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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.
Portal:Gene Wiki - Wikipedia, the free encyclopedia
Welcome to the Gene Wiki portal. This portal is dedicated to the goal of applying community intelligence to the annotation of gene and protein function. The Gene Wiki is an informal collection of pages on human genes and proteins, and this effort to develop these pages is tightly coordinated with the Molecular and Cellular Biology Wikiproject. Our specific aims are summarized as follows:
* To provide a well written and informative Wikipedia article for every notable human gene
* To invite participation by interested lay editors, students, professionals, and academics from around the world
* To integrate Gene Wiki articles with existing Wikipedia content through the use of internal wiki links increasing the value of both
Please browse around the Gene Wiki, make an edit to your favorite gene page, and feel free to ask questions!
EcoliHub - a comprehensive K-12 information resource - Home
Sixty years of study have made Escherichia coli K-12 the most deeply understood organism at the molecular level. Much of what we know about cellular processes can be traced to fundamental discoveries in E. coli. In spite of its great importance as a model organism, information about E. coli is distributed among many online resources. EcoliHub uses web services that are being developed to make seamless bidirectional connections between E. coli resources, thereby enabling the full use of existing knowledge and supporting cutting-edge research into the molecular basis of life.
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EcoliHub is being developed to serve the user community. Users can help teach us what is desirable in future releases by taking our User Survey.
BMC Biology
BMC Biology - the flagship biology journal of the BMC series - publishes research and methodology articles of special importance and broad interest in any area of biology and biomedical sciences. BMC Biology (ISSN 1741-7007) is covered by PubMed, MEDLINE, BIOSIS, CAS, Scopus, EMBASE, Zoological Record, Thomson Reuters (ISI) and Google Scholar.
BioBlocks, Inc.
BioBlocks provides medicinal chemistry services and products to help our pharmaceutical customers accelerate their drug discovery chemistry programs. We are a responsible, experienced partner for custom synthesis and lead optimization projects. In addition, BioBlocks offers catalog sales of a unique collection of scaffolds and building blocks. BioBlocks maintains offices and laboratories in San Diego, California and Budapest, Hungary.
BLAST: Basic Local Alignment Search Tool
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
Bio-Linux
Bio-Linux 5.0 is a fully featured, powerful, configurable and easy to maintain bioinformatics workstation. Bio-Linux provides more than 500 bioinformatics programs on an Ubuntu Linux base. There is a graphical menu for bioinformatics programs, as well as easy access to the Bio-Linux bioinformatics documentation system and sample data useful for testing programs.
You can install Bio-Linux on your machine, either as the only operating system, or as part of a dual-boot setup which allows you to use your current system and Bio-Linux on the same hardware.
Bio-Linux also runs Live from the DVD. This runs in the memory of your machine and does not involve installing anything. This is a great, no-hassle way to try out Bio-Linux, demonstrate or teach with it, or to work with when you are on the move.
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.
PSB 2009 - FriendFeed
Room for discussion and recording of events surrounding the Pacific Symposium on Biocomputing, Hawai'i, January 2009.
A pitfall of wiki solution for biological database...[Brief Bioinform. 2008] - PubMed Result
Not a few biologists tend to consider wiki as a solution to manage and reorganize data by a community. However, in its basic functionality, wiki lacks a measure to check data consistency and is not suitable for a database. To circumvent this pitfall, installation of page dependency through in-line page searches is necessary. We also introduce two existing approaches that support in-line queries.
Bioclipse - Home
The Bioclipse project is aimed at creating a Java-based, open source, visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP). Bioclipse, as any RCP application, is based on a plugin architecture that inherits basic functionality and visual interfaces from Eclipse, such as help system, software updates, preferences, cross-platform deployment etc.
Theoretical and Computational Biophysics Group
Biological cells are surrounded by a highly versatile, yet very feeble cellular membrane and need to balance differences between the cell's interior and exterior that otherwise would burst the membrane. For example, the osmotic pressures inside and outside the cell need to be closely balanced. Thousands of proteins in the membrane act as gatekeepers, opening pores that can also act as safety valves, helping to reduce the interior-exterior difference in pressure rapidly. One such protein, the mechanosensitive channel of small conductance MscS (see the Mar 2008 highlight, "Observation and Simulation Depict Cell's Safety Valve", the Feb 2007 highlight, "Observing and Modeling a Crucial Membrane Channel", the May 2006 highlight, "Electrical Safety Valve", and the Nov 2004 highlight, "Japanese Lantern Protein") opens in response to cellular membrane tension generated due to a drastic imbalance in osmotic pressure as it arises when a bacterial cell suddenly finds itself in fresh water, rather than a highly saline physiological medium. The MscS channel widens then to jettison molecules out of the cell and reduce tension on the cellular membrane quickly. In a recent report, researchers have combined experimental data from electron paramagnetic measurements and computer modeling to reveal in atomic detail how MscS opens and closes its channel. Combining measurement and modeling, the researchers established a highly resolving computational microscope, unmatched by existing microscopes (more on our MscS website).
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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