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Bioinformatics Advance Access originally published online on August 20, 2007
Bioinformatics 2007 23(18):2504-2506; doi:10.1093/bioinformatics/btm365
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

A Laboratory Information Management System (LIMS) for a high throughput genetic platform aimed at candidate gene mutation screening

C. Voegele 1,*, S.V. Tavtigian 1, D. de Silva 1, S. Cuber 1, A. Thomas 2 and F. Le Calvez-Kelm 1

1International Agency for Research on Cancer (IARC), Lyon, France and 2Department of Medical Informatics, University of Utah, Salt Lake City, USA

*To whom correspondence should be addressed.


  Abstract

Summary: High throughput mutation screening in an automated environment generates large data sets that have to be organized and stored reliably. Complex multistep workflows require strict process management and careful data tracking. We have developed a Laboratory Information Management Systems (LIMS) tailored to high throughput candidate gene mutation scanning and resequencing that respects these requirements. Designed with a client/server architecture, our system is platform independent and based on open-source tools from the database to the web application development strategy. Flexible, expandable and secure, the LIMS, by communicating with most of the laboratory instruments and robots, tracks samples and laboratory information, capturing data at every step of our automated mutation screening workflow. An important feature of our LIMS is that it enables tracking of information through a laboratory workflow where the process at one step is contingent on results from a previous step.

Availability: Script for MySQL database table creation and source code of the whole JSP application are freely available on our website: http://www-gcs.iarc.fr/lims/.

Contact: voegele{at}iarc.fr

Supplementary information: System server configuration, database structure and additional details on the LIMS and the mutation screening workflow are available on our website: http://www-gcs.iarc.fr/lims/

Associate Editor: Jonathan Wren

Received on April 16, 2007; revised on June 20, 2007; accepted on July 6, 2007

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