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

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Presentation on theme: "PiMS overview: version 0.3 & beyond Robert Esnouf, PiMS Project Sponsor, Oxford."— Presentation transcript:

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 Robert E Developer Chris M Line Man. Project Steering Board Strategy and priorities Progress and issues Major feature requests Local issues and requirements; daily management Tasks, coordination progress 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









17 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) …




21 PiMS crystallization module Module to cover management of crystallization trials  Shared development with BioXHIT allowing external resources to contribute to PiMS goals  A self contained and well understood module  One of most demanding in terms of database use and user interface performance  Of immediate use to several PiMS sites Four-way grouping: OPPF, NKI, EMBL Grenoble, Paris-Sud

22 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 PiMS and eHTPX hub/portal

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