bioinformatics

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.

Heatmaps are a useful way to visualize matricies of data. Scientists often use green-black-red heatmaps to visualize gene expression data from microarrays. This visualization supports both three color heatmaps (ex: green to black to red) and two color heatmaps (ex: white to yellow).

JUNG provides a common and extendible language for the modeling, analysis, and visualization of data that can be represented as a graph or network.

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

A tool for visualizing abnormal read pairs (i.e. too far apart, forward-forward or reverse-reverse). One of the ways to identify structural variation in a genome is to look at mapping of a read-pair library on a reference genome. Any read-pair (i.e. the ends of the same clone) normally maps in a forward-reverse orientation at a distance from each other that corresponds to the insert size of the clone library. Structural variation between the reference genome used for mapping and the genome used to create the clone library will cause the reads to map in the wrong orientation (i.e. forward-forward or reverse-reverse; indicating an inversion) or at too large or too small a distance (indicating an insertion or deletion in the sample, respectively). pARP basically displays raw read pair mapping data and does not make any assumptions on models as might be required when doing a statistical analysis of the same data. By showing a birds' eye view it helps in interpreting what structural variations are present.

nucleotide blast Search a nucleotide database using a nucleotide query Algorithms: blastn, megablast, discontiguous megablast protein blast Search protein database using a protein query Algorithms: blastp, psi-blast, phi-blast blastx Search protein database using a translated nucleotide query tblastn Search translated nucleotide database using a protein query tblastx Search translated nucleotide database using a translated nucleotide query

BioPuppy is an minimal Linux OS and electronic workbench for bio-informatics and computational biology. It has been designed to meet the needs of beginners, learners, students, staffs and Research scholars. BioPuppy is available as a live CD cum installation CD [and in USB Pen drive] and containing all the required software to boot the computer with ready to use bio-informatics tools. BioPuppy is based of the Puppy Linux. The another objective of this BioPuppy is small in size. Our estimated size of BioPuppy is ~150MB.

A collaborative workflow builder and enactor for e-Sciences, in particular bioinformatics.

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.

Room for discussion and recording of events surrounding the Pacific Symposium on Biocomputing, Hawai'i, January 2009.

SEQanswers is a discussion forum and information source for next generation sequencing.

We are organizing a special session on "Data Mining in Protein Interaction Networks" in ISIBM conference (2009 ISIBM International Joint Conferences on Bioinformatics, Systems Biology and Intelligent Computing). Please refer the call for paper in http://www.isibm.org/IJCBS/sessions.html for more information of this special sessions (The main conference web site is at http://www.isibm.org/IJCBS/index.html).

These Web Services can be used to create applications on Molecules and their Properties. Details of the Web Services can be found here. If you are new to using these Web Services, please take a few minutes to read the instructions here.

Google App Engine enables you to build web applications on the same scalable systems that power Google applications.