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News & Commentary
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DATE: September 4, 2010
LOCALE: Dr DY Patil University, Navi Mumbai, India
CONTACT: dypbioinfo@gmail.com
The Bioinformatics Department of Padmashree Dr. D.Y. Patil University, Navi Mumbai, India has initiated a community called "JanuGanak." The main objective of this community is to educate and spread awareness about bioinformatics and computational biology among students, researchers and scientific fraternities related to Life Sciences. To start with we are organizing a one day hands-on workshop on "Sequence Analysis".
This workshop is the first of a series of workshops which are aimed at giving complete hands-on experience in various tools and techniques used in the fields of Life Science and Bioinformatics. The “Sequence Analysis” Session is aimed at giving practical experience on the basic methods of handling biological sequences using bioinformatics tools. Both under-graduate and post-graduate students can participate in this workshop. Interested candidates from Research Fraternity as well as faculties from various areas of Life Sciences are also welcome. We hope that this workshop will provide fairly good amount of knowledge about handling of biological databases and analysis of the sequences which is essential in all fields of Life Sciences today.
Registration deadline: August 30, 2010
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Computational and Mathematical Biology is a peer-reviewed journal targeting at all aspects of theoretical, methodological and tool development, testing and user evaluation of computational and mathematical tools for the modelling, visualization, analysis and interpretation of biological data at all scales – from molecules and cells to populations and ecosystems. The following areas are also considered: technical and usability reviews, significant updates and improvement of available tools and methods, application of computing, applied mathematics and statistics to actual biological problems, and short reviews consolidating the state of knowledge in the area.
The topics of interest in this journal include (but not limited to):
* Mathematical representation, manipulation and simulation of biological systems
* Computational modeling of molecules, interactions and systems
* DNA, RNA and protein sequence analysis
* Proteomic, interactomic and metabolomic analysis
* Biological database construction and use
* Biomedical literature and health record analysis
* Computational and comparative genomics
* Biological structure representation and analysis
* Theoretical foundation, development and testing of tools and methods
* User evaluation, significant updates and improvement of tools and methods
* Application of tools and methods
Review Process:
The review process is single-blinded (i.e. the reviewers' identities will not be disclosed). We aim to have your paper reviewed within 2 months of receipt of an electronic file.
Publication Fee:
Free.
URL: [link]
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This journal targets senior undergraduates, postgraduates, and researchers who are looking to use, or are currently using, computational and mathematical methods in biology. As we move into the post-genomics era, large datasets are commonplace, and high-throughput computational, mathematical, and statistical tools are essential for analytical studies.
This publication serves two broad themes – Methods and Cases. Current studies and reviews of the employment of computational, mathematical, and statistical methods for the analysis of biological questions will be published under the Methods theme. Hypotheses, successful and on-going cases using computational, mathematical, and statistical methods in biology, as well as usability studies on such tools, will be published under the Cases theme.
You can see it at [link]
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Unipro releases a new version of free, cross-platform and open-source UGENE software suite: http://ugene.unipro.ru
Main features of the release:
* Significant improvement of DotPlot Viewer plugin
* Support for Clustal and MAFFT alignments
* Creation of new Workflow Designer diagram elements using embedded scripting language
* Running workflows on public Amazon EC2 server
* A lot of minor usability improvements and bug-fixes
Watch all the changes in our special video podcast episode:
Part 1: [link]
Part 2: [link]
Download link: http://ugene.unipro.ru/download.html
About the software:
UGENE is a free open-source bioinformatics software. It has friendly
user interface, runs on Linux, Windows, MacOS and Solaris, contains a
library of highly optimized algorithms and have very moderate
hardware requirements to run.
Most of the features that comes with each new release are the result of collaboration of UGENE development team and end-users. The best way to request a new feature or report an issue is using UGENE board: http://genome.unipro.ru/forum/
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DATES: October 4- 6, 2010
LOCALE: Max Planck Institute for Mathematics in the Sciences
URL: [link]
The main objective of this interdisciplinary workshop is to bring together leading scientists in key fields for integrated modeling of the function and evolution of biological networks, namely: gene regulatory networks, epigenomics, metabolic networks, RNA, and evolution of biological networks. While the main focus will be on the theoretical (modeling) side, recent advances from experiments will also be considered to identify important problems that challenge existing modeling paradigms. As a major outcome, we expect the identification of common questions and promising lines of research at the interfaces of functional sub-networks, possibly leading to a future integration into more detailed and more realistic models of biological systems.
Own work can be presented on posters (submission deadline: August 31).
REGISTRATION:
The event is free of charge.
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DATES: September-October, 2010
LOCALE: Distance Learning in Asian Countries (Video Conferencing)
URL: http://www.abren.net/workshop/
Asian Bioinformatics Research and Education Network (ABREN) is opening its 4th Virtual Training Workshop on Bioinformatics for September-October, 2010. A variety of topics in Bioinformatics are covered by experts in the fields mainly from Asian countries. The registered participants can view the multimedia lectures with video and synchronized slides in a video-on-demand (VOD) style from streaming servers located in different parts of Asia. All the lectures are classified into Basic, Intermediate and Advanced levels. Participants can ask teachers questions and get answers any time during the workshop period. The registration is free. Please visit the following site for registration.
Registration site: http://www.abren.net/workshop/
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DATES: November 8-12, 2010
LOCALE: US National Evolutionary Synthesis Center (NESCent) in Durham, NC, USA
URL: http://gmod.org/wiki/GMOD_Evo_Hackathon
This hackathon targets three critical gaps in the capabilities of the GMOD toolbox that currently limit its utility for evolutionary research:
1. Visualization of comparative genomics data
2. Visualization of phylogenetic data and trees
3. Support for population diversity and phenotype data
If you are interested in these areas and have relevant expertise, you are strongly encouraged to apply. Relevant areas of expertise include more than just software development: if you are a GMOD power user, visualization guru, domain expert (comparative, phylogenetics, population, ...), or documentation wizard, then your skills are needed!
REGISTRATION:
Fill out the online application form at http://bit.ly/gmodevohack. Applications are due August 25.
FOR MORE INFORMATION:
Main GMOD EvoHack page, and full proposal: http://gmod.org/wiki/GMOD_Evo_Hackathon
NESCent: http://www.nescent.org/
GMOD: http://gmod.org/
Similar past NESCent events, see: http://hackathon.nescent.org/
GMOD hackathon application: http://bit.ly/gmodevohack
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After last year's success the Blast2GO Team is again very pleased to announce this workshop. It will be offered to 35 participants at 2 locations:
DATES: October 20-22, 2010
LOCALE: Valencia, Spain
DATES: November 16-18, 2010
LOCALE: Florida, USA
The course will provide know-how and bioinformatics resources to assigning rich functional labels to high-dimensional sequence datasets and to extract new knowledge from annotation data. In this course you will learn tools and tips for functional annotation, visualization and analysis of novel sequence data making use of Blast2GO.
FOR MORE INFORMATION:
For more information and registration until the 15th of September please visit: http://bioinfo.cipf.es/blast2gocourse
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URL: http://biofunctionprediction.org/
Genome sequencing and structural genomics projects have generated a wealth of data. However, extracting meaningful information from genomic data is becoming increasingly difficult. Both the number and the diversity of discovered genes is increasing. This increase means that established annotation methods, such as homology transfer, are annotating less data. In addition, there is a need for annotation which is standardized so that it could be incorporated into function annotation on a large scale. Finally, there is a need to assess the quality of the function prediction software. We probably know the sequence of the target for next generation antibiotics or cancer treatment. We just did not recognize that target for what it is: it is currently annotated as a "domain of unknown function".
The mission of the Automated Function Prediction Special Interest Group (AFP-SIG) is to bring together computational biologists who are dealing with the important problem of gene and gene product function prediction, to share ideas and create collaborations.
About the CAFA experiment
The problem: There are far too many proteins in the database for which the sequence is known, but the function is not. The gap between what we know and what we do not know is growing. A major challenge in the field of bioinformatics is to predict the function of a protein from its sequence or structure. At the same time, how can we judge how well these function prediction algorithms are preforming?
The solution: The Critical Assessment of protein Function Annotation algorithms (CAFA) is an experiment designed to provide a large-scale assessment of computational methods dedicated to predicting protein function. We will evaluate methods in predicting the Gene Ontology (GO) terms in the categories of Molecular Function and Biological Process. A set of protein sequences is provided by the organizers. Participants are expected to submit their predictions by the submission deadline. The predictions will be evaluated during the Automated Function Prediction (AFP) meeting, which has been approved as a Special Interest Group (SIG) meeting, at ISMB 2011 conference (Vienna, Austria).
How to participate in CAFA:
1. Register for the experiment at http://biofunctionprediction.org
2. (Recommended) Subscribe to the low-traffic announcement list [link]
3. Download target proteins, available September 15, 2010
4. Submit predictions before January 15, 2011
5. Join us at the AFP-SIG at Vienna July 15-16, 2011 for the fifth protein function prediction meeting to hear the CAFA results, and about the latest research in computational protein function prediction
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We are pleased to announce MetaPred, a webserver which allows users to predict whether their drug molecule will be metabolize or not. It also predicts the cytochrome P450 isoform responsible for metabolizing a drug molecule. This is the first free online server for predicting drug metabolism. It has been published in BMC Pharmacology 2010, 10:8 ([link])
AVAILABILITY:
http://crdd.osdd.net/raghava/metapred/
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| Acknowledgments |
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We wish to thank the following for their support:
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