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Main Page - Open Bioinformatics Foundation
The Open Bioinformatics Foundation or O|B|F is a non profit, volunteer run organization focused on supporting open source programming in bioinformatics.
The foundation grew out of the volunteer projects BioPerl, BioJava and BioPython and was formally incorporated in order to handle our modest requirements of hardware ownership, domain name management and funding for conferences and workshops.The Foundation does not participate directly in the development or structure of the open source work, but as the members of the foundation are drawn from the member projects, there is clear commonality of direction and purpose. Occasionally the O|B|F directors may make announcements about our direction or purpose (a recent one was on the licensing of academic software) when the board feels there is a need to clarify matters, but in general we prefer to remain simply the administrative support organization for our member projects.
Our main activities are:
* Underwriting and supporting the BOSC conferences
* Organizing and supporting developer-centric "hackathon" events
* Managing our servers, colocation facilities, bank account & other assets
We are incorporated in the state of Delaware, USA as a not-for-profit company.
rapodaca's cheminfbenchmark at master - GitHub
Cheminformatics Benchmark Toolkit --------------------------------- Why? Because we want to: 1. measure if a patch improves performance 2. compare cheminformatics toolkits Project ------- This is an open project, and anyone can contribute or patch the tests, in order to attempt to create a balanced and fair test suite impartial to the toolkit being tested. Versioning ---------- When reporting results for a toolkit for a test, always report the version of ChemInfBenchmark release, as well as the test number as listed below. The tests --------- Toolkits should always to the bare minimum; any extra things will only make the outcome unfavourable, but toolkits may do that if they wish. 1. Convert an SD file to XYZ 2. Calculate the molecular mass of the entries in an SD file 3. Convert an SD file to CML 2.5 4. Perform a substructure match on all of the entries in an SD file 5. Parse a collection of SMILES - this will be a measure of performance and completeness 6. Detect rings in a collection of molecules. 7. Parse (not perform the search) for a collection of SMARTS patterns - this will be a measure of performance and completeness Running tests ------------- Each test is run via a configure file. A test can be run by $ ant -Dconfig=test-config.xml run
Jeff Jonas
A collection of thoughts on information management and privacy in the information age, injected with a few personal stories.
National Center for Integrative Biomedical Informatics
The National Center for Integrative Biomedical Informatics (NCIBI) is one of seven National Centers for Biomedical Computing (NCBC) in the NIH Roadmap. NCIBI is based at the University of Michigan and is part of the UM Center for Computational Medicine and Biology (CCMB). Brian Athey is the Principal Investigator for the NCIBI.
Main Page - GenBioWiki
GenBioWiki is the student home page for the Genetics, Bioinformatics, and Computational Biology (GBCB) program at Virginia Tech. Bioinformatics and computational biology provide a research platform to acquire, manage, analyze, and display large amounts of data, which in turn catalyze a systems approach to understanding biological organisms, as well as making useful predictions about their behavior in response to environmental and other perturbations. Moreover, bioinformatics is the study of biological systems and large biological data sets using analytical methods borrowed from computer science, mathematics, statistics, and the physical sciences. This transdisciplinary approach to research requires graduates with extensive cross-cultural professional and technical training and provides ample employment opportunities for Ph.D. graduates. [1]
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