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For a HTS LIMS, a Columbia Lab Built Its Own

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Brent Stockwell’s lab at Columbia University learned the hard way what many pharmaceutical research groups have known for years: “There is no commercial [LIMS] system for high-throughput screening data, and that you always in the end need to build your own.”

The difference, however, between those industry groups and Stockwell’s is that the fruits of his lab’s labors will be available for other research teams facing the same problem. The Columbia researchers have recently released on Sourceforge their home-grown HTS LIMS, called SLIMS (for Small Laboratory Informatics Management System).

“We really did not want to develop our own system in the beginning,” Stockwell says. His team did procure a LIMS system from an undisclosed vendor, and soon found “that it was simply not compatible with the kind of work that we were doing.”

Stockwell chalked up the system’s failings to the inherent differences between pharmaceutical labs — for which most commercial LIMS are designed — and academic groups like his own. “In industry, often there’s a separation between chemists, biologists, and automation specialists … but in the kind of research that we do, it’s continuous collaboration and data exchange between chemists, biologists, and automation specialists,” Stockwell says. “So we needed a system that allowed the rapid and continuous data transfer between those groups.”

SLIMS includes a cheminformatics engine for substructure searching and similarity searching, a database that can be shared between collaborators, and modules for plotting and analyzing assay data via self-organizing maps and other analysis tools.

Other features include a tool that automatically identifies and corrects systematic errors introduced in the experimental process, as well as an algorithm that searches the scientific literature to annotate small molecules with information about their mechanism of action.

— Bernadette Toner

 

PATENT WATCH

US Patent 6,826,296. Method and system for providing a probe array chip design database. Inventors: David Balaban, Earl Hubbell, Michael Mittmann, Gloria Cheung, and Josie Dai. Assignee: Affymetrix. Issued: November 30, 2004.

This patent covers systems and a method “for organizing information relating to the design of polymer probe array chips” and oligo array chips, according to the abstract. “A database model is provided which organizes information interrelating probes on a chip, genomic items investigated by the chip, and sequence information relating to the design of the chip.” The model can be converted into various database languages and scales to allow for storage of high volumes of data.

 

US Patent 6,816,789. Method and system for analyzing chromatograms. Inventor: Jean-Louis Excoffier. Assignee: Varian. Issued: November 9, 2004.

The patent protects an approach for chromatogram analysis, which can be used to identify DNA sequence variations, according to the abstract. The invention can reduce chromatograms to data sets for comparison purposes and provides a user interface for displaying results of the analysis.

 

Datapoint

70.72

In teraflops, the Linpack benchmark performance of a beta version of IBM’s Blue Gene/L system, co-developed by IBM and the Lawrence Livermore National Laboratory. The score earned it the #1 spot on the latest release of the Top500 supercomputing list.

 

The Broad Institute recently made a public release of the browser Argo, a software tool designed to visualize and manipulate whole genomes. Argo is a Java-based program that allows users to build and edit models of genes and test for results of those models on mRNA and protein sequences.

 

The US Department of Energy awarded $2.7 million over three years to Johns Hopkins University, the University of Delaware, and Los Alamos National Laboratory to establish a computational biology research institute. To be known as the Institute for Multi-Scale Modeling of Biological Interactions, the center will have an interdisciplinary staff from all three institutions and will cover research ranging from protein interactions to complex network behavior.

 

Lion Bioscience has endured more shuffling. The company announced late last year it would cut its staff of 142 by more than half, down to between 50 and 70 employees. Meanwhile, Friedrich von Bohlen returned to the company to head its supervisory board, which shifted management roles slightly: Thure Etzold is the new CEO and Peter Willinger is now CFO.

 

UC San Diego Medical School and Massachusetts General Hospital won $32.8 million for biomedical informatics as follow-on funding through the National Center for Research Resources’ Biomedical Informatics Research Initiative.

 

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