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Labkey Launch: Open-Source Proteomics Software Shop


Calling it an unlikely career move would be an understatement.

Labkey, a Seattle-based bioinformatics startup preparing to release the first version of its open-source proteomics analysis system, is the brainchild of several former Microsoft developers — a background generally not associated with proteomics or open-source software, let alone both.

The company’s six founders all left Microsoft in the mid-’90s. Co-founder Mark Igra explains that after a “long road” that included the launch of database software firm Westside and its eventual acquisition by BEA in 2002, the team found its way to the lab of Martin McIntosh at the Fred Hutchinson Cancer Research Center, where it developed the lab’s Computational Proteomics Analysis System.

“Martin wanted professional-quality software, and he built the team here to do that,” Igra says.

CPAS includes the X! Tandem open-source protein search engine, data-mining tools and viewers for mass-spec data, and project-management and sample-tracking tools. The system can also be extended beyond mass-spec data, and the team has already built a set of modules for flow cytometry, with another for gel-based experiments in the works. The idea behind the system is to “expose large data sets in ways that are accessible to researchers,” Igra says. At the Hutch, CPAS currently manages more than 28 million mass spec runs.

CPAS proved to be a success in the McIntosh lab, and Igra says that he and his colleagues “realized that there is a widespread need for this kind of software — a platform for dealing with experiments of any kind.”

Working with the Hutch, which owns one-seventh of Labkey, Igra and his partners decided to launch a business around the system’s underlying technology, which they have dubbed Labkey Portal. The motivation for the company came from a desire “to solve similar problems for other researchers and expand the system and make it more available, more functional and visible,” Igra says.

— Bernadette Toner



US Patent 6,931,396. Biological data processing. Inventors: Thodoros Topaloglou, Anthony Kosky. Assignee: Gene Logic. Issued: August 16, 2005.

This patent claims a multi-database query system that queries a plurality of databases and servers, including an input that receives queries in a structured form and a translation server that translates at least a part of a received query into commands recognized by a data manipulation server.


US Patent 6,950,755. Genotype pattern recognition and classification. Inventor: Douglas Stahl. Assignee: City of Hope. Issued: September 27, 2005.

The patent covers technology to interpret “data obtained by analysis of nucleic acids by obtaining nucleic acid data in a spatial domain, transforming the nucleic acid data from the spatial domain into a frequency domain, and obtaining sequence data of the nucleic acid data by executing a data mining process on the transformed nucleic acid data.”


The National Center for Genome Resources has received a $1.7 million grant from the NSF to develop a Virtual Plant Information Network in collaboration with Cold Spring Harbor Laboratory and TIGR.


GATC Biotech has established a subsidiary in Marseilles, France, and has also hired two new employees for its subsidiary in Cambridge, UK. This brings the 15-year-old company’s total number of employees to 40.


NIH is funding three new National Centers for Biomedical Computing, which will be supported by grants projected to total more than $56 million over five years. The centers include the National Center for Integrative Biomedical Informatics at the University of Michigan, the National Center for Multi-Scale Analysis of Genetic and Cellular Networks at Columbia University, and the National Center for Biomedical Ontology at Stanford University.


Strand Life Sciences, the Bangalore-based company formerly known as Strand Genomics, has announced plans to perform in silico drug discovery research in collaboration with Elan Pharmaceuticals.


Calgary-based United Bioinformatica has made an agreement with Taiwan-based Real Biotech Corporation to market their molecular biology kits in Canada.



$3.2 million

Siga Technologies has received a contract worth $3.2 million to computationally design small-molecule compounds to inhibit biowarfare agents for the United States Air Force.


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