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Topic: Open Bioinformatics Foundation

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	Bioinformatics.Org: The Open-Access Institute
		The course is led by researchers from the Genome Canada Bioinformatics Platform.
		And another is the Supercomputing Facility for Bioinformatics and Computational Biology, in the Chemistry Department (http://www.scfbio-iitd.res.in/).
		Bioinformatics at MACFAST School of Biosciences and Research Centre.
	bioinformatics.org (1396 words)

	Bioinformatics - Encyclopedia.WorldSearch (Site not responding. Last check: 2007-11-06)
		Bioinformatics or computational biology is the use of techniques from applied mathematics, informatics, statistics, and computer science to solve biological problems.
		Bioinformatics is very much involved in making sense of protein microarray and HT MS data; the former involves a number of the same problems involve in examining microarrays targeted at mRNA, the latter involves the bioinformatics problem of matching MS data against protein sequence databases.
		In the genomic branch of bioinformatics, homology is used to predict the function of a gene: if the sequence of gene A, whose function is known, is homologous to the sequence of gene B, whose function is unknown, one could infer that B may share A's function.
	encyclopedia.worldsearch.com /computational_biology.htm (1524 words)

	Synmaxis.Com Weblog » Blog Archive » Bioinformatics (Site not responding. Last check: 2007-11-06)
		A common thread in projects in bioinformatics and computational biology is the use of mathematical tools to extract useful information from data produced by high-throughput biological techniques such as genome sequencing.
		Bioinformatics helps to bridge the gap between genome and proteome projects–for example, in the use of DNA sequences for protein identification.
		In the genomic branch of bioinformatics, homology is used to predict the function of a gene: if the sequence of gene A, whose function is known, is homologous to the sequence of gene B, whose function is unknown, one could infer that B may share A’s function.
	synmaxis.com /blog/2007/03/02/bioinformatics (2776 words)

	Open source - Wikipedia, the free encyclopedia
		Open source politics — is a term used to describe a political process that uses Internet technologies such as blogs, email and polling to provide for a rapid feedback mechanism between political organizations and their supporters.
		Open source journalism — referred to the standard journalistic techniques of news gathering and fact checking, and reflected a similar term that was in use from 1992 in military intelligence circles, open source intelligence.
		Open source movie production is either an open call system in which a changing crew and cast collaborate in movie production, a system in which the end result is made available for re-use by others or in which exclusively open source products are used in the production.
	www.dvd-copy.com /documents/1369-en.wikipedia.org_wiki_Open_source.html (3869 words)

	Main Page - Open Bioinformatics Foundation
		The Open Bioinformatics Foundation or OBF is a non profit, volunteer run organization focused on supporting open source programming in bioinformatics.
		Occasionally the OBF 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.
		Bioinformatics Open Source Conference or BOSC is held annually in conjunction with ISCB's meeting ISMB.
	open-bio.org (138 words)

	BioJava - Wikipedia, the free encyclopedia
		The BioJava Project is an open source project dedicated to providing Java tools for processing biological data.
		The BioJava library is useful for automating those daily and mundane bioinformatics tasks.
		As the library matures, the BioJava libraries will provide a foundation upon which both free software and commercial packages can be developed.
	en.wikipedia.org /wiki/BioJava (99 words)

	bioinformatics standards
		Given the increasingly important role of bioinformatics in life science and pharmaceutical research, as well as the considerable investment that is made into research based on results generated by bioinformatics, quality control standards are becoming absolutely essential.
		As new bioinformatics algorithms and applications are developed and evolve, a rigorous standard must be applied.
		Although bioinformatics methods naturally evolve and are constantly improved, currently there is greater need for proper use of existing algorithms and applications rather than the development of new algorithms.
	janssen-genomics.com /html/standards.html (233 words)

	Blogger: Email Post to a Friend
		The 6th annual Bioinformatics Open Source Conference (BOSC 2005) is organized by the not-for-profit Open Bioinformatics Foundation.
		Because of the power of many Open Source bioinformatics packages in use by the Research Community today, it is not too presumptuous to say that the work of the Open Source Bioinformatics Community represents the cutting edge of Bioinformatics in general.
		If you are involved in the development of Open Source Bioinformatics Software, you are invited to provide a short demonstration to attendees of BOSC 2005.
	www.blogger.com /email-post.g?blogID=8360406&postID=110699152457645250 (660 words)

	[No title] (Site not responding. Last check: 2007-11-06)
		The Open Bioinformatics Foundation is an umbrella group for the various bio*.org projects that grew out of the original BioPerl project.
		The goal of the foundation is to provide financial, administrative and technical assistance for our various open source life science projects and the Bioinformatics Open Source Conference.
		Addendum: In October 2001 the OBF was formally incorporated as a non-profit entity.
	www.dalkescientific.com /news/010930-OBF.html (73 words)

	SUN MICROSYSTEMS AWARDS GRANT TO SUPPORT THE OPEN BIOINFORMATICS FOUNDATION'S OPEN-SOURCE RESEARCH TOOLS - ...
		The Open Bioinformatics Foundation (www.open-bio.org) supports the largest and most active community of volunteer developers dedicated to creating freely available standards-base tools for life science informatics.
		The foundation will use Sun hardware, including Netra rackmount servers, a Netra st A1000 storage array and a Sun Cobalt RAQ 4 rackmount server appliance, to meet its large and growing demand for tools and to create secure protection of its source code.
		Sun is a leading provider of open network computing solutions to colleges and universities around the world, powering academic, research and high performance computing systems, campus administration, digital libraries and student instruction systems.
	www.sun.com /smi/Press/sunflash/2001-09/sunflash.20010910.1.xml?printFriendly=true (602 words)

	O'Reilly Network -- Why I'm Not Supporting the Open Informatics Petition
		Two open source packages may be incompatible, meaning their licensing requirements are such that no software can be distributed which is derived from a combination of the two.
		Open source licenses set no restriction on when, how, or where the source is distributed (with minor exceptions).
		As an open source publisher I am free to release my source code only once a year, at a charge of $1 million paid at least two months in advance, and you have to accept it on paper tape while we are both standing under the Eiffel Tower.
	www.oreillynet.com /pub/a/network/2002/01/12/dalke.html (1491 words)

	New Page 1 (Site not responding. Last check: 2007-11-06)
		While many employers have clauses in their employment contracts that restrict the creation and use of open source software, bioinformatics programmers at universities are often not as attuned to copyright issues as their industry counterparts.
		Realizing that a large number of his colleagues and peers in the bioinformatics community may be facing a similar risk, he and other members of the Open Bioinformatics Foundation have set out to raise awareness of this issue.
		After speaking about his experiences at a talk at the Bioinformatics Open Source Conference in Copenhagen on July 19, Brenner said there was a good deal of interest from people who didn’t realize they were currently violating their institutions’ policies.
	www.bioinfoinstitute.com /newsgenome.htm (1296 words)

	Daenmark: Open Bioinformatics
		Lincoln Stein wrote this as a keynote speech for the 2002 O'Reilly Open Bioinformatics Conference in Tucson, Arizona.
		It is now a strong and stable component of a larger economic unit, the European Union, with which it shares a common currency, a common set of weights and measures, and a common set of rules for national and international commerce.
		My hope is that bioinformatics will one day achieve the same degree of strength and stability by adopting a universal code of conduct along the lines I propose here.
	www.daen.dk /archives/000101.html (348 words)


		The program is open to all registered attendees and includes an introduction to bioinformatics.org, panel discussions, project presentations, and evening "birds of a feather" meetings - bioinformatics.org track.
		The Open Bioinformatics Foundation (OBF) is an umbrella group for the various bio*.org projects that grew out of the original BioPerl project.
		The goal of the foundation is to provide financial, administrative and technical assistance for our various open source life science projects.
	conferences.oreillynet.com /cs/bio2002/pub/w/17/community.html (796 words)

	[Biojava-l] Re: The open bioinformatics foundation. (Site not responding. Last check: 2007-11-06)
		Bioinformatics.org: The Open Lab was established in 1998 to host all sorts of Free and Open projects in bioinformatics research, development, and information.
		I therefore suggest that there may be substantial overlap between the mission of The Open Lab and that of the proposed Open Bioinformatics Foundation.
		Jeff -- J.W. Bizzaro jeff@bioinformatics.org Director, Bioinformatics.org: The Open Lab http://bioinformatics.org/~jeff "Injustice anywhere is a threat to justice everywhere." -- Martin Luther King, Jr.
	www.biojava.org /pipermail/biojava-l/2000-August/000444.html (263 words)

	Pharmaceutical bioinformatics & computational biology glossary
		Bioinformatics is currently undergoing dramatic changes, as high- throughput laboratory methods lead to changes in key approaches, including sequence analysis, gene expression analysis, protein expression analysis, and protein structure prediction and modeling.
		The purpose of the foundation is to act as an umbrella organization for the various bio*.org projects that grew out of the original BioPerl project.
		Bioinformatics offers a means to get to a structure through sequence; while structure- aided drug design offers a means to get to a drug through structure.
	www.genomicglossaries.com /content/Bioinformatics_gloss.asp (5579 words)

	Salon.com Technology \| Genome liberation
		Cynthia Gibas, a bioinformatics professor at Virginia Tech, is very concerned about the way her university and others are using the Bayh-Dole Act to keep her colleagues from contributing to open-source software projects.
		With so many people going into bioinformatics, she notes, it's going to be difficult for them to develop decent software if they're not allowed to participate in already-existing open-source projects.
		Perhaps the only academic to negotiate a blanket open-source contract with his university so far is computational biologist Steven Brenner at U.C. Berkeley, who says that it took several months and hundreds of dollars in legal fees to come to an agreement with the U.C. technology transfer office.
	archive.salon.com /tech/feature/2002/02/26/biopunk/index1.html (1140 words)

	O'Reilly Bioinformatics Conference 2003
		A supporter of free software and open standards for life science research he is a founding member of the Bioperl Project, co-founder of the Bioclusters mailing list, and serves on the board of directors as Treasurer of the Open Bioinformatics Foundation.
		His research interest is the bioinformatics of the proteome, focusing on whole genome analysis in three areas: identification and characterization of Single Nucleotide Polymorphisms (SNPs), detecting alternative splicing across the entire human genome, and protein functional analysis.
		Francis Ouellette is Associate Professor at the University of British Columbia's Biotechnology Laboratory, and Director of the UBC Bioinformatics Centre, in Vancouver, Canada.
	conferences.oreillynet.com /pub/w/21/speakers.html (6859 words)

	Web services for bioinformatics, Part 1
		Document-style Web services are useful in bioinformatics because many bioinformatics applications take so many parameters and produce such complicated structures that RPC becomes cumbersome to the programmer.
		The most popular open source platform for bioinformatics applications are the libraries released by the Open Bioinformatics Foundation.
		She is also a member of the Fungal Genomics Laboratory, where she has worked on several bioinformatics projects, as well as the establishment and integration of their computational and data grids with North Carolina BioGrid.
	www.ibm.com /developerworks/library/ws-bioinfo.html (2630 words)

	BioJava -- Java Technology Powers Toolkit for Deciphering Genomic Codes
		While the foundation does not participate directly in the development or structure of the facilities, the members of the foundation are drawn from the member projects, so there is a clear commonality of direction and purpose.
		The bioinformatics realm is clearly still somewhat in "wild west" mode, prone to disparate and home-brewed formats and facilities.
		Meanwhile, Chris Dagdigian (who was instrumental in forming the Open Bioinformatics Foundation and is on its board of directors), has partnered with several colleagues to form BioTeam, a consulting collective dedicated to delivering vendor-neutral informatics solutions to the life sciences industry.
	java.sun.com /developer/technicalArticles/javaopensource/biojava (3550 words)

	The Open Bioinformatics Foundation (Site not responding. Last check: 2007-11-06)
		We're interested in bioinformatics as one of the fields that our son Sean may pursue in college, so it was interesting to see this article about the use of Macs and XServes in the field.
		Bioinformatics is an interdisciplinary research area loosely defined as the interface between the biological and computational sciences.
		The Herb Research Foundation is the world's first and foremost source of accurate, science-based information on the health benefits and safety of herbs---and expertise in sustainable botanical resource development.
	www.stargeek.com /item/28322.html (4726 words)

	Computer Related : Bio-* Programming Tools : Bioinformatics Links Directory
		The UBC Bioinformatics Centre does not specifically endorse or support any of the links in the directory, nor are we responsible for the content of any of these external sites.
		Bioconductor is an open source and open development software project that aims to provide access to a wide range of powerful statistical and graphical methods for the analysis of genomic data.
		The Open Bioinformatics Foundation is a non profit, volunteer run organization focused on supporting open source programming in bioinformatics.
	bioinformatics.ubc.ca /resources/links_directory/?subcategory_id=46 (901 words)

	BioinformaticsResources < Bioinformatics < myGrid wiki
		This is an interactive exercise that aims to provide a taste of bioinformatics resources around the world.
		KEGG (Kyoto Encyclopedia of Genes and Genomes) is a bioinformatics resource for understanding higher order functional meanings and utilities of the cell or the organism from its genome information.
		Links are also provided to a variety of other sequence and pattern databanks, to numerous bioinformatics sites, and to a unique set of in-house database search facilities.
	www.mygrid.org.uk /wiki/Bioinformatics/BioinformaticsResources (432 words)

	Sun Microsystems Awards Grant to Support the Open Bioinformatics Foundation's Open-Source Research Tools
		The Open Bioinformatics Foundation (http://www.open-bio.org) supports the largest and most active community of volunteer developers dedicated to creating freely available standards-base tools for life science informatics.
		The foundation unites a community of researchers to share information and methods and further their studies while reducing costs." "As leader of the Ensembl project, an effort to annotate eukaryotic genomes, open source software is critical to our mission," said Ewan Birney, team leader, European Bioinformatics Institute.
		"We respect Sun's commitment to facilitating and supporting open data standards in computational biology." Sun in Education Sun is a leading provider of open network computing solutions to colleges and universities around the world, powering academic, research and high performance computing systems, campus administration, digital libraries and student instruction systems.
	www.prnewswire.com /cgi-bin/stories.pl?ACCT=104&STORY=/www/story/09-10-2001/0001569142&EDATE= (533 words)

	Bioinformatics - Open Encyclopedia (Site not responding. Last check: 2007-11-06)
		sequence analysis, sequence motif, structural motif, protein structure prediction, biologically-inspired computing, morphometrics, metabolic network, Important publications in bioinformatics
		Bioinformatics.org: a portal and repository for open source bioinformatics software
		Open Bioinformatics Foundation: umbrella non-profit organization focused on supporting open source programming in bioinformatics
	open-encyclopedia.com /Bioinformatics (973 words)

	Terra Soft -- Linux for Sony PlayStation PS3, IBM Power and pSeries, Mercury Cell, and Apple PowerPC.
		Bioperl: The Bioperl Project is comprised of international volunteers who develop of open source Perl tools for bioinformatics, genomics and related research in the life sciences.
		BioPython: The Biopython Project is comprised of international developers of open source Python tools addressing the current and future needs of bioinformatics and computational molecular biology.
		BioPax: BioPax is a community based open source project in which has the objective of creating a standard data exchange format such that sharing biological pathway data between existing public and private databases becomes possible.
	www.terrasoftsolutions.com /products/ydl/3rd_party/index.php?cat_id=4 (611 words)

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