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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Thursday, December 22, 2011

2012 PASI short course A Systems Biology Approach to Understanding Mechanisms of Organismal Evolution

Satellite short course to the Sixth International Meeting of the Latin American Society for Developmental Biology, April 16-25, 2012, Montevideo, Uruguay. This Pan-American Advanced Studies Institute will be held at the Universidad de la Republica and Institut Pasteur de Montevideo and is funded by a PASI program grant from NSF and DoE. It is aimed for advanced graduate students, postdoctoral fellows and junior faculty interested in enhancing their understanding for evolutionary processes by integrating genomics, systems biology, gene regulatory network with traditional experimental approaches. Latin American citizens, US nationals and permanent residents are invited to apply. Deadline for submission is January 6, 2012, 6 PM Eastern time.
URL: http://www.sdbonline.org/2012Course/course.htm

Contact Person: Ida Chow (ichow@sdbonline.org)

Thursday, December 15, 2011

Protein 3D Structure from High-Throughput Sequencing  

Fifty years after the pioneering discovery hat a protein's three-dimensional structure is determined solely by the sequence of its amino acids, an international team of researchers has taken a major step toward fulfilling the tantalizing promise: predicting the structure of a protein from its DNA alone.

The team at Harvard Medical School (HMS), Politecnico di Torino / Human Genetics Foundation Torino (HuGeF) and Memorial Sloan-Kettering Cancer Center in New York (MSKCC) has reported substantial progress toward solving a classical problem of molecular biology: the computational protein folding problem.

In molecular biology and biomedical engineering, knowing the shape of protein molecules is key to understanding how they perform the work of life, the mechanisms of disease and drug design. Normally the shape of protein molecules is determined by expensive and complicated experiments, and for most proteins these experiments have not yet been done. Computing the shape from genetic information alone is possible in principle. But despite limited success for some smaller proteins, this challenge has remained essentially unsolved. The difficulty lies in the enormous complexity of the search space, an astronomically large number of possible shapes. Without any shortcuts, it would take a supercomputer many years to explore all possible shapes of even a small protein.

The team tested this hypothesis: That evolution can provide a roadmap to how the protein folds. Their approach combined three key elements: evolutionary information accumulated for many millions of years; data from high-throughput genetic sequencing; and a key method from statistical physics.

Using the accumulated evolutionary information in the form of the sequences of thousands of proteins, grouped in protein families that are likely to have similar shapes, the team found a way to solve the problem: an algorithm to infer which parts of a protein interact to determine its shape. They used a principle from statistical physics called "maximum entropy" in a method that extracts information about microscopic interactions from measurement of system properties.

With these internal protein interactions inhand, widely used molecular simulation software generated the atomic details of the protein shape. The team was for the first time able to compute remarkably accurate shapes from sequence information alone for a test set of 15 diverse proteins, with no protein size limit in sight, with unprecedented accuracy.

To test their method, the researchers initially focused on the Ras family of signaling proteins, which has been extensivelystudied because of its known link to cancer. The structure of several Ras-type proteins has already been solved experimentally, but the proteins in the family are larger–with about 160 amino acid residues–than any proteinsmodeled computationally from sequence alone. And there is no reason that the method couldn't work with even larger proteins.

The researchers caution that there are other limits, however: experimental structures, when available, generally are more accurate in atomic detail. And, the method works only when researchers havegenetic data for large protein families. But advances in DNA sequencing have yielded a torrent of such data that is forecast to continue growing exponentially in the foreseeable future.

The next step, the researchers say, is to predict the structures of unsolved proteins currently being investigated bystructural biologists, before exploring the large uncharted territory of currently unknown protein structures; and, collaborating with computational and experimental structural biologists to further refine the "evfolded" proteins and to make structure determination more efficient.

Adapted from text by R Alan Leo, Harvard Medical School.

A full news report: http://www.sciencedaily.com/releases/2011/12/111207175635.htm

_________________________ details:

Supplement, images, 3D structures, restraint lists and more: http://evfold.org
URL: http://bit.ly/tob48p

Contact Person: EVfold team (foldingproteins@cbio.mskcc.org)

Tuesday, November 8, 2011

New Preventing Preterm Birth Initiative

The Global Alliance to Prevent Prematurity and Stillbirth (GAPPS), an initiative of Seattle Childrens, is now accepting letters of inquiry for a new grant program, the Preventing Preterm Birth initiative (PPB).

GAPPS seeks projects that explore gestational origins, biological mechanisms and the immunological response to infection and nutritional deficiency which lead to preterm birth, especially in the developing world.

GAPPS will fund several projects for $1-2 million each to discover the biological mechanisms that lead to preterm birth. The Preventing Preterm Birth initiative was funded by the Bill & Melinda Gates Foundation as part of the Grand Challenges in Global Health.

Details and application instructions are available at http://www.gapps.org/healthybirth. Letters of inquiry are being accepted online until 31 January, 2012.

The PPB review committee will review all letters of inquiry submitted, and selected applicants will be invited to submit a full grant proposal.

We look forward to receiving innovative ideas from scientists around the world and from all scientific disciplines. If you do not submit a letter of inquiry yourself, we hope you will forward this message to someone else who might be interested.

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

Contact Person: GAPPS (gappsgrants@seattlechildrens.org)

EMBO practical course on Bioinformatics and Comparative Genome Analyses 2012 (Stazione Zoologica Anton Dohrn, Naples - Italy. 7 - 19 May, 2012)

Announcement and Call for Application to the EMBO practical Course on "Bioinformatics and Comparative Genome Analyses"
(http://events.embo.org/12-comparative-genomics/index.html) that will take place in the Stazione Zoologica Anton Dohrn, Naples - Italy, 7 – 19 May, 2012.

The main objective of this intensive course is to strengthen capacities of Phd students and young scientists, in Bioinformatics and large-scale genome data analyses skills.

The course will focus on reviews on advanced fundamental algorithms and methods used in Bioinformatics and their applications in genome studies.
The course topics will include among others, theoretical and practical aspects in: large-scale genome comparisons, evolutionary analyses, sequence and genome alignments, Methods for reapeats detection in genomes sequences, orthologs prediction and classification, Genome data visualization, Methods and tools used in Next Generation Sequencing Data analyses.
Practical sessions in a Linux environment will involve Unix and Perl scripting.
Participants are expected to be familiar with this environment.

The topics that will be included in the course programme are similar to those included in previously organized courses: http://www.pasteur.fr/~tekaia/BGA_courses.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 students will have free accommodation and meals and are expected to contribute with 400 euros and to pay for their travel expenses.
All participants (students and invited speakers) will stay in the same hotel.

Detailed indications are available on the course web site: http://events.embo.org/12-comparative-genomics/index.html

Candidates are advised to complete carefully the application form, together with a "one-page CV" and a personal Identity Picture (Photo).

The application deadline is March 30, 2012.

The organizers:
Giuseppe D'Onofrio (Stazione Zoologica Anton Dohrn, Naples - Italy)
Fredj Tekaia (Institut Pasteur Paris, France)
URL: http://www.pasteur.fr/~tekaia/BGA_courses.html
http://events.embo.org/12-comparative-genomics/index.html
URL: http://www.pasteur.fr/~tekaia/BCGA2012.html

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

Monday, October 17, 2011

Benelux Bioinformatics Conference

Putting the Lux on BeNeLux

The BeNeLux Bioinformatics Conference (BBC) will be hosted in Luxembourg for the first time, and CRP-Santé will lead its organization in partnership with other local institutions. BBC will be held on 12 and 13 December 2011, and will showcase research advances from the region and beyond.

A key theme of BBC2011 will be "Bioinformatics: Enabling Translational Biomedical Research".

The conference is an official ISCB affiliated conference.

Go to Conference web-site

Invited speakers

Thomas Lengauer, Max-Planck-Institut für Informatik, Saarbrücken, Germany

Burkhard Rost, Technical University Munich, Germany

Peter van der Spek, Erasmus Medical Center, Rotterdam, The Netherlands

Ioannis Xenarios, Swiss Institute of Bioinformatics and Vital-IT, Lausanne, Switzerland

Monday, October 3, 2011

Genetic Engineering & Biotechnology News (GEN) Celebrates 30 years with Collector's Edition

For Immediate Release
Contact: Linda Muskat-Rim, 914-740-2251, lmuskat@liebertpub.com, Mary Ann Liebert, Inc., publishers

Genetic Engineering & Biotechnology News(GEN)
Celebrates 30 Years with 130-Page Collector's Edition

New Rochelle, NY, October 3, 2011— Genetic Engineering & Biotechnology News (GEN) celebrates 30 years as the world's
first and most widely read magazine for the biotechnology industry. Universally heralded as the definitive information
source in this field, GEN covers the technology, trends, products, services, and advances that shape and drive the industry
forward. GEN's 130-page commemorative issue features articles written by luminaries, and an original poster that
tracks the milestones that have altered the course of biotechnology, leading to today's most groundbreaking scientific and
therapeutic discoveries.

"Genetic Engineering & Biotechnology News was there at the inception of this field and remains the single most useful
resource I use for keeping abreast of new developments," said James Wilson, M.D., Ph.D., Professor of Pathology and
Laboratory Medicine, Gene Therapy Program, University of Pennsylvania School of Medicine.

GEN was founded in 1981 by Mary Ann Liebert, who identified the untapped need for a publication dedicated to the
rapidly evolving biotech industry from applied research through commercialization. David Weiner, Ph.D., Professor of
Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, said, "Mary Ann practically willed
the biotech revolution."

"GEN is biotechnology. It always has been and always will be," said Mary Ann Liebert, president and CEO of the
company that bears her name. John Sterling, GEN's Editor-in-Chief for the past 27 years, confirms that "Genetic
Engineering & Biotechnology News impacts the industry. It fosters critical international collaborations among academia,
industry, and government."

Publishing October 1, the Collector's Edition includes contributions from Leroy Hood, M.D., Ph.D., on Biological
Complexity Under Attack; James M. Wilson, M.D., Ph.D., on The History and Promise of Gene Therapy; Elaine R.
Mardis, Ph.D., on Future of DNA Sequencing Technology; Rita Colwell, Ph.D., on Combating Infectious Disease Agents;
N. Leigh Anderson, Ph.D., on Proteomics: Pathways and Biomarkers; G. Steven Burrill on Tracking Operational
Financing Trends; and articles on bioprocessing and synthetic biology.

Over the years, GEN's guest editorials have been penned by notables including: Presidents Bill Clinton and Jimmy Carter;
Vice Presidents Al Gore and Dan Quayle; Speaker of the House Newt Gingrich; Nobel Prize Winner and co-discoverer of
the structure of DNA, James D. Watson, Ph.D.; former Head of 20th Century Fox and Co-Founder of Stand Up To Cancer,
Sherry Lansing; and J. Craig Venter, Ph.D., leader of a team that decoded the human genome. GEN enjoyed its own
celebrity and a film credit as a scientific consultant for the hit film Jurassic Park.

Genetic Engineering & Biotechnology News is published in print 21 times a year. Its 24/7 website, www.genengnews.
com, provides exclusive editorial online, including news and analysis, podcasts, webinars, polls, videos, and application
notes. The publication's focus, both in print and online, includes the entire bioproduct life cycle from bench to bedside.
Biobusiness, drug discovery, OMICS, bioprocessing, and translational medicine form the core of GEN's global
biotechnology coverage.

GEN's Collector's Edition is available free to subscribers. For individual and bulk purchase contact: Nancy Piscitello
(1-800-M-LIEBERT).
URL:

Contact Person: Linda Muskat-Rim (lmuskat@liebertpub.com)

Monday, September 19, 2011

Announcing Critical Assessment of Genome Interpretation & Prediction season open

The Critical Assessment of Genome Interpretation (CAGI) is a community experiment to assess computational methods for predicting the phenotypic impacts of genomic variation. The CAGI 2011 experiment is now well underway with 11 datasets available at the CAGI website: http://genomeinterpretation.org/. Remaining deadlines to submit predictions start September 30, 2011 and continue until 31 October.

In the CAGI experiment, modeled on the Critical Assessment of Structure Prediction (CASP), participants are provided genetic variants and make predictions of resulting molecular, cellular, or organismal phenotype. These predictions are evaluated against experimental characterizations, and independent assessors perform evaluations. The CAGI Conference 2011 will be held 9 - 10 December at UCSF Mission Bay campus to disseminate results, assess our collective ability to make accurate and meaningful phenotypic predictions, and better understand progress in the field. From this experiment, we expect to identify bottlenecks in genome interpretation, inform critical areas of future research, and connect researchers from diverse disciplines whose expertise is essential to methods for genome interpretation.

The CAGI 2011 challenges include:
• Disease-associated variants of a human metabolic enzyme.
• Variants from the resequencing of breast cancer patients and control subjects.
• Disease-associated variants of a human sodium channel.
• Genome and RNA-seq data from identical twins with discordant disease.
• Multiple genomics data for cancer cell lines, with differential response to drugs.
• Exomes of Crohn's disease patients and healthy individuals.
• Double mutants of p53 to identify mutations that restore the activity of inactive p53.
• Predicting the medical phenotypes of individuals with genome data.
• Microbial dataset measuring the effect of gene disruptions under stress conditions.
• The riskSNPs dataset to identify potential causative SNPs from lists of candidates in the disease-associated loci for seven complex trait diseases.
The CAGI submission deadline for the mouse exomes challenge already passed, but we are accepting submissions for archival purposes.

The first CAGI experiment, called pre-pro-CAGI, was organized in 2010. Assessors are preparing a manuscript to discuss these results. While the identities of the prediction methods have been embargoed for this "training" CAGI, we will de-anonymize methods from predictors who give us the permission to do so and future CAGI experiments will be more open. The next CAGI experiment is anticipated for 2013.

In order to access the challenges, download datasets, and submit predictions to CAGI 2011, please go to the website http://genomeinterpretation.org and register. For more information, contact the organizers at cagi@genomeinterpretation.org.

We are grateful to the following:

Data providers:
Adam Arkin, George Church, Andre Franke, Joe W. Gray, Rick Lathrop, Jasper Rine, Jeremy Sanford, Nicole Schmitt, Jay Shendure, Michael Snyder, and Sean Tavtigian.

Confirmed Assessors:
Rui Chen, Iddo Friedberg, Gad Getz, Sean Mooney, Pauline Ng, and Sean Tavtigian.

Confirmed CAGI Advisory Board:
Russ Altman, George Church, Tim Hubbard, Scott Kahn, and Sean Mooney.

Confirmed CAGI Scientific Council:
Patricia Babbitt, Atul Butte, Garry Cutting, Rachel Karchin, Robert Nussbaum, Michael Snyder, and Liping Wei.

URL: http://genomeinterpretation.org

Contact Person: Susanna Repo (srepo@compbio.berkeley.edu)

Sunday, September 11, 2011

BeNeLux Bioinformatics Conference (BBC) - Enabling Translational Biomedical Research - ISCB affiliated conference


BeNeLux Bioinformatics Conference (BBC) 
Luxembourg - Luxembourg 
Hosted by:CRP-Santé
Venue:Alvisse Parc Hotel
Dates:Dec 12, 2011 through Dec 13, 2011
Call for Papers or Oral Presentations:2011-09-01 through 2011-10-28
Event Registration:2011-08-15 through 2011-11-27
Description
Putting the Lux on BeNeLux

The BeNeLux Bioinformatics Conference (BBC) will be hosted in Luxembourg for the first time, and CRP-Santé will lead its organization in partnership with other local institutions. BBC will be held on 12 and 13 December 2011, and will showcase research advances from the region and beyond.

A key theme of BBC2011 will be "Bioinformatics: Enabling Translational Biomedical Research".

Invited speakers

Thomas Lengauer, Max-Planck-Institut für Informatik, Germany

Burkhard Rost, Technical University Munich, Germany

Peter van der Spek, Erasmus Medical Center, The Netherlands

Ioannis Xenarios, Swiss Institute of Bioinformatics and Vital-IT
Additional Information
Event URL:http://www.bbc11.lu
ISCB Member Discount:15 percent
Contact Person:Francisco Azuaje ( francisco.azuaje@crp-sante.lu)

Wednesday, September 7, 2011

BioVis 2011 registration open

Registration for the 1st IEEE Symposium on Biological Data Visualization (BioVis 2011) is now open. BioVis is an affiliated conference of the ISCB and will take place in Providence, RI (USA), co-located with IEEE VisWeek, the premier forum for visualization advances for academia, government, and industry.

Early registration (reduced rate) for this meeting ends on Friday, 16 September. Single day and two day registrations are available in addition to full week registration. Discounts are available for ISCB, IEEE and ACM members, details are can be found on the registration page.
The goal of BioVis is to create the premier international and interdisciplinary event for all aspects of visualization in biology. This symposium will bring together researchers from the visualization, bioinformatics, and biology communities with the purpose of educating, inspiring, and engaging visualization researchers in biological data visualization, as well as bioinformatics and biology researchers in state-of-the-art visualization research. As the first annual BioVis Symposium, this event seeks to emphasize inclusion and interaction between these communities as its primary impact.
The program of the meeting includes:

  • a keynote by Lynda Chin (MD Anderson Cancer Center / Broad Institute of MIT and Harvard)
  • a primer by Lawrence Hunter (UC Denver) and Kun Huang (Ohio State)
  • a special session on BioVis challenges with invited speakers Arthur Olson (The Scripps Research Institute), Cydney Nielsen (BC Cancer Agency Genome Sciences Centre) and Willy Supatto (California Institute of Technology)
  • four paper sessions with 24 presentations from all areas of biology
  • 27 posters and demos
  • presentation of the results from the BioVis Contest
The full list of accepted papers, posters, demos, and videos is available on the BioVis website.

Thursday, August 18, 2011

Alan T. Waterman Award-Call For Nominations

The National Science Foundation's Highest Honor

The Alan T. Waterman Award is the highest honor awarded by the National Science Foundation. Since 1975, when Congress established the award to honor the agency's first director, the annual award has been bestowed upon individuals who have demonstrated exceptional individual achievement in scientific or engineering research of sufficient quality to place them at the forefront of their peers.

The annual award recognizes an outstanding young researcher in any field of science or engineering supported by the National Science Foundation. In addition to a medal, the awardee receives a grant of $500,000 over a three year period for scientific research or advanced study in the mathematical, physical, biological, engineering, social or other sciences at the institution of the recipient's choice.

Eligibility and Selection Criteria

• Candidates must be U.S. citizens or permanent
residents, 35 years of age or younger, or not more than
seven years beyond receipt of their Ph.D. degree by
December 31 of the year in which they are nominated.

• Candidates should have demonstrated exceptional
individual achievements in scientific or engineering
research of sufficient quality to place them at the
forefront of their peers. Criteria include originality,
innovation, and significant impact on their field.

To nominate a candidate, please go to:
www.fastlane.nsf.gov/honawards/

Information on the award and past recipients is also available at: www.nsf.gov/od/waterman/waterman.jsp
URL: http://www.nsf.gov/od/waterman/waterman.jsp

Contact Person: Mayra N. Montrose, Program Manager (waterman@nsf.gov)

Wednesday, July 13, 2011

Registration open for Therapeutic Applications of Computational Biology and Chemistry (TACBAC) 2012

12-14 March 2012
Wellcome Trust Conference Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

Abstract deadline: 30 January 2012 Registration deadline: 6 February 2012

This conference will bring together leading researchers investigating computational chemistry and biology techniques as applied to advancing our ability to predict, diagnose and modulate human disease. This broad and multidisciplinary meeting will explore the major challenges in drug discovery and development where innovation in computational approaches and tools can really make a significant and tangible contribution towards novel treatments. You should attend this conference if you are a researcher interested in drug discovery, or developing or using computational approaches to the development of therapeutics, or if you are a key decision maker in a pharmaceutical or biotechnology company.

Each of the sessions, which progress from identifying disease mechanisms to implementing new therapeutic and diagnostic approaches in the clinic, will bring together experts in both the biomedical and the computational aspects of the topic under discussion. Sessions chairs will encourage discussion and contribution from the attendees.

Session topics
• Clinical implications of individual genomes
• Metabolism and biomarkers
• Computational systems biology
• Discovery of chemical probes
• Modelling xenobiotic metabolism

Scientific Programme Committee:
Lee Harland, Pfizer, UK
John Overington, EMBL-European Bioinformatics Institute, Hinxton, UK
Christoph Steinbeck, EMBL-European Bioinformatics Institute, Hinxton, UK

Speakers include:
Chas Bountra, Structural Genomics Consortium, UK
Paul Flicek, EMBL-European Bioinformatics Institute, Hinxton, UK
Ronald Frank, Helmholtz Centre for Infection Research, Germany
Bobby Glen, University of Cambridge, UK
Roy Goodacre, University of Manchester, UK
Jules Griffin, University of Cambridge, UK
Lee Harland, Pfizer, UK
Aroon Hingorani, University College London, UK
John Overington, EMBL-European Bioinformatics Institute, Hinxton, UK
Julio Saez-Rodriguez, EMBL-European Bioinformatics Institute, Hinxton, UK
Christoph Steinbeck, EMBL-European Bioinformatics Institute, Hinxton, UK
Olivier Tabourieau, Center for Biological Sequence Analysis, Denmark

URL: http://registration.hinxton.wellcome.ac.uk/display_info.asp?id=263

Contact Person: Jemma Beard (j.beard@hinxton.wellcome.ac.uk)

Sunday, July 3, 2011

Computational Structural Bioinformatics Workshop

Computational Structural Bioinformatics Workshop (CSBW) will be held in conjunction with the IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2011). This workshop aims to bring together researchers with expertise in bioinformatics, computational biology, structural biology, data mining, optimization and high performance computing to discuss recent results, new techniques, and open research problems in computational
structural bioinformatics. Registration of the CSBW will enjoy the benefit of the main conference BIBM2011.
URL: http://www.cs.odu.edu/~lchen/CSBW.htm

Contact Person: Jing He (jhe@cs.odu.edu)

Thursday, June 16, 2011

A new concept in online sequence analysis

I thought I might bring to your attention a revolutionary concept in online research for life sciences.

A website called "Sequilab" has created a virtual research lab for life scientists doing sequence analysis. Sequilab is a sequence-profiling portal with web 2.0 interactivity features built into it. It allows the user to directly link NCBI-BLAST results instantly to an inventory of sequence analysis tools like translate, ORF, CpG islands, View structure (Cn3D), mfold (for RNA) without cutting and pasting.

In addition to the seamless integration of BLAST results with sequence analysis tools, Sequilab also allows users to save the results of their research for later use and they can also create custom toolbars of particular tools that are used most frequently. If assistance is needed, researchers can discuss projects and with peers in the community forums if needed and share research interests via a personal profile.

The portal can be accessed by visiting http://www.sequilab.org. Registration is a free, one-step process.

I think this portal may be of interest to you and your readers. More details on how this concept works can be found at - http://sequilab.org/pages/howItWorks.jsf;jsessionid=6D303B1F5CB0EDACA5AE5F3D6F06E1D4

Thank you

Dr. Natarajan Ganesan,
Sequilab.org
URL: http://www.sequilab.org

Contact Person: Natarajan Ganesan (natarajanganesan@sequilab.org)

Sunday, June 5, 2011

Introducing Predict @proteommetal: A tool for prediction of Metal binding domains in Proteins

"Predict @proteommetal" tool is an informative tool designed to find metal binding sites in proteins structures as well as sequences. It can predict metal binding sites for 16 metals (Cu, Ca, Al, Mo, Ni, Fe Na, K, La, Zn, Mg, Mn, Hg, Cd, Co and Pb) on the basis of coordinating residues specific to the metal.

The information of coordinating residues was gathered in a database. The database was formed on the basis of the binding affinity of metal towards the coordinating residues. At the heart of the tool, effective perl programs had been combined with rich php interface.

This may be used as a platform for the identification and characterization of metal binding site(s) which will further contribute towards a better understanding and evaluation of various facets of contemporary life science areas like protein engineering, epidemiology, evolutionary studies etc. Importantly, In a very less time.

URL: http://www.bitmesra.ac.in/proteommetal/home.php

Contact Person: Shankaracharya, medhavi mallick and A. S. Vidyarthi (shankaracharya@bitmesra.ac.in)

Wednesday, June 1, 2011

Agilent grants for systems biology software development

To: International Society for Computational Biology
This announcement is on behalf of Leo Bonilla, Director of Marketing for Integrated Biology, Agilent Technologies, Inc. Agilent is fostering integrated, whole-systems approaches to biological research through two $75,000 US grants (application deadline August 12, 2011). Funds will support academic or nonprofit research projects covering the development of open source software tools for integrating data from different omics platforms—genomics, transcriptomics, proteomics, and metabolomics.
For full details on eligibility, submission, and review process, please visit www.Agilent.com/lifesciences/emerginginsights.
If you have any questions or would like to interview Leo about the grant program, I'd be happy to set up a phone call. Just reply to my email and I'll connect you with Leo.

Sincerely,
Pia Abola, Ph.D.
Scientific Content Manager
The Linus Group
5900 Hollis St., Suite H
Emeryville, CA 94608
(510) 547-7100

URL: http://www.Agilent.com/lifesciences/emerginginsights

Contact Person: Pia Abola (pabola@thelinusgroup.com)

Sunday, April 24, 2011

Call for Site Proposals - 2012 ACM Conference on Bioinformatics and Computational Biology

Call for Site Proposals: ACM-BCB 2012
Site proposals for the Third ACM Conference on Bioinformatics and Computational Biology (ACM-BCB 2012) are invited from interested groups. ACM-BCB is the official conference of the ACM SIG Bioinformatics (http://www.sigbioinformatics.org/ ) . Site proposals should be no longer than 2 page ASCII text (66 lines, 80 columns). Proposals must be submitted by email to the current ACM SIG Bioinformatics Director of Conferences (Vasant Honavar, honavar@cs.iastate.edu) with the subject: "ACM-BCB site proposal - YEAR" (e.g., "ACM-BCB site proposal - 2012") no later than May 31, 2011. The venue for ACM-BCB 2012 will be announced during ACM-BCB 2011 which is being held in Chicago (http://acmbcb.org/ )
Site proposals should cover the following topics:
• Geographic Region: For 2012, the preferred location is North America. In the future, we will consider rotating the location to other regions (Europe, Asia, etc.)
• Potential dates: Potential dates should be chosen so as to avoid conflicts with major conferences in related areas (ISMB, BIBM, CSB, BIBE, RECOMB, etc.)
• Site city:
➢ The city should be located near a major airport, within 1-2 hours of regular train service and/or 45 minutes of cab/shuttle service. The airport should be served at least two airlines with regular service through a major international airport to the 4 major continents of SIG Bioinformatics attendees: Asia, Europe, North and South America.
➢ The city should have one or more conference venues that can accommodate conferences with 300-600 attendees, including suitable facilities for 4-6 concurrent tutorials or workshops with up to 100 attendees each. The venues should include facilities with one to 3 large center screens, with unobstructed views, and projectors and audiovisual equipment appropriate for plenary sessions. The venue should include suitable reception and banquet facilities. Please do NOT contact possible venues regarding availability or cost. ACM negotiates the cost, availability, and contracts directly with candidate venues. However, you may include estimates based on your knowledge of recent conferences, especially ACM conferences (if any), held at the venues under consideration. A sample list of possible venues with a 1-line description addressing logistics (time to get there, need for transportation) would be useful. The availability of low-cost or subsidized venues e.g., the conference facilit ies at a major university would be a plus.
➢ The city should have hotels that can house 500-700 people (attendees and their guests) within easy access to the possible venue. The availability of inexpensive accommodations for student participants is a plus.
• Conference Organizers:
➢ The proposal must include the name and affiliation of an active member of the SIG Bioinformatics community based in or very close to the proposed site city who is willing to serve as general chair; this may eventually require a statement of support from the chair's institution, and possibly administrative and organizational support.
➢ The proposal may include: 2 co-chairs, one of whom must be local; The names and affiliations of a few other candidates that the chair can enlist to serve on the committee, notably a local person as local arrangements chair, a publicity chair, treasurer, etc.
➢ The proposal must not include the names of program committee chairs (The ACM SIG Bioinformatics Board of Directors will select the program chairs).
• Dates and conflicts: Please indicate which dates have conflicts with major local events, etc. that could interfere with the availability of either the proposed site or the proposed conference organizers. The proposed dates should consider conflicts with major conferences on related topics (ISMB, AAAI, IEEE BIBE, IEEE BIBM, RECOMB, PSB, etc.) The dates of ACM-BCB will ultimately be selected by the SIG Bioinformatics Executive Committee, based on the proposals received and feedback from surveys conducted by SIG Bioinformatics.
URL: http://www.sigbioinformatics.org/

Contact Person: Vasant Honavar (honavar@cs.iastate.edu)

Thursday, April 21, 2011

Bioinformatics writing contest on en.bioinformatyk.eu

We are happy to announce a writing contest for beginner-friendly articles on bioinformatics. The web magazine http://en.bioinformatyk.eu collects articles for bioinformatics students that are easy to understand. You are welcome to participate by contributing a short article about a topic of your choice, e.g.:

* Fancy algorithms & bioinformatics tools you have used.
* Amazing discoveries you read about.
* Present your lab and what it has achieved.
* How you survived your BSc, MSc, or PhD thesis.
* Books, events, science news.

You don't need to describe original research (we'd even suggest you save this up for your first paper). What matters more important is to explain bioinformatics in a clear or entertaining way.

To submit an article, prepare a MS Word, OpenOffice or PDF document with your text in English (200-1000 words). Prepare eventual figures as separate files (.jpg or .png). Finally send everything by email to contest[at]bioinformatyk.eu - We will take care of the rest.

The submission deadline for the contest is September 18th, 2011.

Remember that you need to have copyright of everything you are submitting. Also, if your article contains results from your research, please make sure that your supervisor agrees with that.

The best articles will be awarded by an international board of referees:

* 1st prize: 150,- USD
* 2nd prize: 50,- USD
* Reader's prize: 50,- USD
* Book prize sponsored by the Dean of the Biological Faculty, UAM Poznan: ~300 USD


You can find the detailed regulations of the contest on:
http://en.bioinformatyk.eu/the-contest/


The Organizers,
Justyna Wojtczak (Chief Editor)
Teresa Szczepińska (ISCB-SC Vice Chair)
Kristian Rother (Faculty Advisor)

URL: http://en.bioinformatyk.eu

Contact Person: Kristian Rother (krother@genesilico.pl)

Wednesday, April 20, 2011

Announcing grant writing sessions @ISMB

Dear colleagues,

We would like to invite you to join us for
information sessions about grant writing during
ISMB/ECCB, July 15-19, 2011 in Vienna, Austria.

Tutorial
Grant-writing 101: how to write a winning grant proposal
Saturday July 16, 1:30 pm - 5:30 pm

Workshop
Navigating the Granting Jungle
Sunday July 17, 2:30 pm – 4:25 pm
  • Funding availability
  • Reviewer’s recommendations
  • Speaking from experience
  • Finding/selecting funding schemes

Looking forward to seeing you in Vienna!


Yana Bromberg, Rutgers University
Magali Michaut, University of Toronto
Venkata P. Satagopam, EMBL
Andrea Schafferhans, Technical University of Munich

Monday, April 11, 2011

Publication on Virtual workshops for Africa and future prospects

A paper concerning the Basic Molecular evolution training that virtually took place in July 2010 across Africa has just been published. This can be accessed at the following url

http://onlinelibrary.wiley.com/doi/10.1002/bies.201000139/abstract

A lot of experience was garnered that brought forth the publication which is an aftermath on the "ten simple rules to organize a virtual conference-anywhere".

There are plans to have an on site workshop on molecular evolution early 2012 with a wide range of participants from other regions connected virtually.

Further information will be communicated in due course and it is hoped that more regions will participate this time round.

It is hoped that this will lead to a series of such workshops in different subjects within the field of bioinformatics and computational biology.

Let us endeavor to support and make virtual workshops a success and reality in order to benefit more students/scientists within the developing countries.

URL: http://onlinelibrary.wiley.com/doi/10.1002/bies.201000139/abstract

Contact Person: Sheila Ommeh (scecily@yahoo.com)

Sunday, April 10, 2011

Career Advice from a Rock Star of Science

Elizabeth Blackburn spoke about careers to young scientists during AACR (American Association for Cancer Research) meeting. Jade attended the session and shares useful advice with us on her blog.
  • How Deep into a Topic should you go?
  • Choosing a Postdoc
  • On a Failure
  • On Collaborations and Letters of Recommendations
  • Publishing in High Profile Journals
  • "Alternative" Careers in Science
  • Mommy Guilt
  • Chasing Ideas
Read the details...

Friday, April 1, 2011

Call for Tutorials and Demos: IEEE International Conference on Healthcare Informatics, Imaging and Systems Biology (HISB'011)

First IEEE International Conference on
Healthcare Informatics, Imaging, and Systems Biology (HISB)
July 27-29, San Jose, California
http://www.ieee-hisb.org/

*** Call for Tutorials and Demos ....
URL: http://www.ieee-hisb.org/
Contact Person: HISB Tutorial and Demo Chairs (hisbdemo@eecs.umich.edu)


First IEEE International Conference on
Healthcare Informatics, Imaging, and Systems Biology (HISB)
July 27-29, San Jose, California
http://www.ieee-hisb.org/

*** Call for Tutorials and Demos ***

The First IEEE International Conference on Healthcare Informatics, Imaging and Systems Biology now invites proposals for tutorials and demonstrations at the conference to be held in San Jose, July 26-29, 2011.

The purpose of tutorials is to provide a comprehensive overview by subject matter experts on topics relevant to HISB, keeping in mind the inter-disciplinary audience. The purpose of demos is to give researchers the opportunity to showcase the state of the art in areas relevant to HISB. Industrial exhibitors may also demonstrate their products through demos as long as they are relevant to the topic areas of the main conference.

We encourage submissions of tutorial and demonstration proposals on all topics relevant to the conference in the general areas of healthcare informatics, biomedical imaging, bioinformatics, and systems biology. A full list of topics is available in the call for papers for HISB at (http://www.ieee-hisb.org). Specialized subtopics that address computational or clinical aspects of the main topics will also be considered.
Please refer to the main conference site (http://www.ieee-hisb.org) for further details.

Key Dates:

Submission deadline (for both tutorials and demos): April 20, 2011
Notification of Acceptance: May 20, 2011
Conference Dates: July 27-29, 2011
URL: http://www.ieee-hisb.org/

Contact Person: HISB Tutorial and Demo Chairs (hisbdemo@eecs.umich.edu)

Monday, March 28, 2011

Intech Launches Open Access Journal "Nanomaterials and Nanotechnology"

InTech, the Open Access publisher, has announced the launch of a new Open Access journal, "Nanomaterials and Nanotechnology". The quarterly journal will be available online for free full-text download on the reading platform www.InTechOpen.com.

Open Access publications which are not subsidized by institutional funding are usually financed by payments met by the institutions researchers work for. However, "Nanomaterials and Nanotechnology" will be a "Free for All" publication, with no costs incurred by contributors or readers.

Thanks to the "one at a time" publishing model, accepted papers will be published online immediately following peer review. The complete process from submission to publication will take approximately one month.

The journal's Editor in Chief is Dr. Paola Prete of the Institute for Microelectronics and Microsystems at the Italian National Research Council, Lecce, Italy. Dr. Prete expects that the journal will be a useful source of information for researchers in all areas of nanoscience since it will cover a wide range of topics, such as the synthesis of nanosized materials, nano-characterization techniques, nanobiotechnology and nanomedicine.

The Editorial Board is comprised of international experts, including C. N. R. Rao - Linus Pauling Research Professor at the Jawaharlal Nehru Centre for Advanced Scientific Research and Honorary Professor at the Indian Institute of Science, Bangalore, India. Professor Rao is a member of the Royal Society and the US National Academy of Sciences, and is renowned for his contribution to solid state chemistry and nanomaterials over the last two decades.

The first issue of the Journal is expected to go live in June 2011. The call for papers for inclusion in the first issue is open until 10 May, 2011.

Researchers interested in submitting their papers for consideration for the first issue are invited to find out more at http://www.intechweb.org/nn-first-issue.html.


ABOUT INTECH

InTech (www.intechweb.org) is an Open Access publisher of journals and books covering the fields of Science, Technology and Medicine. InTechOpen is an Open Access reading platform for InTech publications, a space where all users can read, share and download more than 300 books and 8,000 book chapters. All content at InTechOpen (www.intechopen.com) is distributed under the Open Access label and under the Creative Commons license - freely accessible to anyone, anywhere in the world.




URL: http://www.intechweb.org

Contact Person: Nataly Anderson (anderson@intechweb.org)

Sunday, March 27, 2011

Announcing RECOMB-BE 2011 in Vienna, Austria, July 20-21, 2011

Third RECOMB Satellite Conference on Bioinformatics Education
Vienna, Austria
July 20-21, 2011
in Conjunction with ISMB 2011


OVERVIEW

The Third Annual RECOMB Conference on Bioinformatics Education (RECOMB-BE) will be held in Vienna, Austria, July 20-21, 2011 as an ISMB/ECCB 2011 Satellite Meeting (http://www.iscb.org/ismbeccb2011). The conference follows the first two RECOMB-BE meetings: http://casb.ucsd.edu/bioed/ and http://casb.calit2.net/bioed10/ . RECOMB-BE 2011 will consist of invited presentations, oral presentations selected from submitted abstracts and papers, a poster session, and discussion panels, all of which focus on improving bioinformatics education.


INVITED SPEAKERS

Partial List: Laurie Heyer (Davidson College), Larry Hunter (University of Colorado), Fran Lewitter (Whitehead Institute for Biomedical Research) Ran Libeskind-Hadas (Harvey Mudd College), Florian Markovetz (CRUK Cambridge Research Institute), Bernard Moret (École Polytechnique Fédérale de Lausanne), Tal Pupko (Tel Aviv University), Pavel Pevzner (University of California at San Diego), Ben Raphael (Brown University), Ron Shamir (Tel Aviv University), Beth Simon (University of California at San Diego), Terry Speed (University of California at Berkeley), and Jens Stoye (Bielefeld University).


THEME AND SCOPE

The goal of RECOMB-BE is threefold: to showcase best practices of teaching bioinformatics ideas to biology undergraduates, to discuss existing challenges in bioinformatics education (with an emphasis on undergraduate education), and to promote collaboration among educators with the aim to develop a mature bioinformatics curriculum. In keeping with the focus on undergraduates, the conference will also showcase selected bioinformatics research projects conducted by undergraduate students.

While biology has been transformed into a computational science in the last decade, the biological curriculum remains largely unchanged with respect to computational issues. The question: "How should we teach bioinformatics to biology students?" has become of the utmost importance, since many universities have not only founded undergraduate bioinformatics programs but are considering the addition of new computational courses to the standard biology curriculum—a change which would represent a dramatic paradigm shift in biology education. However, as the first two RECOMB-BE meetings demonstrated, there is a great divide in how even the world's top bioinformaticians thought the subject should be taught, and therefore the above pedagogical question has not been answered satisfactorily to date.

RECOMB-BE therefore aims to demonstrate the intricacy, practicality, and beauty of modern bioinformatics at the undergraduate level, and advance the discussion about its curriculum in the biology classroom. For a summary of RECOMB-BE discussions and the educational challenges that lie ahead for bioinformatics, see Computing has changed biology--biology education must catch up (Science 2009, v.325: 541-542).


FORMAT

RECOMB-BE will have a somewhat unusual format, inspired by the biennial mathematical conference called Gathering for Gardner (G4G) At G4G, leading mathematicians give high-school and undergraduate level lectures; the goal of G4G is therefore to present complex mathematical ideas in a simple form. This objective is one for which the bioinformatics community must also strive in order to establish meaningful future collaborations with biologists and to bridge the cultural gap between computational and experimental scientists.

Unlike previous meetings on bioinformatics education, which have focused on how bioinformatics should be taught, RECOMB-BE showcases how leading bioinformaticians actually teach. Speakers will give short, introductory-level lectures, aimed at undergraduates. These lectures will be complemented by discussion panels focusing on existing challenges in bioinformatics education as well as poster presentations given by undergraduate students on their research projects.


BIOINFORMATICS FOR BIOLOGISTS TEXTBOOK PROJECT

The participants of RECOMB-BE in 2009 and 2010 formed the Bioinformatics Education Alliance, a group of sixteen leading bioinformaticians who have recently collaborated to produce a textbook, called Bioinformatics for Biologists (B4B). The first edition of B4B will be published by Cambridge University Press in the summer of 2011, and test copies will be available at ISMB 2011. Please see the official B4B website for more details: http://cseweb.ucsd.edu/~ppevzner/B4B/

B4B is an open project that will be continuously expanded by new chapters. Therefore, RECOMB-BE invites submissions of proposals for new chapters; accepted chapters will be included in the second edition of B4B which is scheduled for publication in 2012 (see "Important Dates" below).


CALL FOR PARTICIPATION

We invite submissions in four categories:

1. Bioinformatics Education Papers
2. Bioinformatics for Biologists Textbook Chapter Proposals
3. Bioinformatics Education Abstracts (submitted by educators)
4. Undergraduate Bioinformatics Research Abstracts (submitted by undergraduate or first-year graduate students)

Selected papers and abstracts in the first three categories will be invited for either oral or poster presentations. Undergraduate bioinformatics research abstracts will be invited for a poster presentation.

Bioinformatics Education Papers should be submitted via the RECOMB-BE website and must be received by May 5, 2010. Each paper should cover a single biological problem and focus on didactic ways to convey the computational ideas needed to address it. Papers should be self-contained and aimed at advanced undergraduate biology students. Submissions that focus either solely on computational topics or solely on biological topics will not be considered. RECOMB-BE imposes no explicit restrictions on format, length, or notation, as we encourage contributors to choose the style they feel is the most appropriate; however, we anticipate that each contributed paper will be at least 10 pages long.

Authors of selected papers will be invited to submit their paper in the journal PLOS Computational Biology (in the Education Article category) as well as a chapter in the second edition of the Bioinformatics for Biologists textbook, which is described above.

Bioinformatics for Biologists (B4B) Chapter Proposals should be submitted via the RECOMB-BE website and must be received by May 15, 2011. Each submission in this category should constitute a brief description of the proposed chapter. Authors of selected proposals will be invited either for oral or poster presentations at RECOMB-BE 2011. In addition, these authors will be asked to submit a full-length chapter for the second edition of B4B shortly after RECOMB-BE. Proposals should cover a single biological problem and focus on didactic ways to convey the computational ideas needed to address it. Submissions that focus either solely on computational topics or solely on biological topics will not be considered. We anticipate that each chapter proposal will be 1-2 pages long.

Bioinformatics Education Abstracts (submitted by educators) should be submitted via the RECOMB-BE web site and must be received by May 20, 2011. Submissions in this category can discuss practice, challenges, or perspectives in bioinformatics education (e.g., curricula, integration of bioinformatics programs, online courses, etc.) or represent a proposal for a short 20-30 minute introductory lecture aimed at undergraduates. We are specifically looking for lectures that begin with a description of an interesting biological problem, such as "Did we evolve from Neanderthals?" and then show how computational techniques can be used to solve this biological problem. Each abstract should be at most 1 page long.

Undergraduate Bioinformatics Research Abstracts (submitted by undergraduates or first-year graduate students reporting their undergraduate work) should be submitted via the RECOMB-BE website and must be received by May 20, 2011. Each abstract should be at most 1 page long.


TRAVEL SUPPORT

RECOMB-BE and the Howard Hughes Medical Institute offer travel support to undergraduate students interested in bioinformatics. All undergraduate students are invited to apply for travel support. RECOMB-BE will have a poster session showcasing undergraduate bioinformatics research, and we encourage undergraduate students interested in participation to submit an undergraduate bioinformatics research abstract. Students who submit abstracts will be given a priority with regards to travel support. First-year graduate students who wish to present their undergraduate work are also welcome to apply for travel support. All applications for travel support should be made via RECOMB-BE website.

In addition to supporting undergraduate students, RECOMB-BE also has limited funds to support authors of accepted RECOMB-BE papers and B4B chapter proposals.


IMPORTANT DATES

Paper submission deadline: May 5, 2011
Notification of paper acceptance: May 15, 2011
Bioinformatics for Biologists textbook chapter proposals deadline: May 15, 2011
Notification of proposal acceptance: May 25, 2011
Abstract submission deadline: May 20, 2011
Notification of abstract acceptance: May 25, 2011
Application for travel support deadline: June 5, 2011
Notification of travel support: June 15, 2011


RECOMB-BE ORGANIZERS

RECOMB-BE was founded by Pavel Pevzner (UCSD) and Ron Shamir (Tel Aviv University) in 2009.

RECOMB-BE 2011 Program Committee: Fran Lewitter (Whitehead Institute for Biomedical Research), Ran Libeskind-Hadas (Harvey Mudd College), Pavel Pevzner, (UCSD) and Ron Shamir (Tel Aviv University).

RECOMB-BE Organizing Committee: Phillip Compeau (Chair), Sangtae Kim, and Son Pham.

Email contact: pcompeau@math.ucsd.edu


RECOMB-BE SUPPORT

RECOMB-BE is supported by the Howard Hughes Medical Institute (HHMI), the International Society for Computational Biology (ISCB), and the California Institute for Telecommunications and Information Technologies (CalIT2).


ABOUT RECOMB

The RECOMB International Conference on Research in Computational Molecular Biology was founded in 1997 to provide a scientific forum for theoretical advances in computational biology and their applications in molecular biology and medicine. The conference arose from the need to advance research on the mathematical and computational side of molecular biology, and today the conference maintains its focus on state-of-the-art computational advances in this field. The 15th Annual RECOMB conference (RECOMB 2011) will be held March 28-31, 2011 in Vancouver, Canada. The conference website can be found at http://compbio.cs.sfu.ca/recomb2011/.

The RECOMB Satellites Series was founded by Pavel Pevzner in 2001. It contains today nine focused meetings covering various specialized aspects of bioinformatics: RECOMB Comparative Genomics, RECOMB Regulatory Genomics, RECOMB Computational Cancer Biology, RECOMB Computational Proteomics, RECOMB SNPs and Haplotypes RECOMB Systems Biology, RECOMB Massively Parallel Sequencing and of course RECOMB Bioinformatics Education.
URL: http://casb.ucsd.edu/bioed11/index.php

Contact Person: Phillip Compeau, University of California-San Diego Dept. of Mathematics (pcompeau@math.ucsd.edu)

Thursday, March 17, 2011

NEW NSF Solicitation: AVAToL

AVAToL, Assembling, Visualizing and Analyzing the Tree of Life

The Assembling, Visualizing and Analyzing the Tree of Life (AVAToL) activity supports novel and transformative approaches to the development of an integrated and robust tree of life, as well as visualization and analysis on a dynamic tree of life. This will take place through the Ideas Lab project development and review process. The goal of this activity is to identify opportunities for investment to significantly advance the state-of-the-art in tree construction, visualization, and analysis across the tree of life. Participants selected through an open application process will engage in an intensive five-day residential workshop to generate project ideas through an innovative, real-time review process. New multidisciplinary teams will form during this workshop to engage in creative problem solving directed at outstanding problems concerning the tree of life. Multidisciplinary integrative approaches calling for communication and interaction among diverse scientists are key to the success of the approach. For example, in addition to those working in systematics and phylogenetics, AVAToL might benefit from mathematicians and computer scientists to contribute algorithms and models, bioinformaticians or genomicists to contribute data pipelines and novel molecular characters, or statisticians and artists with an interest in novel methods of visualization and interactive use of the tree of life. Therefore, members of the systematics research community, bioinformaticians, genomicists, morphologists, paleontologists, computer scientists, statisticians, mathematicians, educators involved in training the next generation of researchers, and representatives of any other disciplines that might contribute important ideas are all strongly encouraged to apply.
URL: http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=503629&org=BIO&from=home

Contact Person: Tim Collins (bio-AVAToL@NSF.gov)

Thursday, March 10, 2011

SIB Swiss Institute of Bioinformatics Awards 2011-Call for Applications

The SIB Swiss Institute of Bioinformatics is happy to announce the SIB 2011 Awards, two prizes assigned to young scientists in bioinformatics.
Two categories: SIB Young Bioinformatician Award and SIB Best Graduate Paper Award.


SIB 2011 Young Bioinformatician Award

Prize of CHF 10,000 and award certificate.

Open to any graduate student or young researcher in Europe who has carried out a research project centered on the in silico analysis of biological sequences, structures and processes.
Candidate must not be more than 32 years old at the time of submission and must have worked on a project with a partner in Switzerland for at least 6 months in 2010.

Submitted project must be completed or subject to publication within the period from 1 June 2010 to 1 June 2011.

Applications for the award may be submitted by the candidate, any faculty member or SIB group leader.



SIB 2011 Best Graduate Paper Award

Prize of CHF 5,000 and award certificate.

Open to any graduate student who has not yet completed his/her PhD, at the time the paper was published.

Applicant must have studied in Switzerland for at least 6 months in 2010.
Submitted paper must have been published or be subject to publication within the period from June 1, 2010 to June 1, 2011.

Applications for the award may be submitted by the candidate, by any SIB group leader or by a Swiss university or federal institute of technology.


Both winners will receive their prizes during the [BC]2
Basel Computational Biology Conference on 23-24 June 2011.
Winners will also be invited to present their projects during the conference.

Closing date for entries: 30 March 2011


More information and submission form at:
http://www.isb-sib.ch/research/sib-awards.html


Contact:
Irene Perovsek
00 41 (0)21 692 40 54
Irene.perovsek@isb-sib.ch
URL: http://www.isb-sib.ch/research/sib-awards.html)

Friday, February 25, 2011

Web Publishing of Scientific Data and Services Training Courses

This series of training courses is mandated to train service providers in the use of modern semantic approaches to publishing informatics resources on the Web using the semantic web services paradigm. The first Web Publishing of Scientific Data and Services Training Course will be held in Fredericton, NB, CANADA on May 19-20th, 2011.

Semantic Web Services have rich descriptions of functional requirements that facilitate service interoperability and make it easier for users to discover and access relevant services in real time. The course provides both theory and practical training in the semantic technologies that underpin the development of semantic web services.The training course is divided into the following modules:

* Semantic Web
* Knowledge Representation and Reasoning
* Web Services
* SADI Semantic Web Services

At the end of the training, attendees will know how to:

* publish their data and algorithms on the Web in a manner that is easy for others to find and access using state of the art toolkits.

* ensure their data and tools integrate well with other resources on the Web.

* enhance query access and service discoverability for target end-user communities.


Target Audience
===============

This training course is primarily of interest to providers of bioinformatic resources seeking to extend the utility and usability of thier data and services. Researchers interested in learning state of the art semantic technologies and their deployment to facilitate web scale interoperability are strongly encouraged to attend. Priority will be given to students and professionals with working knowledge of Perl and/or Java.

Profile of Target Audience:

* Grid Computing Architects and Developers interested in building globally interoperable systems;

* Web Developers and Bioinformatics researchers seeking to ensure the adoption of their technologies in the knowledge discovery;

* Workflow system developers coordinating computational and data resources across the web using semantics;

* Industry pioneers in Workflow, Grid and Semantic technologies;

* Researchers involved in Web-based Knowledge Discovery in Bioinformatics.

URL: http://sadiframework.org/training/

Contact Person: Silvane Paixao (silvane.cbrass@gmail.com)

Thursday, February 17, 2011

12th MRC SGDP Centre Summer School: Bioinformatics for Geneticists

Bioinformatics for Geneticists: This course will teach how to handle data and conduct basic analysis, QC and annotation. It will cover the most common analysis packages and methods and how to do systems biology with each of these datasets singly or in combination. It will teach the essentials of GWAS and web data resources, pathway and network analysis, but a primary focus this year will be on next generation sequencing analysis. It will consider methods for analysis of transcriptome sequencing and exome/whole genome sequencing.

Scientific Directors: Gerome Breen & Richard Dobson
URL: http://www.kcl.ac.uk/schools/summerschool/si/sgdp/index.html

Contact Person: Gerome Breen, Richard Dobson (gerome.breen@kcl.ac.uk)

Thursday, February 3, 2011

Announcing New Master of Biostatistics at Duke

The Duke University Department of Biostatistics and Bioinformatics is excited to launch the new Master of Biostatistics Program in Fall 2011. This two-year degree program seeks to provide students with the analytical, biological, and communication skills that will ensure successful contribution to the rapidly-expanding field of biomedical research.

The program offers both degree and non-degree options. The two-year master degree option leads to a Master of Biostatistics, a professional degree awarded by the School of Medicine at Duke University.

Fall 2011 applications now available.

Application review begins January 31, 2011. Priority is given to Applications received by March 1, 2011. After March 1, 2011, Applications are considered on a space-available basis.

For more details about the Master of Biostatistics Program, please visit the program website: http://biostat.duke.edu/master-biostatistics-program/program-overview


URL: http://biostat.duke.edu/master-biostatistics-program/program-overview

Contact Person: Jonathan Hecht (jonathan.hecht@duke.edu)

Book Release: ADVANCES IN GENOMIC SEQUENCE ANALYSIS AND PATTERN DISCOVERY

ADVANCES IN GENOMIC SEQUENCE ANALYSIS AND PATTERN DISCOVERY
edited by Laura Elnitski (National Human Genome Research Institute, USA), Helen Piontkivska (Kent State University, USA), & Lonnie R Welch (Ohio University, USA)

Mapping the genomic landscapes is one of the most exciting frontiers of science. We have the opportunity to reverse engineer the blueprints and the control systems of living organisms. Computational tools are key enablers in the deciphering process. This book provides an in-depth presentation of some of the important computational biology approaches to genomic sequence analysis. The first section of the book discusses methods for discovering patterns in DNA and RNA. This is followed by the second section that reflects on methods in various ways, including performance, usage and paradigms.

Contents:

1 Pattern Discovery Methods:
1.1 Large-Scale Gene Regulatory Motif Discovery with NestedMICA (M Piipari et al.)
1.2 R'MES: A Tool to Find Motifs with a Significantly Unexpected Frequency in Biological Sequences (S Schbath & M Hoebeke)
1.3 An Intricate Mosaic of Genomic Patterns at Mid-range Scale (A Fedorov & L Fedorova)
1.4 Motif Finding from Chips to ChIPs (G Pavesi)
1.5 A New Approach to the Discovery of RNA Structural Elements in the Human Genome (L Hua et al.)

2 Performance and Paradigms:
2.1 Benchmarking of Methods for Motif Discovery in DNA (K Klepper et al.)
2.2 Encyclopedias of DNA Elements for Plant Genomes (J Lichtenberg et al.)
2.3 Manycore High-Performance Computing in Bioinformatics (J-S Varré et al.)
2.4 Natural Selection and the Genome (A L Hughes)

Readership: Those who perform biological, medical and bioinformatics research.

236pp Pub. date: Jan 2011
ISBN: 978-981-4327-72-5
981-4327-72-7 US$90 / £56
URL: http://www.worldscibooks.com/lifesci/7972.html

Contact Person: Lonnie Welch (welch@ohio.edu)

Monday, January 31, 2011

2nd Bioinformatics for Regulatory Genomics Special Interest Group (BioRegSIG)

CALL FOR PAPERS and POSTERS for the 2nd Bioinformatics for Regulatory Genomics Special Interest Group (BioRegSIG).

The meeting will be on July 16, 2011 in Vienna, in conjunction with The Nineteenth International Conference on Intelligent Systems for Molecular Biology (ISMB) and the 10th European Conference on Computational Biology.

BioRegSIG is a one-day workshop that focuses on bioinformatics for regulatory genomics. It provides a broad, deep perspective on developments in research, and addresses the topic more extensively than can be done in the main conference.

Extended abstracts (in English) should not exceed 4 pages (2 pages for posters). Submit abstracts (in pdf format) to Sophie.Schbath@jouy.inra.fr. Submission deadline is February 21, 2011. Details about BioRegSIG are available at http://light.ece.ohio.edu/bioreg/2011/.
URL: http://light.ece.ohio.edu/bioreg/2011/

Contact Person: Lonnie Welch (welch@ohio.edu)

Thursday, January 27, 2011

VIZBI 2011 workshop on visualizing biological data - early registration closes Jan 31

Early registration for VIZBI 2011 closes next Monday (Jan 31) – after this date, registration costs $100 more.
URL: http://vizbi.org

Contact Person: Seán O'Donoghue (sean.odonoghue@embl.de)

Tuesday, January 11, 2011

EMBO practical course on Bioinformatics and Comparative Genome Analysis (Institut Pasteur Paris, France, June 27 - July 9, 2011.

Announcement and Call for Application to the EMBO practical Course on "Bioinformatics and Comparative Genome Analysis" (http://cwp.embo.org/pc11-09/index.html) that will take place in the Institut Pasteur Paris, France, June 27 – July 9, 2011.
The main objective of this intensive course is to strengthen capacities of Phd students and young scientists, in Bioinformatics and large-scale genome data analyses skills.

The course will focus on reviews on advanced fundamental algorithms and methods used in Bioinformatics and their applications in genome studies. The course topics will include theoretical and practical aspects in: large-scale genome comparisons, evolutionary analyses, sequence and genome alignments, orthologs prediction and classification, Genome data visualization and statistical methods needed in Genome Wide Association Studies.
Practical sessions in a Linux environment will involve Unix and Perl scripting.
Participants are expected to be familiar with this environment.

The topics that will be included in the course programme are similar to those included in previously organized courses: http://www.pasteur.fr/~tekaia/BGA_courses.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 their expressed motivations.
Selected students will have free accommodation and meals and are expected to contribute with 300 euros and to pay for their travel expenses.
All participants (students and invited speakers) will stay in the same hotel.
Details are available on the course web site: http://cwp.embo.org/pc11-09/index.html

Candidates are advised to complete carefully the application form, together with a one-page CV and a personal Identity Picture (Photo).

The deadline application is April 30, 2011.

Fredj Tekaia (Institut Pasteur Paris, France)
URL: http://www.pasteur.fr/~tekaia/BGA_courses.html
URL: http://cwp.embo.org/pc11-09/index.html

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