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Open Access Research article

PIMS sequencing extension: a laboratory information management system for DNA sequencing facilities

Peter V Troshin1*, Vincent LG Postis25, Denise Ashworth3, Stephen A Baldwin25, Michael J McPherson45 and Geoffrey J Barton1

Author Affiliations

1 College of Life Sciences, University of Dundee, Dundee, DD1 4HN, UK

2 Institute of Membrane and System Biology, University of Leeds, Astbury Centre for Structural Molecular Biology, Leeds LS2 9JT, W Yorkshire, UK

3 DNA Analysis and Protein Production Facility, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK

4 Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK

5 Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK

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BMC Research Notes 2011, 4:48  doi:10.1186/1756-0500-4-48

Published: 7 March 2011

Abstract

Background

Facilities that provide a service for DNA sequencing typically support large numbers of users and experiment types. The cost of services is often reduced by the use of liquid handling robots but the efficiency of such facilities is hampered because the software for such robots does not usually integrate well with the systems that run the sequencing machines. Accordingly, there is a need for software systems capable of integrating different robotic systems and managing sample information for DNA sequencing services. In this paper, we describe an extension to the Protein Information Management System (PIMS) that is designed for DNA sequencing facilities. The new version of PIMS has a user-friendly web interface and integrates all aspects of the sequencing process, including sample submission, handling and tracking, together with capture and management of the data.

Results

The PIMS sequencing extension has been in production since July 2009 at the University of Leeds DNA Sequencing Facility. It has completely replaced manual data handling and simplified the tasks of data management and user communication. Samples from 45 groups have been processed with an average throughput of 10000 samples per month. The current version of the PIMS sequencing extension works with Applied Biosystems 3130XL 96-well plate sequencer and MWG 4204 or Aviso Theonyx liquid handling robots, but is readily adaptable for use with other combinations of robots.

Conclusions

PIMS has been extended to provide a user-friendly and integrated data management solution for DNA sequencing facilities that is accessed through a normal web browser and allows simultaneous access by multiple users as well as facility managers. The system integrates sequencing and liquid handling robots, manages the data flow, and provides remote access to the sequencing results. The software is freely available, for academic users, from http://www.pims-lims.org/ webcite.