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This blog collects news, announcements or other information which could be of interest to our ISCB members. We are a group ISCB members who volunteer to populate this blog on a regular basis. In case you want to become an "ISCB-News Reporter" yourself, let us know: contact ISCB
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Tuesday, March 19, 2013

FASEB BRINGS SCIENTISTS TO CAPITOL HILL TO DISCUSS IMPACT OF FUNDING CUTS ON LOCAL RESEARCH

FASEB BRINGS SCIENTISTS TO CAPITOL HILL TO DISCUSS IMPACT OF FUNDING CUTS ON LOCAL RESEARCH; RELEASES NEW SEQUESTRATION FACT SHEET

Bethesda, MD – Over 40 scientists from 21 states are in Washington DC today as part of The Federation of American Societies for Experimental Biology (FASEB) annual Capitol Hill Day.

· Representatives of FASEB member societies are meeting with more than 70 congressional offices to share personal stories and experiences about how federal funding cuts affect their research and that of their colleagues. They are also discussing how sequestration—combined with several years of flat funding for the National Institutes of Health (NIH)—is damaging our capacity for biomedical research.

· In addition, FASEB released a new sequestration fact sheet illustrating the extent to which the NIH budget is being cut and how these cuts will affect every state and describing the many ramifications of the lost opportunities for scientific progress.

"Capitol Hill Day is part of FASEB's ongoing efforts to inform members of Congress about the irreparable harm sequestration will do to biomedical research," stated FASEB President, Judith S. Bond, PhD.

FASEB is composed of 26 societies with more than 100,000 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:

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

Monday, March 18, 2013

Exploring Computational Biology as a Service, in the Cloud

This is an invitation to join us in April for the 3rd round of the open and free UberCloud CompBio Experiment, applying the cloud computing services model to Computational Biology.

This open, humanitarian, and collaborative Experiment is making computing resources available as a service, for everybody, on demand, at your fingertip, by exploring the end-to-end process of accessing and using remote computing resources as a service, and learning how to resolve the many roadblocks.

Now, for round 3 starting in April with so far 370 organizations worldwide, we invite industry end-users, software providers, HPC and computational bio experts, and computing resource providers, to join the experiment. For every end-user application we are building a small expert and resource team to collaboratively explore the end-to-end process of remote Computational Biology as a Service, hands on, in 22 well-defined, well-guided, easy steps.

You can register at http://www.compbioexperiment.com or read more in HPC in the Cloud at http://goo.gl/5BhMg
URL: http://www.compbioexperiment.com

Contact Person: Wolfgang Gentzsch (wolfgang.gentzsch@hpcexperiment.com)

Tuesday, March 12, 2013

Russ Altman quoted in New York Times on finding hidden side effects of drugs using web search data

Russ Altman quoted in New York Times on finding hidden side effects of drugs using web search data

http://www.nytimes.com/2013/03/07/science/unreported-side-effects-of-drugs-found-using-internet-data-study-finds.html

The New York Times reports on a study published in JAMIA, Web-scale Pharmacovigilance: Listening to Signals From the Crowd, authored by Ryen W. White, ISCB members Nicholas P. Tatonetti and Nigam H. Shah, ISCB Fellow Russ Altman, and Eric Horvitz.
http://jamia.bmj.com/content/early/2013/02/05/amiajnl-2012-001482.abstract
URL: http://www.nytimes.com/2013/03/07/science/unreported-side-effects-of-drugs-found-using-internet-data-study-finds.html

Contact Person: Suzi Smith (admin@iscb.org)

Monday, March 11, 2013

CS2Bio 2013: 4th International Workshop on Interactions between Computer Science and Biology

[We apologise for multiple copies]

NOTE THE SPECIAL ISSUES OF "THEORETICAL COMPUTER SCIENCE" JOURNAL
AND FOR PAPERS CONTRIBUTING TO THE EU FP7 DyM-CS SESSION
THE SPECIAL ISSUE OF "MATHEMATICAL STRUCTURES IN COMPUTER SCIENCE" JOURNAL

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

                         Second call for papers

                               CS2Bio'13
                     4th International Workshop on
           Interactions between Computer Science and Biology

                       Affiliated to DisCoTec'13

                           06th of June 2013
                            Florence, Italy

                      http://cs2bio13.di.unito.it/

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

Systems Biology is a stimulating field of application for computer
scientists and a promising resource for biologists. The aim of this
workshop is to gather researchers in formal methods that are
interested in the convergence of Computer Science and Life Sciences.
In particular, in this forth edition, we solicit the contribution of
original results, from any research areas, such as Mathematics,
Physics, Complex Systems, and Computational Sciences that address both
theoretical aspects of modelling and applied work on the comprehension
of biological behaviour. Furthermore, to facilitate the integration of
different research areas we encourage the presentation of the main
objectives and preliminary results of active projects on the CS2Bio
topics conducted by interdisciplinary teams.


*** SCOPE ***

Contributions selected for presentation at CS2Bio should either present
the modelling of a specific biological phenomenon using formal
techniques, or a modelling, 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. Topics of interest include, but shall
not be limited to:

- Formal Biological Modelling
  - Formal methods for the representation of biological systems and
    their dynamics;
  - Theoretical links and comparisons between different formal models
    for the modelling of biological processes;
  - Quantitative (probabilistic, timed, stochastic, etc.) languages
    and calculi;
  - Spatial (geometrical, topological) languages and calculi;
  - Prediction of biological behaviour from incomplete information;
  - Model checking, abstract interpretation, type systems, etc.

- Novel Computational Paradigms for Understanding Biological Complex
  Systems
  - Quantum information and life sciences;
  - Geometry, algebraic and computational topology and
    biomathematics;
  - Information processing and biomedicine;
  - Statistical mechanics and biophysics.

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


*** INVITED SPEAKERS ***

  - Giuseppe Longo (ENS Paris, France)
  - Mario Rasetti (ISI Foundation, Italy)


*** SUBMISSION GUIDELINES ***

We solicit three kinds of contributions:
  - Regular papers: must report previously unpublished work and not be
    submitted concurrently to a journal or to another conference with
    refereed proceedings (limited to 14 pages).
  - Tool presentations: describing new tools or platforms for the
    modelling of biological systems (limited to 7 pages).
  - Dissemination of project results: concern recent or ongoing work
    on topics relevant to CS2Bio and are intended to provide discussion
    and stimulate feedback during the workshop. The focus of a
    dissemination should be put on the main objectives and preliminary
    results of active projects on topics relevant to the workshop. There
    are no restrictions about previous or future publication of the
    contents of a dissemination, it could also be based on a recently
    published paper or on a work which has not yet been submitted
    (limited to 4 pages).

Authors should submit their contributions via EasyChair
(http://www.easychair.org/conferences/?conf=cs2bio13) in the form of a
pdf file compiled using the ENTCS style for the workshop proceedings
(http://www.entcs.org/files/cs2bio/prentcsmacro.sty). If necessary,
detailed proofs or other additional material can be added in an appendix
(referees might review it at their discretion).


*** DISSEMINATION ***

The proceedings of the workshop will be published in a volume of the
Elsevier series "Electronic Notes on Theoretical Computer Science". After
the event, papers presented at the workshop will be invited to be
furtherly extended and submitted to an open special issue of the journal
"Theoretical Computer Science".

A special issue of the journal "Mathematical Structures in Computer Science"
will be open for papers that will contribute to the session on
EU FP7 DyMCS - Dynamic Modelling of Complex Systems -
that will be held on the 5th of June.



*** IMPORTANT DATES ***

- Submission deadline: 26 March 2013
- Notification to authors: 03 May 2013
- Workshop: 06 June 2013


*** PROGRAM COMMITTEE ***

  - Erik de Vink
  - Jasmin Fisher
  - Paola Giannini
  - Radu Grosu
  - Jean Krivine
  - Pietro Lio'
  - Daniele Manini
  - Emanuela Merelli (Co-chair)
  - Paolo Milazzo
  - Ion Petre
  - Marco Pettini
  - Christian Reidys
  - David Safranek
  - Luca Tesei
  - Angelo Troina (Co-chair)
  - Verena Wolf


*** STEERING COMMITTEE ***

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

URL: http://cs2bio13.di.unito.it

Contact Person: Emanuela Merelli (emanuela.merelli@unicam.it)

Wednesday, March 6, 2013

Bioinformatics and Comparative Genome Analyses Course


Practical Course on "Bioinformatics and Comparative Genome Analyses"
(http://www.pasteur.fr/~tekaia/BCGA2013.html): University of La Reunion, Saint-Denis - France, 6 – 18 May, 2013.


The course will be organized within the frame of Run-Emerge objectives in order to train in La RĂ©union local, regional and international young scientists and PHD students in Bioinformatics and Genomics.
The course will focus on reviews on advanced fundamental algorithms and methods used in Bioinformatics and their applications in genome studies.
The course will involve genome comparisons, evolutionary analyses, phylogenomics and statistical methods needed in RNAiseq data analyses and Next Generation sequencing methods. The course program includes a series of lectures related to recent hot topics in Bioinformatics and Genome studies.
Practical sessions in a Linux environment will involve Unix and Perl scripting. Participants are expected to be familiar with this environment.
(Final programme:http://www.pasteur.fr/~tekaia/BCGA2012/BCGA2013_Prog.html).

The course is aimed at motivated Ph.D students and Post-Doctoral Researchers in Academic Institutions, with background in Mathematics, Statistics, Biology or Computer Science and who are involved in Bioinformatics and Genomes studies.

Selection of participants will be based on their background, running research projects and on expressed motivations.
Selected academic students will have free accommodation and meals and are expected to pay for their travel expenses. Selected students from the south western Indian Ocean region will be offered transport grants.

Candidates are advised to complete carefully the application form together with a "one-page CV" (see: http://www.pasteur.fr/~tekaia/BCGA2013.html to download the application form).

The application deadline is March 30, 2013 (European time) and the selected list of participants will be available by April 6, 2013.

With our best wishes.

The organizers:
Pablo Tortosa, Universite de la Reunion, Saint-Denis – France
Koussay Dellagi, CRVOI, Saint-Denis, France
Fredj Tekaia (Institut Pasteur Paris, France)
URL: http://www.pasteur.fr/~tekaia/BGA_courses.html
URL: http://www.pasteur.fr/~tekaia/BCGA2013.html

Contact Person: Fredj Tekaia (tekaia@pasteur.fr)