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

Nearly 35 years since Stanford researcher Leonard Herzenberg and colleagues developed the first fluorescence activated cell sorter (FACS), the instrument has become the immunologists' key tool. Immunology journals are chock-full of flow-cytometry profiles, the characteristic plots that such instruments produce.But cytometry is just half the story. The instruments also allow researchers to purify specific cell populations based on the presence or absence of particular characteristics. And therein

Fifteen years into the microarray revolution, biochip images – row upon row of red and green spots on a field of black – have become as ubiquitous as DNA gels once were.But how are those pictures generated? Arrays are imaged using one of two classes of equipment: array imagers and array scanners. Both use lasers to excite the fluorphors on the chip, but where imagers capture a snapshot of the glowing array using a charge-coupled device (CCD camera), scanners read the chip point-by-po

MOLECULAR CARTOGRAPHY:Recognizing that much of the cell's work is done not by individual proteins but by large macromolecular complexes, researchers increasingly are trying to map protein-protein interactions throughout the cell. This map of the C. elegans interaction network, or "interactome," links 2,898 proteins (nodes) by 5,460 interactions (edges). (reprinted with permission, Science, 303:540–3, 2004.)If you want a sense of one of the hottest trends in biology today, open the hood of

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.,

Courtesy of Quantum DoWhen it comes to gene-expression analysis, researchers seem always to be sacrificing something. With real-time quantitative PCR, it's gene number: Though inexpensive enough to apply to large numbers of samples, each assay can test, at best, three or four transcripts simultaneously. Microarrays, on the other hand, sacrifice sample throughput, probing tens of thousands of genes in a single sample.Quantum Dot http://www.qdots.com has developed a compromise solution. According

Repligen and MIT sue ImClone over 1987 Tonegawa mammalian cell protein production patent

CRYSTAL CITY:Courtesy of FluidigmFluidigm's TOPAZ 1.96 screening chips employ microscale channels and valves for diffusive mixing of protein and crystallization reagents. Future chip designs will steadily increase parallel throughput.Protein structure determination using X-ray crystallography typically suffers from two major bottlenecks: producing sufficient quantities of material, and finding appropriate crystallization conditions. The TOPAZ™ Crystallizer, released last year by microfluid

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,

Perhaps no tool has been as instrumental to the proteomics revolution as the mass spectrometer. With the ability to deconvolute highly complex mixtures over a wide range of abundance levels, these machines enable researchers to identify and quantify proteins and to determine if and how those proteins have been post-translationally modified.The basic mass spectrometer measures an ion's mass-to-charge (m/z) ratio only. This enables peptide mass fingerprinting, which is the identification of a prot

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