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Consolidation continues: Agilent buys Silicon Genetics


The gene expression analysis software market will undergo a seismic shift in a few months, when Silicon Genetics — the most well-known company in that segment of the bioinformatics sector — becomes part of Agilent Technologies under an acquisition deal the companies announced in late August.

Silicon Genetics is a rare bioinformatics success story. The privately held firm has been profitable ever since it launched its flagship GeneSpring software in 1998, and now claims more than 4,000 users for that product. But the company’s acquisition (the terms of which have not been disclosed) sends a bit of a mixed message to the remaining vendors in the gene expression analysis market: It illustrates the value that large platform vendors — and their customers — are placing on bioinformatics tools, but it’s an additional reminder that the wave of consolidation that began last year within the sector has not yet run its course. In addition, this deal could even accelerate the pace of the shakeout: With the formidable sales and marketing force of Agilent behind Silicon Genetics’ software, how will smaller software firms compete?

Agilent spokeswoman Christina Maehr says that Agilent expects to take on nearly all of Silicon Genetics’ 50 or so employees, which will nearly double the size of Agilent’s current bioinformatics group. She says the companies will follow a “reverse integration” model that will keep the smaller firm organizationally intact “to minimize disruption,” while the Agilent informatics employees will be folded into that group. “In terms of the organizational structure, we’re going to try and keep that as much the same as possible so that we don’t wreck a good thing,” she says. The acquisition was scheduled to close within two to three months.

— Bernadette Toner


US Patent 6,760,715. Enhancing biological knowledge discovery using multiple support vector machines. Inventors: Stephen Barnhill, Isabelle Guyon, Jason Weston. Assignee: Barnhill Technologies. Issued: July 6, 2004.

The patent described covers multiple support vector machines used to extract essential information from vast quantities of biological data. The method includes pre-processing of training data and test data to add dimensionality or to identify missing or erroneous data points. After training has been confirmed, live biological data can be pre-processed and then entered into the identified support vector machine that provides the optimal solution for extraction of useful information.

US Patent 6,743,576. Database system for predictive cellular bioinformatics. Inventors: James Sabry, Cynthia Adams, Eugeni Vaisberg, Anne Crompton. Assignee: Cytokinetics. Issued: June 1, 2004.

This patent covers a “system for acquiring knowledge from cellular information” using a database made up of various management (DBMS) and other modules to categorize and store various sets of data from an imaging instrument. According to the patent abstract, “the system has a translation module coupled to the DBMS for defining a descriptor from a set of selected features. … A prediction module is coupled to the DBMS for selecting one of a plurality of a descriptors from known and unknown compounds from the database based upon a selected descriptor from a selected compound.”


$ 240 million
Size of estimated global market for analytical bioinformatics software this year, according to a prediction from Research and Markets. They further expect growth to continue at 9.3 percent, bringing the same market to $375 million in 2009.

Last month Indiana University broke ground in Indianapolis for its Medical Information Sciences Building. The new facility will house various university programs, including the Center for Computational Biology and Bioinformatics, the Division of Biostatistics, and the Center for Bioethics.

New Mexico State University received a $4.5 million grant over five years from NSF to start a new bioinformatics center consisting of faculty from computer science, biology, biochemistry, agronomy, and horticulture. The university plans eventually to offer both master’s degree and PhD programs in the discipline.

Using its statistical modeling and analysis technology, Accelrys will work with aerospace firm Northrop Grumman in its effort to develop bioagent detectors to monitor bacteria, viruses, and toxins for the US Department of Homeland Security.

The UK has launched two new bioinformatics initiatives: the Biosystems Informatics Institute, led by Ian Humphery-Smith and subsisting on $7.3 million in seed funding from the UK’s Department of Trade and the One NorthEast regional economic development agency, will develop genomics-related software with a goal of spinning off companies down the road. Meantime, the new UK National Text Mining Center has close to $2 million from various British science agencies and aims to design text-mining tools targeted at biomedical research.

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