PIMS sequencing extension

a laboratory information management system for DNA sequencing facilities

Peter V. Troshin (Lead / Corresponding author), Vincent L. G. Postis, Denise Ashworth, Stephen A. Baldwin, Michael J. McPherson, Geoffrey J. Barton

    Research output: Contribution to journalArticle

    5 Citations (Scopus)

    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/.
    Original languageEnglish
    Article number48
    Number of pages9
    JournalBMC Research Notes
    Volume4
    DOIs
    Publication statusPublished - 7 Mar 2011

    Fingerprint

    Clinical Laboratory Information Systems
    Management Information Systems
    Information Management
    DNA Sequence Analysis
    Information management
    DNA
    Robots
    Software
    Proteins
    Web Browser
    Liquids
    Robotics
    Data handling
    Web browsers
    Costs and Cost Analysis
    Managers
    Throughput
    Communication

    Cite this

    Troshin, Peter V. ; Postis, Vincent L. G. ; Ashworth, Denise ; Baldwin, Stephen A. ; McPherson, Michael J. ; Barton, Geoffrey J. / PIMS sequencing extension : a laboratory information management system for DNA sequencing facilities. In: BMC Research Notes. 2011 ; Vol. 4.
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    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/.",
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    PIMS sequencing extension : a laboratory information management system for DNA sequencing facilities. / Troshin, Peter V. (Lead / Corresponding author); Postis, Vincent L. G.; Ashworth, Denise; Baldwin, Stephen A.; McPherson, Michael J.; Barton, Geoffrey J.

    In: BMC Research Notes, Vol. 4, 48, 07.03.2011.

    Research output: Contribution to journalArticle

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    T1 - PIMS sequencing extension

    T2 - a laboratory information management system for DNA sequencing facilities

    AU - Troshin, Peter V.

    AU - Postis, Vincent L. G.

    AU - Ashworth, Denise

    AU - Baldwin, Stephen A.

    AU - McPherson, Michael J.

    AU - Barton, Geoffrey J.

    N1 - Copyright 2011 Elsevier B.V., All rights reserved.

    PY - 2011/3/7

    Y1 - 2011/3/7

    N2 - 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/.

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