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| News & Commentary |
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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I, Librarian is a free tool to build a web-based annotated library of scientific PDF articles. It is suitable for individuals as well as for small collaborative groups, like science labs or departments.
The features include the ability to:
- Perform diacritics-neutral searches in reference data
- Search for words in PDF full texts
- Search and seamlessly import data from PubMed, PubMed Central, NASA ADS, arXiv, JSTOR, and HighWire Press
- Store attached files, like supplementary data or full resolution figures
- Attach personal notes
- Access all stored data and PDF files through WWW
- Export records into RIS, Endnote, BibTex, CSV and plain text files
- Create personal reference lists in the shared library
- Organize your PDFs into multiple categories
- Create collaborative projects by placing PDFs at virtual Desk
- Create collaborative groups for a project and discuss your progress using the built-in chat
The new version brings various small improvements, bug fixes, and integrated search of JSTOR. For the first time, a full-featured version for Mac OS X is also available for download.
The installers for Windows and Ubuntu are available. Other Linux platforms and Mac OS X require manual installation.
AVAILABILITY:
http://www.bioinformatics.org/librarian
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DATES: 6-8 pm, Monday, Feb. 22nd
LOCALE: Moscone Center, Room 124, 747 Howard St., San Francisco, CA
Simbios invites you to attend its ancillary meeting on RNA 3D Modeling & Simulation, to be held as part of the 2010 Biophysical Society Annual Meeting. We have lined up 6 diverse presentations on RNA computational tools, which will be followed by an informal discussion on the technical challenges to the field of RNA structural computation.
You do *not* need to be registered for the Biophysical Society meeting in order to attend this session.
Agenda:
- Kwok Yan Chan, Building RNA Structures for Molecular Dynamics Simulations
- Nikolay V. Dokholyan, Predicting 3D RNA Structure and Dynamics Using Discrete Molecular Dynamics
- Samuel Flores, RNABuilder: Multibody Mechanics for Versatile RNA Modeling
- Bruce Shapiro, 3D Modeling of the Turnip Crinkle Virus Translational Enhancer with RNA2D3D
- Yun-Xing Wang, Rapid Global Structure Determination of Large RNA and RNA Complexes Using NMR and Small Angle X-Ray Scattering (SAXS)
- Magdalena Jonikas, The Nucleic Acid Simulation Tool: Coarse Grain Modeling with Atomic Refinement
FOR MORE INFORMATION:
Simbios is an NIH National Center for Physics-Based Simulation of Biological Structures. For more information about this event, contact Joy Ku at joyku@stanford.edu.
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Unipro UGENE is a free open source multiplatform software tool for molecular biologists.
Version 1.6.1 changes:
- Got new aligner: KAlign algorithm is integrated
- Improved Phylip package integration
- Improvements in PhyTree and Alignment editors
- A lot stability and bug fixes
AVAILABILITY:
Pre-built packages for different platforms and complete source code is available here: http://ugene.unipro.ru/download.html
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To improve our knowledge of the various primary and secondary metabolisms of Fungi, we have mapped curated groups of orthologous proteins on to steps in the metabolic pathways published in the public databases KEGG and MetaCyc. FUNGIpath is a web service allowing to recover specific metabolic data and to compare them along a wide taxonomical range of sequenced fungal species.
AVAILABILITY:
This Open Source tool, including its source code, is freely available at the address http://www.fungipath.u-psud.fr/.
REFERENCES:
Grossetete S, Labedan B, Lespinet O. FUNGIpath: a tool to assess fungal metabolic pathways predicted by orthology. BMC Genomics 2010, 11:81
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