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PiMS overview: version 0.3 & beyond

PiMS overview: version 0.3 & beyond. Robert Esnouf, PiMS Project Sponsor, Oxford. PiMS mission statement…. “To produce a commercial-quality freely available laboratory information management system (LIMS) suitable for use in structural biology laboratories”

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PiMS overview: version 0.3 & beyond

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  1. PiMS overview: version 0.3 & beyond Robert Esnouf, PiMS Project Sponsor, Oxford

  2. PiMS mission statement… • “To produce a commercial-quality freely available laboratory information management system (LIMS) suitable for use in structural biology laboratories” • Many (partially) failed efforts in the past • Process is very complex (by previous LIMS standards) • Research processes rapidly evolve (need configuration rather than customization) • No two laboratories have the same working practices

  3. The story of PiMS so far… • PiMS is a loose consortium involving labs in UK, France and elsewhere • PiMS is also the name of a BBSRC SPoRT grant in the UK and is heavily supported by CCP4 • PiMS SPoRT grant required reapplication supported by other SPoRT award holders (SSPF and MPSI) • PiMS effectively started Apr 2005, Bill Lin Feb 2006 • Management structure re-investigated late 2005 • Created part-time ‘Project Sponsor’ role late Jan 2006 • Version 0.3 released ~25 February 2006 • Developer meeting to start new structure 17 March

  4. PiMS (and associated) staff • Supported directly by PiMS grant • Ed Daniel (Daresbury), Anne Pajon (EBI), Katya Pilicheva (OPPF), Susy Griffiths (York – not full time) • Supported by CCP4 • Chris Morris (Daresbury – project manager), Bill Lin (Daresbury) • Supported by BBSRC at SSPF, MPSI and OPPF • Jo van Niekerk (Dundee), Petr Troshin (Daresbury), Jon Diprose (OPPF) • Not available full-time to PiMS • Supported by MRC • Robert Esnouf (OPPF – part time)

  5. Diagram of new PiMS structure Project Steering Board Major featurerequests Major featurerequests Line Man. Line Man. Robert E Local issues andrequirements;daily management Progress and issues Strategy andpriorities Chris M Developer Developer Developer Developer Developer Tasks, coordinationprogress monitoring

  6. Components of PiMS (1) • Standardized, consistent user interface • Multiple views onto database • Detailed view of experiments (processes) • Tracking of ‘target’ / ‘construct’ progress • Simplified view of project / laboratory progress • Views based on samples / users / locations / activities • Administration (configuration and management roles) • Security / authorization module / access control / roles • Interface for multiple databases and web services • Locations / people / groups / projects • Sample and reagent description / tracking • Integration of robotic platforms • run sequence files • output files

  7. Components of PiMS (2) • Potential target collection / annotation • Target selection and construct design • Project progress / target tracking • Non-plate experiments • Expression, purification, custom experiments • Plate experiments • PCR, cloning, crystallization • QA experiments • Gels, mass spectroscopy, sequencing, DLS • Reporting / virtual lab book • Crystallization setup and imaging (eHTPX and BioXHIT) • Links to x-ray data collection (eHTPX) • Reagent management • … more sophisticated features …

  8. Where is PiMS currently? • PiMS version 0.3 ‘released’ 25 February 2006 • Logging on • Target tracking • Reagent management • A basic, but generic, user interface • (Ability to record experimental information) • (Definition of work required for crystallization) • MPSI target data from Leeds have been entered

  9. PiMS releases 2006 • PiMS version 0.4, 24 May 2006 • Provide DB support for SPoT • Beginnings of consistent user interface / better web site • Target progress / tracking • PiMS version 0.5, 2 October 2006 • Major upgrade of database machinery • Consistent user interface throughout • Experiments and protocols • PiMS version 1.0, 4 December 2006 • Plate experiments • Crystallization interface (work with BioXHIT) … • Crystal shipping (draw on eHTPX) …

  10. PiMS crystallization module • Module to cover management of crystallization trials • Shared development withBioXHIT allowing externalresources to contribute toPiMS goals • A self contained and well understood module • One of most demanding interms of database use anduser interface performance • Of immediate use to several PiMS sites • Four-way grouping: OPPF, NKI, EMBL Grenoble, Paris-Sud

  11. PiMS and eHTPX hub/portal • PiMS primarily intended to cover protein production • Molecular biology, protein expression, purification • This is only part of the whole process • Target annotation precedes production • Crystallization follows production (for most PiMS sites) • Both parts should eventually be integrated into PiMS to give extended framework • Structure solution / refinement / deposition • eHTPX hub/portal covers getting crystals to beam lines • Cryo-treatment of crystals • Links back to crystallization data • Links forward to x-ray experiment data • Beam line logs

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