings of the workshop will be published in ENTCS. Quality
permitting, a special issue of a Computer Science journal is planned.

*** SUBMISSION GUIDELINES ***

Papers must report previously unpublished work and not be submitted
concurrently to another conference with refereed proceedings.
Authors should submit their papers via EasyChair
(http://www.easychair.org/conferences/?conf=cs2bio12). Papers
should take the form of a pdf file in ENTCS style and should not
exceed 12 pages. If necessary, detailed proofs or other additional
material can be added in an appendix (referees might review it at
their discretion). We also encourage the submission of short papers,
limited to 7 pages, presenting new tools or platforms for the
modelling of biological systems.


=================================================================


*** INVITED SPEAKERS ***

- Jane Hillston (Lab for Foundation of Computer Science -
Edinburgh, UK)
- Gianluigi Zavattaro (Department of Computer Science -
University of Bologna, IT)


*** PROGRAM COMMITTEE ***
- Luca Cardelli
- Gabriel Ciobanu
- Francesca Cordero
- Erik de Vink (Co-chair)
- Francois Fages
- Jerome Feret
- Jasmin Fisher
- Paola Giannini (Co-chair)
- Jane Hillston
- Jean Krivine
- Giancarlo Mauri
- Emanuela Merelli
- Paolo Milazzo
- Gethin Norman
- Ion Petre
- David Safranek
- Angelo Troina
- Adelinde Uhrmacher
- Verena Wolf

*** STEERING COMMITTEE ***

- Erik de Vink
- Paola Giannini
- Jean Krivine
- Angelo Troina



URL: http://cs2bio12.di.unipmn.it/

Contact Person: Paola Giannini (giannini@di.unipmn.it)

Monday, March 26, 2012

ISCB congratulates Dr. Atul Butte on being named a Top Ten Biotech Techie by FierceBiotech IT.

FierceBiotech IT has named ISCB member Dr. Atul Butte as a Top 10 Biotech Techie. See full announcement at: http://www.fiercebiotechit.com/special-reports/dr-atul-butte-fierce-s-top-10-biotech-techies.
URL: http://www.fiercebiotechit.com/special-reports/dr-atul-butte-fierce-s-top-10-biotech-techies

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

Monday, February 27, 2012

Call for Submissions: FASEB BioArt Competition

The Federation of American Societies for Experimental Biology (FASEB) is seeking the submission of captivating, high resolution images that represent the cutting edge of 21st century biomedical research. Each day scientific investigators produce thousands of images during the course of their research. FASEB believes that these images are an important, yet underutilized, resource in the community's effort to engage and educate the general public and policy makers about biomedical research.

Winning images will be featured on the FASEB and National Institutes of Health websites and displayed before Members of Congress at FASEB's centennial celebration.

The submission deadline is March 25, 2012. To find out more about the competition, please go to www.faseb.org/BioArt or see the attached flyer.
URL: http://www.faseb.org/BioArt

Contact Person: Public Affairs Office (opa@faseb.org)

Thursday, February 16, 2012

Encyclopedia of Life Education Innovation Challenge

The Encyclopedia of Life (EOL) is pleased to announce the EOL Education Innovation Challenge, an international competition to foster development of educational software tools, services, or games using EOL content. The challenge is to use EOL content and services to create an engaging and educational application that will promote global learning activities focused on discovering and understanding the living world.

The competition will award funding to the most scalable and innovative applications. Target audiences can include the general public, citizen scientists and learners of all ages in both formal and informal settings. The platform can be the web and/or mobile devices.

The Challenge is a two-stage process. In Stage 1, applicants submit a product idea that includes an overview of the concept. Applicants who are selected to continue to Stage 2 will be asked to submit a development plan and budget required to complete a working product. One or more prizes will be awarded to successful Stage 2 proposals.

The prize total is $50,000 USD, which may be divided among one or more successful applicants. In addition to the cash award, the winners\\\' work will be promoted and distributed by EOL. 



For more information about deadlines, guidelines and eligibility, please visit the EOL Innovation Challenge page (http://eol.org/info/290?language=en).

The Encyclopedia of Life (EOL) operates as an ongoing collaboration of individuals and organizations who share the vision to provide global access to knowledge about life on Earth. EOL is supported by founding sponsors the John D. and Catherine T. MacArthur Foundation and the Alfred P. Sloan Foundation. Additional support comes from EOL member institutions and donations from around the world.

URL: http://eol.org/info/290?language=en

Contact Person: Tracy Barbaro (tbarbaro@eol.org)

Monday, February 13, 2012

Announcement of CS2Bio'12

==========================================================

Call for papers
CS2Bio'12
3rd International Workshop on Interactions
between Computer Science and Biology

Affiliated to DisCoTec'12

16th of June 2012
Stockholm, Sweden

http://cs2bio12.di.unipmn.it/

===========================================================

The aim of this workshop is to gather researchers in formal methods
that are interested in the convergence of Computer Science, Biology
and life sciences. In particular, we solicit contribution of original
results that address both theoretical aspects of modeling and applied
work on the comprehension of biological behavior. We encourage
presentations of interdisciplinary work conducted by teams composed of
both life and computer scientists.

Papers selected for presentation at CS2Bio should either present the
modeling a specific biological phenomenon using formal techniques, or
a modeling, simulation, testing or verification approach in computer
science that leads to a novel and promising application to a range of
biological or medical systems. In the latter case, some emphasis on
the scope and scalability of the approach will be required. The
workshop intends to attract researchers interested in models,
verification, tools, and programming primitives concerning the complex
interactions encountered.

*** SCOPE ***

In general, topics of interest include, but are not limited to:

Formal Biological Modeling:
-- Formal methods for the representation of biological systems and
their dynamics (rewrite systems, process calculi, graph grammars,
hybrid systems, etc.);
-- Theoretical links and comparison between different formal
models for the modeling of biological processes;
-- Quantitative (probabilistic, timed, stochastic, etc.) languages
and calculi.
-- Spatial (geometrical, topological) languages and calculi.

Formal Testing and Validation of Biological Properties:
-- Prediction of biological behavior from incomplete information;
-- Model checking, abstract interpretation, type systems, etc.

Tools and Simulation
-- Modeling, analysis and simulation tools for systems biology;
-- Emergence of properties in complex biological and medical systems;
-- Tools for parallel, distributed, and multi-resolution simulation
methods;
-- Detailed biological case-studies.

*** Invited Speakers (to be completed) ***

- Jane Hillston (University of Edinburgh)

*** DISSEMINATION***

Proceedings of the workshop will be published in ENTCS. Quality
permitting, a special issue of a Computer Science journal is planned.

*** SUBMISSION GUIDELINES ***

Papers must report previously unpublished work and not be submitted
concurrently to another conference with refereed proceedings.
Authors should submit their papers via EasyChair
(http://www.easychair.org/conferences/?conf=cs2bio12). Papers
should take the form of a pdf file in ENTCS style and should not
exceed 12 pages. If necessary, detailed proofs or other additional
material can be added in an appendix (referees might review it at
their discretion). We also encourage the submission of short papers,
limited to 7 pages, presenting new tools or platforms for the
modelling of biological systems.

*** IMPORTANT DATES ***

- Submission deadline: April 2, 2012
- Notification to authors: May 16, 2012
- Workshop: June 16, 2012

*** STEERING COMMITTEE ***

- Erik de Vink
- Paola Giannini
- Jean Krivine
- Angelo Troina

*** PROGRAM COMMITTEE ***

- Luca Cardelli
- Gabriel Ciobanu
- Francesca Cordero
- Erik de Vink (Co-chair)
- Francois Fages
- Jerome Feret
- Jasmin Fisher
- Paola Giannini (Co-chair)
- Jane Hillston
- Jean Krivine
- Giancarlo Mauri
- Emanuela Merelli
- Paolo Milazzo
- Gethin Norman
- Ion Petre
- David Safranek
- Angelo Troina
- Adelinde Uhrmacher
- Verena Wolf
URL: http://cs2bio12.di.unipmn.it/

Contact Person: Angelo Troina (troina@di.unito.it)

Thursday, February 9, 2012

[BIBM 2012] Call for Workshop Proposals

The Program Committees of the 2012 IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM 2012) invite proposals for Workshops. Workshops selected will hold a central position within the larger Conference, which will bring together top academic and industrial researchers from all over the world to exchange cutting edge research ideas in bioinformatics and biomedicine. Within these fields, workshops at BIBM form crucial focal points for emerging communities and forums for the examination of new results.

In addition to bringing people together, papers submitted to BIBM 2012 workshops, and selected by workshop program committees, will be included in the Workshop Proceedings. This mechanism enables research communities to publish their new findings in a focused context and to jointly publicize their results to the wider community.

Workshop organizers will be responsible for advertising the workshop, forming program committees, reviewing and selecting workshop papers, and guaranteeing a high quality worthy of the prestige and breadth of the Conference. Other workshop activities can include poster sessions and inviting keynote speakers. Papers accepted for the Workshop Proceedings will be published by the IEEE Computer Society Press and made available at the Conference.

The workshop organizers will also have the discretion of editing selected papers (after their expansion and revision) into books or special journal issues. Workshops should cover at least a single session (6 regular papers). The workshop organizers should ensure registration and presence of authors of accepted papers.



Workshop Topics:

Each workshop subject will focus on new research challenges and initiatives in Bioinformatics and Biomedicine. The workshops should provide an informal and vibrant forum for researchers and industry practitioners to share their research results and practical development experiences in these two fields. Workshop topics may be narrow, e.g., "reverse-engineering" of gene regulatory networks from experimental data, computational approaches to drug discovery, mathematical modeling of signaling pathways, analysis of the next-generation sequencing data, oscillations and synchronization of biological rhythms; or broad, e.g., computational proteomics, in-silico diagnosis and prognosis, data mining and machine learning algorithms for biomedical applications, application of network research to biology etc. Prospective workshop organizers are encouraged to contact workshop chairs for feedback.



Important Dates

April 20, 2012: Workshop proposal submission due: A workshop proposal is sent by e-mail to any of the Workshop Chairs

April 31, 2012: Notification to workshop proposers

May 30, 2012: Each workshop organizer sends out Call for Workshops Papers



For further information on preparing and submitting a workshop proposal, please visit the following website or contact the Workshop Chairs.

http://www.ischool.drexel.edu/ieeebibm/bibm12/workshop.htm

Workshop Chairs:

Prof. Brian Y. Chen
Lehigh University
chen (at) lehigh.edu

Prof. Kun Huang
The Ohio State University Medical Center
kun.huang (at) osumc.edu

Prof. Bernard Offmann,
Université de La Réunion France,
bernard.offmann (at) univ-reunion.fr
URL: http://www.ischool.drexel.edu/ieeebibm/bibm12

Contact Person: Brian Y. Chen (____see_email_in_workshop_information_above_____@a.com)

Tuesday, February 7, 2012

Genome Sequencing and Annotation Symposium

The UF Computational Biology Initiative is pleased to announce

Genome Sequencing and Annotation.

a two-day symposium focusing on the computational and analytical
challenges involved in the sequencing and annotation of genomes, and
on their impact on biological and biomedical research. The symposium
will take place on April 12th and 13th 2012, in the main auditorium of
the Cancer Genetics Research Center at the University of Florida.

Speakers:

John Quackenbush, Harvard School of Public Health (keynote)
Srinivas Aluru, Iowa State University
Steven Jones, University of British Columbia
Matias Kirst, University of Florida
Ian Korf, UC Davis Genome Center
Eric Lyons, University of Arizona
Leonid Moroz, University of Florida


See the following website for more information on the symposium and to
register for it:

http://compbio.ufl.edu/symposium/

Note that registration is required, but attendance is free.
URL: http://compbio.ufl.edu/symposium/

Contact Person: Alberto Riva (ariva@ufl.edu)

Announcing the 2012 Life Sciences and Healthcare Venture Summit

A select group of 50 Top Innovators from the will be chosen to present their breakthrough investment opportunities to VCs, investors and strategic partners at the summit. To be considered for inclusion in this group, read the submission requirements in the "Call for Top Innovators" section below.

Join leading industry influencers, VCs, Corporate VCs, angel investors, investment bankers, incubator managers and CEOs of some of the most promising early stage and emerging growth companies at the 2012 Life Sciences & Healthcare Venture Summit being held on March 28th at Digital Sandbox in New York City.

This exclusive Venture Summit will bring together over 350 Top-tier Venture Capitalists, Private Investors, Corporate VCs, CEOs of cutting edge startups and Strategic Service Firms and will feature more than 40 leading VCs on interactive panels; Presentations by 50 Top Innovators; and high-level networking opportunities.
A partial list of VCs confirmed to speak includes:

Isaac Ciechanover Partner Kleiner Perkins Caufield & Byers, David Coats Managing Director Correlation Ventures, Suzette Dutch Managing Partner Triathlon Medical Ventures, Bill Harrington Managing Partner Osage Ventures, Bosun Hau Investment Partner MVM Life Science Partners, Mike Kaplan Founder and Managing Director Altos Health Management, Daniel Kosoy Partner Athenian Venture Partners, Noah Kroloff Partner NGN Capital, Al Lauritano Director / Technology Licensing & Collaboration BD Technologies, Corey McCann Principal MPM Capital, Ilya Nykin Managing Director Prolog Partners, Heather Preston Managing Director TPG Biotech, Brian Underdown Managing Director Lumira Capital, Robert Weisskoff Partner Fidelity Biosciences, Tom Weldon Chairman, Managing Director Accuitive Medical Ventures,and many more.


CALL FOR TOP INNOVATORS!
Get Noticed > Get Funded > Grow Faster
A select group of 50 Top Innovators from the Biotech, Pharma, Healthcare, Healthcare IT, Medical Devices, Diagnostics, and Life Science sectors will be chosen to present their breakthrough investment opportunities to an exclusive audience of Venture Capitalists, Private Investors, Investment Bankers, Corporate Investors, and Strategic Partners.

Advance applicants for presenting slots are eligible to be chosen during the early-bird selection process ending on February 22, 2012.

Apply to Present:
To be considered for one of the Top Innovator slots, please e-mail iwant2present@youngstartup.com for an application.

To Nominate a Company:
To nominate a company please forward: company name, main contact at firm, contact details and why you think they should present to nominations@youngstartup.com.

URL: http://www.youngstartup.com

Contact Person: Jennifer Dell (jennifer@youngstartup.com)

Monday, January 30, 2012

CFP: 2012 IEEE International Conference on Bioinformatics and Biomedicine (BIBM12)

2012 IEEE International Conference on Bioinformatics and Biomedicine (BIBM12)

http://www.ischool.drexel.edu/ieeebibm/bibm12/
October 4-7, 2012, Philadelphia, PA, USA,


The IEEE International Conference on Bioinformatics and Biomedicine
(BIBM) has established itself as the premier research conference in
bioinformatics and biomedicine. IEEE BIBM 2012 provides a leading
forum for disseminating the latest research in bioinformatics and
health informatics. It brings together academic and industrial
scientists from computer science, biology, chemistry, medicine,
mathematics and statistics.

We solicit high-quality original research papers (including
significant work-in-progress) in any aspect of bioinformatics and
biomedicine. New computational techniques and methods in machine
learning; data mining; text analysis; pattern recognition; knowledge
representation; databases; data modeling; combinatorics; stochastic
modeling; string and graph algorithms; linguistic methods; robotics;
constraint satisfaction; data visualization; parallel computation;
data integration; modeling and simulation and heir application in life
science domain are especially encouraged Relevant topics include but
are not limited to:

1. Genomics and Molecular Structure, Function and Evolution
a. Next-Gen Sequencing and Metagenomics
b. Evolution, Phylogeny, Comparative  Genomics
c. SNPs and haplotype analysis, GWAS
d. Protein/RNA Structure, Function and Interactions

2. Computational Systems Biology
a. Transcriptomics - Microarray Data Analysis
b. Gene Regulation, Alternative Splicing, Network/Pathway Analysis
c. Proteomics, PTMs, Metabolomics
d. Epigenomics, non-coding RNA analysis, DNA methylation analysis

3. Medical Informatics and Translational Bioinformatics
a. Biomedical Intelligence, Clinical Data Analysis, and Electronic
Health Record
b. Biomedical Signal/Image Analysis
c. Genome-Phenome Analysis
d. Biomarker Discovery

4. Cross-Cutting Computational Methods and Bioinformatics Infrastructure
a. Biomedical Text Mining and Ontologies
b. Biological Data Mining and Visualization
c. Computational Modeling and Data Integration
d. High Performance Computing

5. Healthcare Informatics
a. Healthcare knowledge representation & reasoning
b. Health data acquisition, analysis and mining
c. Healthcare information systems
d. Clinical Decision Support and Informatics


INDUSTRIAL Track

The Industrial Track solicits papers describing implementations of
Bioinformatics and Biomedicine solutions relevant to industrial
settings. The focus of industry track is on papers that address the
practical, applied, or pragmatic or new research challenge issues
related to the use of bioinformatics and biomedicine technologies in
industry.

* Journal special issues: IEEE BIBM has a tradition to publish
selected papers as special issues in highly respected journals. So
far we have confirmed the special issues publications with 7
journals: IEEE Transactions on Information Technology in
Biomedicine, IEEE Transactions on  System, Men and Cybernetics,
International Journal of Data Mining and Bioinformatics, BMC
Bioinformatics, BMC Proteomics, BMC Genomics, BMC Proteomics
Science,  Proteomics, Journal of Network Modeling and Analysis in
Health Informatics and Bioinformatics (In the past BIBM conference,
the number of special issues is: BIBM 2011-8 special issues, BIBM
2010-7 special issues, BIBM 2009-4 special issues; BIBM 2008-4
special issues)

* Student Travel Award: BIBM 2012 will offer as many as possible
student travel awards to student authors (including post-doc) (BIBM
2011-28 student travel awards, BIBM 2010-22 student travel awards,
BIBM 2009-16 student travel awards )


* Panel on Bioinformatics and Biomedicine Research Challenges and
Opportunities led by top researchers and program managers from NSF
and NIH


Conference Co-Chairs:

Prof. Lyle Ungar, University of Pennsylvania, USA, ungar@cis.upenn.edu
Prof. Cathy Wu, University of Delaware, USA, wuc@dbi.udel.edu

Program Co-Chairs:

Prof. Reda Alhaij, University of Calgary, Canada, rsalhajj@gmail.com
Prof. Jean Gao, University of Texas at Arlington, USA, gao@uta.edu
Prof. Dubitzky Werner, University of Ulster, UK, W.Dubitzky@ulster.ac.uk

Industry Program Committee Chair:

Dr. Anastasia Christianson, AstraZeneca, USA,
anastasia.christianson@astrazeneca.com

BIBM Steering Committee Chair:

Prof. Xiaohua Tony Hu, Drexel University, USA, thu@cis.drexel.edu


Paper Submission:

Please submit a full-length paper, up to 8 pages in IEEE double-column
format, through the online submission system. Formatting instructions
for Latex and Word are available at the online submission
site. Electronic submissions (in PDF or Postscript format) are
required. Selected participants will be asked to submit their revised
papers in a format to be specified at the time of acceptance.


Online Submission:

http://wi-lab.com/cyberchair/2012/bibm12/cbc_index.html


Important Dates:

Electronic submission of full papers: May 10, 2012
Notification of paper acceptance: July 20, 2012
Camera-ready of accepted papers: August 15, 2012
Conference: October 4-7, 2012

URL: http://www.ischool.drexel.edu/ieeebibm/bibm12/

Contact Person: Umit V. Catalyurek (catalyurek.1@osu.edu)