Critical Assessment of protein Function Annotations

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

http://biofunctionprediction.org/

MetaPred, a server for predicting drug metabolism

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

AVAILABILITY: http://crdd.osdd.net/raghava/metapred/

Microsoft Biology Foundation available for free download

On July 10, in Boston, the External Research division of Microsoft Research introduced the Microsoft Biology Initiative, resources designed to help biological scientists and programmers conduct research more efficiently and affordably. These include the first post-beta release of the Microsoft Biology Foundation (MBF), a language-neutral bioinformatics tool kit built as an extension to the Microsoft .NET Framework.

In addition to a new genome assembler, performance enhancements, and other improvements, MBF builds upon the vision and goals that drove the development of the beta versions. Those included a commitment to community involvement, extensibility, cross-platform and interoperable functionality, language neutrality, and support for best practices.

While there are other libraries of biological functionality available, MBF supports universally accepted standards of the bioinformatics community and implements a range of unique functionality derived from original Microsoft research. The code for MBF and supporting documents is available on CodePlex[RK1] .

FULL STORY:
For the full story check out the External Research Blog at: http://blogs.msdn.com/b/msr_er/

a2zbioinformatics.com

This website seeks to apply multidimensional approaches to solve statistical and combinatorial problems in biosciences. It provides important information and links in the fields of genome analysis, genetics, protein sequence analysis and genetic epidemiology. The website provides links to all the major software used in the analysis of biological information. It also provides detailed information on all the Government/Semi government Institutes as well as private companies dealing with bioinformational analysis and training. Detailed tutorials on selected topics have also been provided.

Link: http://www.a2zbioinformatics.com

Professional development online

At the University of Manchester, UK, we have over 10 years experience in teaching a range of online courses in computational biology. These courses are designed to enable those with a background in the life sciences, computer science, mathematics or related disciplines to update their skills, while remaining in the workplace. The courses are also very suitable for home study, helping you to keep in touch with a research environment while taking a career break.

The modules running next semester, from October 2010, include :

Introduction to software development in Java
Bioinformatics for Systems Biology
Introduction to Health Informatics
Biocomputing
Computational Systems Biology

These modules can be studied individually, or you can choose to register for a formal qualification. Those wishing to progress to the MSc will complete a supported research project. Examples of projects that have been published in a range of journals are listed here : [link]

For further information, please visit our programme website :http://octette.cs.man.ac.uk/bioinformatics/index.html

National Cancer Institute caBIG® Annual Meeting, Building a Collaborative Biomedical Network

Join the National Cancer Institute for its 2010 caBIG® Annual Meeting – Building a Collaborative Biomedical Network
- Learn about the critical importance of biomedical informatics and information technology in facilitating multidisciplinary collaboration across institutional barriers and advancing biomedical research
- Discover caBIG® capabilities that can support your work and share lessons learned with others who have developed and applied caBIG® technology to advance basic and clinical research
- Engage in unparalleled opportunities for networking and information exchange with leaders in biomedical informatics
- Investigate innovative tools and explore the caBIG® services-oriented architecture during hands-on sessions and demonstrations

REGISTRATION:
This meeting is free to attend and open to the public:
https://cabig.nci.nih.gov/2010AnnualMeeting

Influence of virtual conferences on bioinformatics in developing nations

Organizing on-site conferences requires substantial expense including the costs of the venue, labour, and accommodations for speakers invited from other countries. Scientific institutions in developing nations can find these costs prohibitive, thus limiting the number of conferences that they can afford to host.

We at Bioinformatics.Org, in collaboration with Bioclues.org, a partner of Asia Pacific Bioinformatics Network (APBioNet.org), recently organized a virtual conference on bioinformatics in India (Inbix'10) featuring an impressive collection of distinguished speakers. Although the bandwidth and network stability in India is modest relative to that of Western nations, the advantages of lower cost and effort outweighed these technical difficulties, and the virtual conference was considered a success by the organizers and participants.

A meeting report of this conference has been recently published in India's journal Current Science, a publication of the Indian Academy of Science. The report is available at http://www.ias.ac.in/currsci/10jun2010/1428.pdf