Photolithography Advances; Updating Bioperl ; Data Collection Goes Mobile

PATENT WATCH | Photolithography Advances Affymetrix Affymetrix, the Santa Clara, Calif.-based manufacturer of GeneChip® microarrays, has developed a new device to create microarrays, according to a recently awarded patent.1 The new technique replaces physical photolithographic masks with computer-generated ones, and will, according to the application, "significantly improve the cost, quality, and efficiency of polymer array synthesis." GeneChip arrays typically consist of hundreds of thousands of 25-base-long oligonucleotide probes. These probes are synthesized on-chip, in parallel, using a process that employs photoreactive nucleotide building blocks. When exposed to light, these precursors become "deprotected," meaning they are available for coupling to the next nucleotide in the chain. Affymetrix (www.affymetrix.com) employs photomasks--small wafers riddled with holes-- to selectively illuminate, and thereby deprotect, different regions of the array that are to react with the next added nucleotide. In this way, each probe can be synthesized with a unique sequence. The new process replaces the old photomasks with a computer-controlled spatial-light modulator that dynamically creates and alters the illumination pattern. This modulator may be either a microelectronic device, such as a liquid crystal display, or a micromechanical device, such as an array of independently controlled mirrors or micromachined elements, each of which can be programmed to be reflective or diffractive. The system can also include an array of microlenses, which focus light on each "pixel" of the developing microarray. Though Affymetrix currently has no plans to switch its manufacturing process to accommodate the new method, the company has indicated its willingness to collaborate with others or license the device. 1. C.F. Quate, D. Stern, "Methods involving direct write optical lithography," US Pat. 6,480,324, Issued Nov. 12, 2002. SOFTWARE WATCH | Updating Bioperl In mid-December the Bioperl project (www.bioperl.org) released version 1.2 of its freely available, open-source bioinformatics application framework.1 Containing Perl modules for manipulating, parsing, and managing biological data, Bioperl is "a programming toolkit for bioinformatics," says Jason Stajich, a core project developer. Bioperl focuses mainly on sequence analysis and text-file parsing, explains Stajich. Normally, a bioinformaticist must deal with the minutiae of extracting data from databases such as GenBank before getting to actual sequence analysis. With Bioperl's object-oriented abstraction layer however, the programmer does not need to know exactly how a particular database record is formatted. "We've done ... all the work for parsing in the data," Stajich says, "so ... you can focus your efforts on looking for the particular part of the data that you're interested in." Other modules provide functions for database input and output; parsing output from such analysis programs as BLAST, HMMER, and ClustalW; and generating graphical sequence information--to build, for instance, a Web-based genome browser. Version 1.2 has a variety of bug fixes and performance enhancements, and adds modules to map sequences between different coordinate systems (e.g., from contig coordinates to assembly coordinates); modules to handle Gene Ontology information; and to parse UniGene clusters, among others. 1. J.E. Stajich et al., "The Bioperl toolkit: Perl modules for the life sciences," Genome Res, 12:1611-8, October 2002. GADGET WATCH | Data Collection Goes Mobile Courtesy of Biobserve Bonn, Germany-based Biobserve (www.biobserve.com) is angling to take field data collection high-tech. In place of the traditional clipboard, paper, and pencil, the company offers a range of mobile data acquisition systems using handheld computers. Current products include: Spectator GO!, to collect notes on 14 different behaviors on up to five subjects; Collector, to collect animal data such as size, weight, and gender; Outdoor Explorer, to collect behavioral, environmental, and spatial information about animals in the wild; and TMT GO!, for mobile Trail Making Tests (commonly used in neuropsychological research and assessment). Each software package works on Palm OS-based devices, but Biobserve also offers a Pocket PC-based version of Spectator GO! The company also sells peripherals to enhance the usability of these products, including a one-handed keyboard; a solar panel to replace batteries; software to print data directly from the Palm device; and a global positioning system (GPS) antenna. Both Spectator GO! and Collector can log GPS data, allowing field researchers to correlate observations with precise positional information. --Articles by Jeffrey M. Perkel

Photolithography Advances; Updating Bioperl ; Data Collection Goes Mobile

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