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Courtesy of Filippo RusconiWhile a graduate student, Filippo Rusconi couldn't come up with the money to pay for a Microsoft developer's license to continue work on his mass spectrometry program. So instead he rewrote the whole program in GNU/Linux. It turned out to be the best thing that happened to him, he says. "It allowed me to make the program a thousand times more powerful."The program, now called GNU polyxmass http://www.polyxmass.org is a complete software suite for mass spectrometrists t

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IBM Goes for Unity

By | August 30, 2004

Courtesy of IBMA new effort to unify the naming conventions of biological data is now underway in labs and companies throughout the world. The Life Science Identifier (LSID) Resolution Protocol Project consists of two software programs and a set of naming standards http://www.ibm.com/developerworks/oss/lsid.The first program is a server application called LSID Authority, which allows database and Web-site managers to identify their data with LSID URNs (uniform resource names, similar to URLs). T

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Reactome Explores Biological Processes

By | August 2, 2004

Courtesy of http://www.reactome.orgReactome, a new knowledgebase of human biological processes, launched on June 2 http://www.reactome.org. An NIH-funded collaboration between Lincoln Stein's lab at Cold Spring Harbor Laboratory (CHSL), NY, and Ewan Birney's lab at the European Bioinformatics Institute (EBI), Hinxton, UK, the Reactome supersedes an earlier project called the Genome Knowledgebase.Flexible searching tools allow users to explore biological processes and pathways in a variety of way

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Mining Cancer Arrays with Oncomine

By | July 19, 2004

Courtesy of OncomineEach week it seems a new study comes out about applying DNA microarrays to cancer. The data are generally publicly accessible, but not conveniently so, as they are scattered about the Web or available only by E-mail.Arul Chinnaiyan, director of the University of Michigan Pathology Microarray Center in Ann Arbor, decided to collect all the data and put it in a single place, along with some bioinformatics tools to help cancer biologists interpret the information.The result is O

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Systems Biology on the Grid

By | July 5, 2004

Courtesy of CellwareThere are more than 60 in silico modeling programs available to systems biologists, including expensive proprietary packages and niche open-source projects. Most of them, though, rely on one kind of algorithm to calculate a model.That's why Pawan Kumar Dhar, a senior research scientist at the Bioinformatics Institute in Singapore, designed Cellware http://www.bii.a-star.edu.sg/research/sbg/cellware/index.asp. "In gene expression, you would usually use deterministic algorithms

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Biopython Hits Version 1.3

By | June 21, 2004

Cindy MageeThe Biopython project http://www.biopython.org released its new version 1.3 last month. Hosted by the Open Bioinformatics Foundation (OBF), Biopython is an international effort to build reusable, open-source tools and libraries for bioinformaticians using an interpreted language called Python http://www.python.org.Like its sister projects (BioPerl, BioJava, and BioRuby) at OBF, Biopython includes code to manipulate and annotate sequences, communicate with remote databases, parse file

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BNS Provides Faster Symbol Mapping

By | June 7, 2004

Biological databases typically tag their records with unique identifiers called accession numbers. These locators simplify record retrieval, but they are also database-specific, presenting a headache for bioinformaticians who want to map records in one database with their equivalents in another. Typically this is done manually, a tedious, error-prone task, especially when applied genome-wide.A few years ago, Robert Kincaid, a senior research scientist at Agilent Laboratories, Palo Alto, Calif.,

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Gel Annotation on a Budget

By | May 24, 2004

Proteomicists who want to share their data, take heed: A team at the University of Alberta has a software tool for you. GelScape http://www.gelscape.ualberta.ca is a free, cross-platform, browser-based tool for annotating, manipulating, comparing, and storing 1-D and 2-D protein images.1 Users can run the Java-based software off servers in Edmonton or install a local copy on their individual PC, according to David Wishart, a bioinformatics professor at the University of Alberta who oversaw the p

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Taking Control of the Cluster

By | May 10, 2004

When Gernot Stocker noticed that the biologists in his lab were not using the department's brand-new, 24-node computer cluster, he started taking notes. Running sequences on a desktop computer could take days, yet these scientists preferred that to the cluster for a simple reason. "Biologists don't like command-line software," says Stocker, a graduate student at the Institute for Genomics and Bioinformatics at Graz University of Technology in Austria. "They're used to using Web browsers."So Stoc

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To siRNA with Love

By | April 26, 2004

Just as the use of RNA interference has mushroomed throughout the world over the last six years, the number of bioinformatics tools to screen for siRNA has blossomed, too. More than a half-dozen proprietary and open-source programs are available, many sponsored by siRNA and reagent vendors.So Jonathan Rux, a bioinformatician at the Wistar Institute at the University of Pennsylvania, was surprised to find that all these resources lacked a critical tool: They didn't account for gene specificity. S

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