Array Analysis Online

2001-2002 VizX Labs As a graduate student, Eric Olson learned something about DNA microarrays: Biochip data management can be vexing. His graduate adviser abandoned a number of microarray experiments because it was too difficult to manage the data using the software supplied with the arrays. Now Olson is director of science for a company that is trying to change that. Seattle-based VizX Labs offers a Web-based, platform-independent microarray data analysis package called GeneSifter. Net™. Originally developed by NeoBase, a start-up company formed by a group of University of Washington biologists who were frustrated with conventional microarray analysis software, GeneSifter. Net is designed to be accessible to researchers with little computer expertise. Olson, one of the program's developers, explains that he and his colleagues found array analysis software too complicated to use and "not worth the time and effort" it took to gain the level of computer literacy required to work with it. Olson decided that the best way to solve the main problems--managing and analyzing data and making sense of gene lists--with existing array analysis software was to adopt Web-based technologies. GeneSifter.Net is accessible through the Web via a secure password, rather than installed on an individual computer, eliminating the need for seat-specific licenses. "A lot of the software in this field goes all the way back to having dongles that plug into the back of a machine, so you are locked to that one workstation," says Elon Gasper, senior vice president at VizX Labs. "Our software runs on any computer that's hooked up to the World Wide Web," he says. As a result, scientists can upload data to the Web and access analysis tools from any computer at any time. Part of the appeal of GeneSifter.Net is its simplicity; Gasper explains that the software was designed to be convenient to use for general microarray data analysis rather than for specialized tasks and, therefore, does not include unnecessary features that may limit ease-of-use. Gasper adds that the product went through extensive market testing, including one-way mirror testing and time-and-motion optimizations, before its formal launch last October. The testing ensured that the software would be easy to use by scientists without formal training and that investigators who do not extensively use microarrays in their research can easily go back to the software after a long absence. 2001-2002 VizX Labs Because the software and data are located on an externally maintained server, there is no need to set up a laboratory server or to institute a laboratory backup protocol. Olson emphasizes that GeneSifter.Net is aimed at the bench scientist rather than bioinformatics support personnel and does not require the user to make a commitment for system administration and hardware support. "Most scientists would rather do science than information technology," adds Gasper. GeneSifter.Net is compatible with any operating system, including Macintosh, Windows, and Linux, and is fully integrated with online public genomics data-bases such as GenBank, UniGene, and LocusLink, so the most current information is always available to users. "The software that was originally developed for microarray analysis did not see these databases as being central to the research process," says Gasper. "Our product was written with that integration in mind from the very beginning." In addition, because data can be accessed through any Internet-ready computer, researchers can use GeneSifter.Net to collaborate with other scientists anywhere in the world at any time. The software includes a gene navigation feature that allows the user to group results by function using the GeneOntology™ Consortium database. In addition, GeneSifter.Net accepts any type of data format, including custom; features automatic quality control and data backup; and produces publication-quality graphics complete with standard error bars. And, its Web-based format facilitates instant software updates. Concludes Gasper, "There's very low impact on your work process [with GeneSifter.Net]." --Aileen Constans

Array Analysis Online

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