perspective: standard protein information management system
TRANSCRIPT
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Perspective: standard
Protein information Management System www.pims-lims.org
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Perspective: standard
Protein information Management System www.pims-lims.org
Why PiMS?Chris Morris
STFC Daresbury Laboratory…
…and the PIMS development team
St Andrews University 18/01/2011
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Perspective: standard
Protein information Management System www.pims-lims.org
Outline of talk
■ Why use a LIMS?■ Use of PiMS for real projects■ PiMS concepts■ xtalPiMS for crystallization■ Future work
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Perspective: standard
Protein information Management System www.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
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Perspective: standard
Protein information Management System www.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”
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Perspective: standard
Protein information Management System www.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
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Perspective: standard
Protein information Management System www.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"
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Perspective: standard
Protein information Management System www.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, ...
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Perspective: standard
Protein information Management System www.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
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Perspective: standard
Protein information Management System www.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
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Perspective: standard
Protein information Management System www.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
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Perspective: standard
Protein information Management System www.pims-lims.org
How it all links together
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Protein information Management System www.pims-lims.org
Target: sequences and annotations
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Perspective: standard
Protein information Management System www.pims-lims.org
Construct: starting point for experiments, links to target
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Perspective: standard
Protein information Management System www.pims-lims.org
Sample: has type, owner, location
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Perspective: standard
Protein information Management System www.pims-lims.org
Experiment: samples in, samples out
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Protein information Management System www.pims-lims.org
Protocol: template for experiment
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Perspective: standard
Protein information Management System www.pims-lims.org
A workflow derived from PIMS
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Perspective: standard
Protein information Management System www.pims-lims.org
Experiments can read/write data
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Protein information Management System www.pims-lims.org
Simple reports of how samples are made
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Perspective: standard
Protein information Management System www.pims-lims.org
Interface being
reworked for
next release
of PiMS
Graphical interface for plate experiments
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Perspective: standard
Protein information Management System www.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
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Perspective: standard
Protein information Management System www.pims-lims.org
Boxes show
latest updates
for projects
that you have
access to
The xtalPiMS home page
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Perspective: standard
Protein information Management System www.pims-lims.org
Fast, web-
based access
to images
including
time courses
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Perspective: standard
Protein information Management System www.pims-lims.org
Fast, web-
based access
to images
including
time courses
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Perspective: standard
Protein information Management System www.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
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Protein information Management System www.pims-lims.org
Future work: Design adoption path
■ Booking instruments ■ Freezer index■ Reagent stocks■ Archive of files■ Protocols■ Experiments
“Outlook for structural biology”
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Perspective: standard
Protein information Management System www.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 -> ?
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Protein information Management System www.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
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Supplementary material
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Protein information Management System www.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
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Protein information Management System www.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
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Perspective: standard
Protein information Management System www.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
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Protein information Management System www.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.
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Protein information Management System www.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.
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Perspective: standard
Protein information Management System www.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
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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
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Protein information Management System www.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
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Perspective: standard
Protein information Management System www.pims-lims.org
Diagnosis?
■ Adopting PiMS is like swallowing a cow■ Could be a bite at a time
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Protein information Management System www.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”
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Perspective: standard
Protein information Management System www.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