1. Perspective: standard Protein information Management Systemwww.pims-lims.org

2. Perspective: standard Protein information Management Systemwww.pims-lims.org Why PiMS? Chris Morris STFC Daresbury Laboratory… …and the PIMS development team St Andrews University 18/01/2011

3. Perspective: standard Protein information Management Systemwww.pims-lims.org Outline of talk ■ Why use a LIMS? ■ Use of PiMS for real projects ■ PiMS concepts ■ xtalPiMS for crystallization ■ Future work

4. Perspective: standard Protein information Management Systemwww.pims-lims.org Why use a LIMS for protein production? ■Traceability, Searchability, Manageability, Continuity, Integration ■Flexibility, Future Proofing ■- lucky that we worked for two consortia ■Alternative 1: a combination of lab notebook and MS Office ■Alternative 2: Electronic Lab Notebook ■LIMS for: HTP, long term projects, scattered collaborations, automated work, services

5. Perspective: standard Protein information Management Systemwww.pims-lims.org Potential problems with LIMS ■ IT overhead ■ Shared data should be on backed-up server – use a web-based service ■ Data loss ■ Hardware failure or data corruption – hardware failures manageable ■ Data integrity ■ Data need to be entered properly or LIMS can default to being ELN ■ Recording data takes time for no immediate benefit – easy input essential ■ Unrecorded data are lost and incomplete data may break data “chain”

6. Perspective: standard Protein information Management Systemwww.pims-lims.org Who uses PiMS? ■MPSI 1064 Targets, 2536 Experiments, 3467 Samples ■SSPF 392 Targets, 3709 Experiments, 1344 Samples ■OPPF 352 Targets, 20,559 Experiments, 18,714 Samples ■PiMS adopted at IRB (Barcelona), Institute of Biophysics (Beijing)‏, EMLB Hamburg, IQTB (Lisbon), TCD, … ■XtalPiMS adopted in OPPF, York. ■Free for academic use

7. Perspective: standard Protein information Management Systemwww.pims-lims.org What do they say about PiMS? 17 replies / 18 academic licenses ■4: "I love PiMS" / "PiMS is brilliant" / "of great use for us" / “it is a key application that we do not want to miss anymore!” ■4: "time investment needed to start using it" / "too much time had to be put in initially" / "energy needed to get into it" / "the learning curve was too steep for us"

8. Perspective: standard Protein information Management Systemwww.pims-lims.org Technologies used in PiMS ■ PiMS is a web application ■ Client is Mozilla Firefox or Internet Explorer ■ No client software to install (perhaps plugins) ■ Windows, Macintosh and Linux clients ■ PiMS requires a server ■ Web server uses Apache Tomcat ■ Database server uses PostgreSQL or Oracle ■ Windows and Linux servers ■ Managed public PiMS server hosted at RAL ■ Technologies used by developers ■ Java1.5, Hibernate, JUnit, BioJava, dot, batik, AJAX,...

9. Perspective: standard Protein information Management Systemwww.pims-lims.org PiMS 4.2 supports.... ■work on ORF targets, complexes, promoters, protein from natural source... ■Gateway, Infusion,... ■individual experiments, groups of experiments, and work with plates ■Acquisition of data from Akta ■Tracking samples ■Tracking reagents used ■Crystallogenesis in xtalPiMS extension

10. Perspective: standard Protein information Management Systemwww.pims-lims.org Access rights ■ Each PiMS record belongs to a “lab note book” ■ Each user can write in one or more lab note books ■ Your lab note book may be: ■ Private to you ■ Or readable by your supervisor ■ Or shared with colleagues

11. Perspective: standard Protein information Management Systemwww.pims-lims.org PiMS uses simple key concepts ■ Complexes & Targets ■ Descriptions of proteins and complexes ■ Can contain bioinformatics annotations ■ Constructs ■ Starting point for real experiments ■ Describes actual sequences ■ (Typed) Samples ■ Tracked samples made & used by experiments ■ Samples have types, owners, locations etc. ■ Experiments & Protocols ■ Consume (input) and produce (output) samples ■ Protocols are user-defined reusable templates

12. Perspective: standard Protein information Management Systemwww.pims-lims.org How it all links together

13. Perspective: standard Protein information Management Systemwww.pims-lims.org Target: sequences and annotations

14. Perspective: standard Protein information Management Systemwww.pims-lims.org Construct: starting point for experiments, links to target

15. Perspective: standard Protein information Management Systemwww.pims-lims.org Sample: has type, owner, location

16. Perspective: standard Protein information Management Systemwww.pims-lims.org Experiment: samples in, samples out

17. Perspective: standard Protein information Management Systemwww.pims-lims.org Protocol: template for experiment

18. Perspective: standard Protein information Management Systemwww.pims-lims.org A workflow derived from PIMS

19. Perspective: standard Protein information Management Systemwww.pims-lims.org Experiments can read/write data

20. Perspective: standard Protein information Management Systemwww.pims-lims.org Simple reports of how samples are made

21. Perspective: standard Protein information Management Systemwww.pims-lims.org Interface being reworked for next release of PiMS Graphical interface for plate experiments

22. Perspective: standard Protein information Management Systemwww.pims-lims.org Access rights ■ Each PiMS record belongs to a “lab note book” ■ Each user can write in one or more lab note books ■ Your lab note book may be: ■ Private to you ■ Or readable by your supervisor ■ Or shared with colleagues

23. Perspective: standard Protein information Management Systemwww.pims-lims.org Boxes show latest updates for projects that you have access to The xtalPiMS home page

24. Perspective: standard Protein information Management Systemwww.pims-lims.org Fast, web- based access to images including time courses

25. Perspective: standard Protein information Management Systemwww.pims-lims.org Fast, web- based access to images including time courses

26. Perspective: standard Protein information Management Systemwww.pims-lims.org Plans for 2011 ■Support for INSTRUCT centres ■Support for ThermoElectron/Rhombix ■Sending data to DLS ■In plate screening CM funded by CCP4 to July 2013 have to say “no” to some requests Also part of “BioMedBridges” FP7 application

27. Perspective: standard Protein information Management Systemwww.pims-lims.org Future work: Design adoption path ■Booking instruments ■Freezer index ■Reagent stocks ■Archive of files ■Protocols ■Experiments “Outlook for structural biology”

28. Perspective: standard Protein information Management Systemwww.pims-lims.org The long term vision A unified and extensible set of software tools for molecular biology, offering seamless data transfer and a consistent user experience, from target selection to extraction of biological significance from the structure ? -> PiMS -> xtalPiMS -> ISPYB -> Xia -> CCP4 -> ?

29. Perspective: standard Protein information Management Systemwww.pims-lims.org Acknowledgments ■ The PiMS project people ■ Kim Henrick, Dave Stuart, Keith Wilson, Colin Nave, Neil Isaacs, Jim Naismith, Richard Blake ■ Chris Morris, Ed Daniel, Alain Da Souza, Jon Diprose, Susy Griffiths, Bill Lin, Anne Pajon, Katya Pilicheva, Marc Savitsky, Petr Troshin, Jo van Niekerk ■ xtalPiMS people ■ Ian Berry ■ PiMS and xtalPiMS users

30. Perspective: standard Protein information Management Systemwww.pims-lims.org Supplementary material

31. Perspective: standard Protein information Management Systemwww.pims-lims.org Crisis of Drug Discovery ■Closure of many in-house R&D groups ■Sharing risk with academic groups ■Market in drug candidates Product could includes methods ■Use of Contract Research Organisations Need for collaborative knowledge management solutions

32. Perspective: standard Protein information Management Systemwww.pims-lims.org Survey of PiMS Licensees ■17 replies / 18 academic licenses ■5: never able to get a good installation ■5: one useful addition would be... / very small incremental improvements / increase the bioinformatics tools / plugins / A friendly browser-based user management would be very helpful ■4: I love PiMS / PiMS is brilliant / of great use for us / it is a key application that we do not want to miss anymore! ■4: time investment needed to start using it / too much time had to be put in initially / energy needed to get into it / the learning curve was too steep for us ■2: finding the right way to use it / We think that some training would be needed now. ■2: weird java error messages / there are still many (small) bugs ■until we are told to use it

33. Perspective: standard Protein information Management Systemwww.pims-lims.org Feedback from funding bodies ■FP7: A major risk... is lack of adoption by the European user community ■BBR: lack of evidence showing support for the resource from current users Funding bodies will not tell scientists to use PiMS

34. Perspective: standard Protein information Management Systemwww.pims-lims.org Dissemination of new technology ■The greatest credibility gap is from visionaries (~5%) to pragmatists (~33%)‏ ■This is the stage that PiMS is at.

35. Perspective: standard Protein information Management Systemwww.pims-lims.org Five types of technology user ■Enthusiasts: enjoy Unix installation... ■Innovators: want to get ahead; accept risk; competent at IT; act now. === we are here === ■Pragmatists: want to be up to date; “did you get continuation funding?”; “no weird java error messages”; wait and see. ■Conservatives: want the tried-and-tested; trouble free; expect full support. ■Skeptics: a lab note book was good enough for James Sumner.

36. Perspective: standard Protein information Management Systemwww.pims-lims.org Contradictions in requirements = key design challenges 1)Easy installation v. reliable backup 2)139 feature requests v. “day to day problems of finding the right way to use it” 3)Scientists' autonomy v. sharing laboratory space

37. Perspective: standard Protein information Management Systemwww.pims-lims.org Contradiction 3: autonomy v. sharing I won't tell them to use it v. Please write down start/finish times so others may use the shaker when it is free

38. Perspective: standard Protein information Management Systemwww.pims-lims.org Need to prioritise ■5 requests to travel in November – PSDI – PSB – Universities of Vienna, Helsinki, St Andrews ■CM prepared to travel 3 times a month ■Team was 9, now 2, soon 1 ■139 outstanding feature requests ■7 PY development ~ 1 FTE maintainance

39. Perspective: standard Protein information Management Systemwww.pims-lims.org Diagnosis? ■Adopting PiMS is like swallowing a cow ■Could be a bite at a time

40. Perspective: standard Protein information Management Systemwww.pims-lims.org Design for piecemeal adoption ■Highlight “next step” ■Module: Booking instruments ■Module: Freezer index ■Module: Reagent stocks ■Module: Archive of files ■Module: Protocols ■“Please fix” page ■Better installer 6 weeks “Outlook for structural biology”

41. Perspective: standard Protein information Management Systemwww.pims-lims.org What we are not doing ■Site visits, beyond 3 per month ■User support, beyond 1 day per week ■Backlog of new feature requests ■BioPiMS – unless in BioMedBridges