Researchers at the Virginia Bioinformatics Institute recently assessed several microarray-analysis software packages based on their ability to provide researchers with “biological insight” — a seemingly subjective term that the VBI team painstakingly broke down into eight measurable characteristics in order to glean quantifiable feedback from participants.
While the study was limited in its scope — it evaluated only five visualization packages — industry observers applauded the effort as the first such usability study in bioinformatics, and hailed it as a sign that the field may finally be coming of age.
“I think usability is one of the barriers that keeps these tools from a much larger percentage of true biological users — not bioinformaticists or cheminformaticists or computational biologists, but bench biologists,” says Evan Steeg, a life science data-mining and IT consultant. “In order to get to the point where these tools become ubiquitous for biologists … there is a definite usability burden [that] has to be surmounted, and these kinds of studies will help.”
Michael Lelivelt, senior manager for informatics applications at Affymetrix, says that the VBI study is “a great start” toward quantifying visualization performance — as well as other features of microarray analysis software. “I think the best service to the community is to have independent parties continue to bring visibility to these issues.”
Karen Duca, co-author of the study, says that human-computer interaction evaluations are common in other fields, but are still a rarity in bioinformatics. One reason for this, she suggests, is that “the biology field in general hasn’t been used to dealing with dense data, so I won’t say that we never had the need for good interface design, but perhaps we’ve never been quite as demanding” as users in other fields.
— Bernadette Toner
US Patent 6,850,846. Computer software for geno-typing analysis using pattern recognition. Assignee: Affymetrix. Inventors: Eugene Wang, Teresa Webster. Issued: February 1, 2005.
This patent covers software and a system to determine the genotype of a sample “using a plurality of probes,” according to the abstract. “In one preferred embodiment, a tentative genotype call is made based upon the relative allele signals. Pattern recognition is then used to validate the tentative call.”
US Patent 6,847,995. Security architecture for distributed processing systems and associated method. Assignee: United Devices. Inventors: Edward Hubbard, Sriram Mandyam. Issued: January 25, 2005.
Under this patent, inventors describe a security architecture and method for enabling secure transmissions within distributed processing systems, the abstract states. “More particularly, a server system is coupled to a network that is configured to be coupled to a plurality of distributed devices. The server system utilizes a security measure that is partitioned and distributed to multiple distributed devices. The distributed device receiving electronic information reconstructs the security measure by obtaining the various partitioned portions from the multiple distributed devices.”
Increase in bookings, worth $37.9 million, reported by Accelrys for the quarter ending Dec. 31, over the same quarter the year before. However, the company’s revenue for the same period saw a 30 percent decrease to $22.2 million. This is attributed to the transition to a subscription accounting model that began in 2004.
The European Union has awarded €8.3 million to a consortium of European bioinformaticists to improve access to bioinformatics databases. The group consists of 17 institutes across 11 countries and is headed by EBI Associate Director Graham Cameron. The group expects to build a data grid that will provide for standardized access to informatics databases.
The Whitehead Institute plans a spring launch for the open-source image analysis package CellProfiler. The project has been in the works with Anne Carpenter, David Sabatini, Polina Gollard, and Thouis Jones.
Incyte got rid of the last of its database unit by selling its subsidiary, Proteome, to Germany’s Biobase. Biobase will have access to the databases for Proteome’s BioKnowledge Library and LifeSeq Foundation.
OmniViz signed a development deal with Infocom to jointly develop genetic network analysis software.
The Arizona Disease Control Research Commission awarded a three-year contract for a total of $300,000 to 5AM Solutions, a Phoenix-based Web applications developer for life sciences research. 5AM will use the money to build the System for Collaborative Translational Research — a Web-based application to support clinical research — and the Microarray Enterprise Manager — a Web-based information-management system for microarray core labs.