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LSBC: Large Scale Bioinformatics Company? A Proteomics Shop Dabbles in Software Sales


Large Scale Biology Corporation, a proteomics company not known in the industry as a software provider, has begun to market several of the computational tools it developed for in-house use, the company told BioInform last week. The move is unrelated to a recent restructuring that eliminated 31 percent of LSBC’s staff and forced its highest-paid executives to take a 10-20 percent salary reduction, according to Gary Wolfe, vice president of informatics systems. But while the company began discussing plans to commercialize its software months before the belt-tightening began, additional revenues from software sales sure couldn’t hurt right now.

One of the applications LSBC is making available is a classification clustering algorithm called Biomarker Amplification Filter. It is the product of an internal project to re-analyze mass spectra from a paper published in The Lancet earlier this year that reported protein profiles for classifying ovarian cancer. Wolfe said that LSBC found several new markers for the disease state that went undiscovered in the publication using its own algorithm, which involves a “unique way of classification and feature enhancement.” LSBC researchers have since analyzed data sets from mass spec and other methods for a number of biotechnology and instrumentation companies, several of which are interested in licensing the software, Wolfe said. Potential users can test a slimmed-down version of the algorithm for free at

NaviGene, a visualization tool for sequence comparison developed for gene shuffling analysis, is another of LSBC’s software products.

Furthermore, Wolfe said that the number of biotechnology and pharmaceutical companies who have already expressed an interest in LSBC’s laboratory information management system is in the “double digits.” The system — called LSIMS for Large Scale Information Management System — is fast and scalable, he claimed, and LSBC will also offer custom-built workflows to accommodate special needs. Wolfe said he first saw signs of interest in the system last fall when he presented examples of LSBC’s workflows in talks and presentations. Internal discussions to make LSIMS available as a commercial product started at the beginning of this year.

What distinguishes LSBC from pure-play software companies, said Wolfe, is that product development costs were minimal — four programmers constitute the company’s entire informatics workforce, and all products were originally developed for internal use.

LSBC does not view the sale of its in-house technology to potential competitors as a signifiant risk. “I can’t think of a reason why that would hurt us in the way we sign deals and bring revenue into the company,” said Wolfe. “I think it can only help it.”

— JK

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