| News & Commentary |
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This past January, requests for nominations for the 2010 Benjamin Franklin Award in the Life Sciences were sent out to more than 27,000 members of Bioinformatics.Org, and we thank everyone who participated in the process. This will be the ninth presentation of the humanitarian and bioethics award, which is given annually by the members of the Bioinformatics Organization to an individual who has worked to promote open access to the materials and methods used in the life sciences.
And the nominees are...
- Alex Bateman, Wellcome Trust Sanger Institute ([link]). Alex has lead the freely available and very useful Pfam (http://pfam.sanger.ac.uk/), Rfam (http://rfam.sanger.ac.uk/) and MEROPS (http://merops.sanger.ac.uk/) databases at the Wellcome Trust Sanger Institute since moving there in 1997. He was also the Executive Editor for the open-access Database issue of the journal Nucleic Acids Research for many years ([link]). Furthermore, Alex helped initiate the RNA Families track at the journal RNA Biology ([link]), where a Wikipedia article is required for each published RNA family.
- Don Gilbert, Indiana University, Bloomington ([link]). Don has made long and varied contributions to bioinformatics, from his initial establishment of the IUBio archive and Bio-Mirror (http://www.bio-mirror.net/), to the development and release of the widely used program readseq ([link]); and from 'loopdloop' to the SeqPup application, to his current work in comprehensive database organization with the Eugenes project (http://iubio.bio.indiana.edu:8089/). Don was one of the first, if not the first, to use the Internet to provide biological information and software tools to the biological community. Forget the web -- Don was using gopher and email protocols to provide usable biotools well before http came round.
- David J. Lipman, NCBI ([link]). For many years David has been at the forefront of open access for biomedical data of several categories. David is also a driving force behind PubMed Central, a repository of full-text, peer-reviewed articles from life science journals. And much of the power of NCBI's resources derives from David's vision of integrating the resources so that users can seamlessly move, for example, from a genetic sequence to the scientific literature discussing a related gene, to related protein structures, etc. Additionally, David is Editor-in-Chief of the Open Access journal Biology Direct (known for its novel approach to peer review) and a moderator for PLoS Currents: Influenza, a new project developed during the recent H1N1 influenza epidemic that allows scientists to share results and ideas immediately while ensuring that the results will be permanently archived (in PubMed Central) and citable.
- John Quackenbush, Harvard School of Public Health ([link]). John has a long history of promoting open-source and publicly available software tools in various area of bioinformatics/computational biology, emphasizing and evangelizing several areas that have become pillars of good bioinformatics research: accessibility, reproducibility, scalability, and biological applicability. Particularly in the past few years, John has been starting to apply these in the area of cancer treatment and personalized medicine (e.g. [link]), an area where both transparency and rigorous community analysis will be even more critical in the years to come. John has also been a pioneer in gene expression microarray software development (MeV), providing it free to the public. And he started Center for Cancer Computational Biology (CCCB) to help Greater Boston Area biology labs and clinicians with research and therapeutics (http://cccb.dfci.harvard.edu/).
- G.P.S. Raghava, Institute of Microbial Technology ([link]). Dr. Raghava has developed 10 curated databases and more than 100 web services, which serve immunology researchers around the world. He has been at the forefront of bioinformatics in India, where his efforts to make scientific information freely accessible have greatly helped the scientific community there. His group builds upon free and open source software, and all of the resulting resources are free for academic use. For example, his group recently created the Computational Resources for Drug Discovery (CRDD) Web portal at the Open Source Drug Discovery Foundation (http://crdd.osdd.net/).
The ceremony for the presentation of the award will be held at the 2010 Bio-IT World Conference & Expo in Boston (http://www.bio-itworldexpo.com/). It involves a short introduction, the presentation of the certificate, and the laureate seminar. Ceremony attendance is free with early registration.
If you're a member of Bioinformatics.Org, you may vote on the Bioinformatics.Org website: [link].
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CHANGES:
- The current version of the bioLegato user interface is 0.6.2. This version includes major improvements in features and usability: allows copying and pasting with system clipboard; multiple alignment canvas can now be split horizontally into two windows; now supports grouping of sequences, for simultaneous editing of multiple alignments; now supports rectangular selection of blocks of subsequences from a multiple alignment.
- Added biolegato documentation to Documentation menu.
- bioLegato versions of all tutorials are now available.
- And more.
AVAILABILITY:
The latest release of BIRCH (2.6) is available at the BIRCH Web site http://home.cc.umanitoba.ca/~psgendb under the link 'BIRCH Administrator's Guide'.
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DATES: May 10-11, 2010
LOCALE: Ghent, Belgium
URL: [link]
By discussing the latest developments and potentially new applications in text mining amongst scientists in both academia and industry, this workshop aims to provide a broad view on text mining tools in biology and biomedicine. We are reaching out to a broad public, including researchers with an interest in text mining but with little or no experience in this domain. To this end, the workshop will start with an extensive tutorial on text mining in the bio-sciences, providing sufficient background knowledge for novices.
IMPORTANT DATES:
Submission deadline: April 1, 20101
Notification of acceptance: April 15, 2010
Camera-ready abstracts due: April 30, 2010
Workshop in Ghent: May 10-11, 2010
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DATES: August 12-15, 2010
LOCALE: Dalian, China
URL: http://icicip.dlut.edu.cn/
ICICIP 2010 aims to provide a broad international forum for scientists, engineers, and educators working in the areas of information and control to discuss state-of-the-art science and technologies, and their applications in diverse areas. The conference will feature plenary speeches given by worldwide renowned scholars and some special sessions focused on some popular topics.
Topics of contributing papers include but are not limited to the following areas: intelligent information processing, adaptive filtering & signal processing, higher order spectral analysis, neural signal processing, array signal processing, time series analysis, design and implementation of signal processing systems, image and multidimensional signal processing, computer vision & pattern recognition, bioimaging and signal processing.
IMPORTANT DATES:
Paper submission deadline: May 1, 2010
Notification of paper acceptance: June 1, 2010
Final paper submission deadline: July 1, 2010
Conference dates: August 12-15, 2010
FOR MORE INFORMATION:
Email: icicip@dlut.edu.cn
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DATES: August 16-18, 2010
LOCALE: Stanford University, Stanford, CA, USA
URL: http://csb2010.org/
You are invited to submit papers to the 9th annual Computational Systems Bioinformatics Conference (CSB2010, http://csb2010.org/). The conference’s goal is to facilitate exchange of ideas and collaborations between computational scientists and biologists by presenting cutting-edge computational and systems biology research findings. Such research has an interdisciplinary character. Computer science and mathematical modeling papers must contain a concise description of the biological problem being solved, and biology papers should show how computation or analysis affects the results. Topics of interest include broad areas of bioinformatics and computational biology.
Pubmed indexes papers appearing in CSB Proceedings. A select subset of accepted papers will be invited to publish an extended version in the Journal of Bioinformatics and Computational Biology. The Best Paper will be selected by the program committee and announced at the awards ceremony.
IMPORTANT DATES:
Submission deadline: March 26, 2010
Paper acceptance decision: April 30, 2010
Final revised draft due to publisher: May 18, 2010
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DATES: March 29, 2010, 9am to 5pm
LOCALE: University of Illinois at Chicago
URL: [link]
Learn new tools to generate structures and dynamical trajectories based on hypotheses, limited experimental information, and/or initial coordinates. The presented molecular modeling and simulation tools were designed to be easily applied by experimentalists to problems of current biological interest:
- Nucleic Acid Simulation Tool (NAST)- Generates a large number of conformationally diverse coarse-grained 3D structures that satisfy user-provided secondary and tertiary contacts. http://simtk.org/home/nast
- RNABuilder - Constructs structural models of RNA by enforcing user-provided base pairing interactions and other structural constraints. http://simtk.org/home/rnatoolbox
- OpenMM Zephyr - Generates a full atomic simulation using a version of the GROMACS molecular dynamics package that can be accelerated on GPUs. http://simtk.org/home/zephyr
REGISTRATION:
Free to attend. Registration is required, though, and spaces are limited.
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The following editorial has been published about the First African Virtual Conference on Bioinformatics 2009 (AFBIX09), organized by Bioinformatics.Org and several ISCBSC RSGs in Africa:
``The aim was to provide students and scientists in the bioinformatics and computational biology fields a chance to network through a unique platform conceptualized as `hubs.' These hubs then gave participants the opportunity to foster both physical and virtual interactions as well as develop collaborations, irrespective of geographical location.
``Virtual conferencing may prove to be an effective low-cost strategy for conveying bioinformatics and computational biology education to African scientists who otherwise would be deprived of the opportunity. Unlike conventional conferences, virtual conferencing permits the involvement of a greater number of participants who would otherwise be unable to participate in events of this breadth owing to (1) limited travel fellowships, if any; (2) lack of time to travel to distant conference locations; and (3) insufficient accommodation and subsistence funds. These factors apply in general to the post-/undergraduate student community and especially to the target audiences that reside in developing countries. Minimizing the requirement to travel also means that the availability of invited speakers is greatly increased, improving the chances of attracting highly relevant and high-impact presenters.''
FULL EDITORIAL:
[link]
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DATE: July 9, 2010
LOCALE: Boston, MA (ISMB 2010)
URL: http://symposium.iscbsc.org/
Submit your abstract today to participate in the 6th Symposium of the International Society for Computational Biology Student Council on July 9th 2010 in Boston!
Submission website: [link]
Travel fellowship information: [link]
IMPORTANT DATES:
Abstract and travel fellowship submission opens: February 22, 2010
Abstract submission closes: April 23, 2010
Travel fellowships submission closes: April 30, 2010
Travel fellowship winners and abstract acceptance notification: May 14, 2010
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GEB (Gene Expression Browser) is an efficient tool for searching and viewing large-scale microarray data from diverse experiments. GEB is composed of a set of software tools, including microarray data management system, data annotation tools, microarray data processing pipeline and data search and visualization tool. The current GEB web service integrates 301 ATH1 microarray experiments from GEO and NASC. This set of GEB software tools can be easily used in the microarray data from other platforms and species.
AVAILABILITY:
http://www.ExpressionBrowser.com/
EXAMPLES:
Here are several examples of Arabidopsis functions:
- All 301 Arabidopsis ATH1 experiments are listed at: [link]
- Gene View displays all treatments that affect the expression of a selected gene. An example Gene View of Arabidopsis PR-1 gene is at: [link]
- T/C View (Treatment over Control View) displays the expression of all genes under a selected T/C condition. An example of T/C view is at: [link]
- The user can get co-regulated genes of any specific gene. For example, PR-1 has 1305 co-regulation genes that are listed in the order of relationship with PR-1 (refer to [link]); COR15A has 1467 co-regulated genes (refer to [link]). GEB also provide experiment condition network (T/C network) so that users can get all conditions (T/Cs) that have similar expression profile with a selected experiment condition (T/C). For example, a T/C "16 hr Pseudomonas infection" has 199 T/Cs that have similar expression profiles ([link]); "cold 24 hr effects" has 49 T/Cs that have similar expression profiles with it ([link]). The gene network and T/C network (condition network) provides a cross-experimental and systematic understanding on Arabidopsis gene expression as totality.
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DATES: March 22-24, 2010
LOCALE: Churchill College, University of Cambridge, United Kingdom
URL: [link]
This sixth meeting on Integrative Bioinformatics has an exciting programme of supporting workshops and tutorials along with demonstrations of new software that will be of interest to Bioinformaticians, Computer Scientists and other working in, or interested in finding out more about, the developing area of integrative bioinformatics.
Biological Data Integration and Visualisation for Systems Biology
DATE: March 22, 2010, 09:30-12:00
URL: [link] (PDF)
EMERALD - Enhancing Data Quality
DATE: March 22, 2010, 10:00-12:00
Please register (for free) by sending an email to vidar.beisvag@ntnu.no at the latest by March 11, 2010.
Gene Networks for Bench Scientists Workshop
DATES: March 24, 14:00-17:30 plus March 25, 09:30-12:00
In order to register at this workshop, please email Paul Verrier (paul.verrier@bbsrc.ac.uk).
FOR MORE INFORMATION:
Further information can be obtained from Paul Verrier (paul.verrier@bbsrc.ac.uk) or Chris Rawlings (chris.rawlings@bbsrc.ac.uk).
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| Acknowledgments |
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We wish to thank the following for their support:
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