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PIMS: The Problems of Project Management

The PIMS initiative aims to develop a high-quality laboratory information management system (LIMS) tailored for structural biology research. With the complexities associated with evolving research processes and diverse laboratory practices, PIMS facilitates efficient project management and data recording, supporting thousands of experiments and samples. The initiative emphasizes collaboration across institutions, data sharing, and compatibility with existing software and robotic platforms. Through continuous user feedback, PIMS strives to enhance usability and meet the unique needs of research laboratories.

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PIMS: The Problems of Project Management

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  1. PIMS: The Problems ofProject Management Robert Esnouf, Scientific Sponsor for PIMS OPPF/STRUBI, University of Oxford strubi .ox.ac.uk

  2. PIMS “mission statement”… • “To produce a commercial-quality freely available laboratory information management system (LIMS) suitable for use in structural biology research 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. Information to be managed… • Potential targets / bioinformatics annotation • Target selection and construct design • Project planning and progress • Experiments and protocols (templates) • Non-plate: expression, purification, “traditional” work • Plate-based: PCR, cloning, crystallization • QA: gels, mass spectroscopy, sequencing, DLS • Samples and sample descriptions (e.g. sequences) • Holders and locations • Stocks, reagents and reference data • Health and safety information • Users, roles, access / sharing and security • Databases and external references • X-ray diffraction / structure solution

  4. Functionality required… • An interface for entering data • Simple to use, intuitive • Minimal client software • Secure storage of well defined data (database) • An interface for recovering / analyzing data • An interface for project management • Administration (configuration and management roles) • Interface to external software (e.g. web services) • Integration of robotic platforms • parsing output files • producing run sequence files • direct robotic control

  5. Scientific goals for PIMS… Recording laboratory information • A lot of data recording • 10,000s of experiments • 1,000,000s of samples Data interchange and interoperation • Collaboration in protein production • Share data between stages and sites • Data transfer to beam line or NMR operations Data mining and reporting • Analysis of positive and negative results • Data deposition • Scientific publications

  6. The story of PIMS so far… • PIMS started as a loose consortium involving labs in the UK, France and elsewhere • PIMS BBSRC SPoRT grant (3.62 FTE) • in collaboration with and in support of other SPoRTaward holders (SSPF and MPSI) with heavyinvolvement of CCP4 (2 FTE), OPPF and others • PIMS effectively started 4/2005 (one post 2/2006) • Management structure re-investigated late 2005 • Part-time ‘Scientific Sponsor’ (Robert E)who works with ‘Project Manager’ (Chris M) • Version 1.0 released 15/1/2007 • Version 1.1 due 17/4/2007

  7. PIMS version 1.0: January 2007… • Improved performance • Adequate for small-to-medium scale • Barely adequate for scale of OPPF target data • 10,000 targets, 4,000 constructs imported, 3 genomes • Support for plate-based experiments • Simplified user interface • “Generic” interface became “Expert” interface • Development guided by end-user feedback • First sample tracking to link experiments together • Create a pipeline of data • Workshop to introduce users to PIMS • Now focusing on SPoRT/OPPF use

  8. PIMS management structure… Project Steering Board Major featurerequests Major featurerequests Line Man. Line Man. Robert E Local issues andrequirements;daily management Progress & issues Strategy &priorities Chris M Developer Developer Developer Developer Developer Tasks, coordinationprogress monitoring

  9. Short-term / long-term issues… • Meeting the needs of SPoRT consortia / OPPF / YSBL etc. • Implementations of established experimental procedures • Interfacing existing software • Each lab gets a custom interface • Developing a truly generic LIMS for end of project • Balancing competing interests • One size fits all/no one • Model is comprehensive/cumbersome • Interface is complex • Lack of early user input • Shared goals • Common way of representing data underneath • Contributed software • Extensible application

  10. Current interaction with CCPN… Object Domain User Interface Complete Data model Business Logic PIMS model PIMS API ‘Hibernate’ API PIMS/CCPN Autogeneration Software Hibernate Mapping Files Hibernate Persistence Layer PostgreSQL DB • Review of data model/data base • ObjectDomain has ceased trading

  11. Problems of distributed projects… • Isolated developers • Need good support • Face contradictory demands • Developers not near experimentalists • Relevance of developments • Usability of developments • Focus is provided by real use • Needs “big picture” vision to get to “real use” stage • First experience of users can be brutal • Need developers to spend time together • Code camps / teleconferencing • Email is poor communication

  12. Problems of distributed projects… • Management by a distributed PSB • Requires consent/indulgence of collaborating groups • Hard to get PSB together for meetings • Interaction between PSB and developers • Need for clear minutes/actions • Scientific sponsor could easily be full time role • Assessment by BBSRC • Review not by computer scientists (not bad!) • Original review process contained no demo (very bad!) • Visiting group assessed PIMS in November • ‘Mid-term’ review will consist of demo at BBSRC

  13. PIMS non-plate experiments…

  14. PIMS plate-based experiments…

  15. Oxford Protein Production Facility… • Example follows 96 constructs through PCR, Gateway cloning and expression screening with two cell lines and two protocols: • Top shows plate usage • Bottom shows the number of 96-lane agarose gels, 24-well colony-plate images and 26-lane SDS–PAGE gels • 96 constructs uses 34 96-well plates and 36 24-well plates… • …generates 480 images of colony wells,1536 lanes on agarose gelsand 416 lanes on SDS–PAGE gels

  16. Working with MPSI to increase use… • Target annotation (largely covered in PIMS 0.4) • Target selection (not planned for PIMS) • Construct design (using VectorNTI) • Obtain/store source strain genomic DNA • Describe selected genes • Describe primers, link to VectorNTI output • Describe entry clones as plasmids • Describe expression constructs • Describe high-throughput expression trials • Describe solubilization trials…

  17. Solubilization trials (Leeds)… • Solubilization trials performed in 96-well format • Perform 24-trials per target, therefore four targets per set Detergent concentration gradients… Det 1 Det 2 Target 1 Target 2 Det 3 Det 4 Det 1 Det 2 Target 3 Target 4 Det 3 Det 4

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