Software Watch

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

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

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

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

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

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

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.,

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

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

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

If you've been intrigued by Linux but want to avoid the hassle of repartitioning your hard drive, Bioknoppix http://bioknoppix.hpcf.upr.edu may be just what you need. A bioinformatics-themed version of Knoppix, Bioknoppix, unlike most Linux distributions, does not install to the hard drive; instead it runs from a CD.As a result, the existing operating system is untouched, says Bioknoppix codeveloper Humberto Ortiz of the University of Puerto Rico. "You just pop the CD in and reboot the computer,

For every model organism whose genome is being sequenced, a community of researchers clamors for the data. Model organism databases often provide the necessary interface to such information, but they can be difficult to set up, maintain, and make conversant with other databases. Enter the Generic Model Organism Database (GMOD) project http://www.gmod.org.GMOD's long-term goal, says project coordinator Scott Cain, is to create a suite of application tools (e.g., for browsing, curation, annotation

Creating a protein crystal structure diagram from raw X-ray diffraction data is a labor-intensive task that can take weeks to months. A new program called ELVES http://ucxray.berkeley.edu/~jamesh/elves from the Lawrence Berkeley National Laboratory in California automates the process and can churn out the diagram in only a few hours."When humans deal with a complex system with hundreds of things to keep track of, they make mistakes," says James Holton, the creator of the UNIX-compatible program

Most bioinformatics programs churn out raw text files bursting with data, but devoid of interpretation. Programmers spend much of their time slogging through these files-computationally speaking – to extract useful information. For nearly 10 years, the bioperl project http://www.bioperl.org has labored to relieve bioinformaticians of this burden, building an object-oriented toolkit that handles the nitty gritty of data format and access so that developers can concentrate on their bioinform

Biological databases are everywhere. From protein libraries in Switzerland to genome repositories in Maryland, one could spend hours tracking down all the sources of information on the Internet. An ambitious new project at the San Diego Supercomputer Center, University of California, aims to bring them all into one easy-to-use, centrally hosted place that is open to all.Culling data from over a dozen databases, the Encyclopedia of Life project (EOL, http://eol.sdsc.edu/) seeks "to catalog the co

When Glen Otero worked as a postdoc at the San Diego Supercomputer Center, he noticed a project called NPACI Rocks, which fine-tunes the operating system for cluster computing. That software now forms the core of Otero's own Linux distribution called BioBrew http://www.bioinformatics.org/biobrew.Based on Red Hat Linux kernel 7.3, BioBrew is optimized for cluster computing and bioinformatics. Besides the usual collection of networking and programming tools, the distribution includes such clusteri