Perspective: standard
Protein information Management System
www.pims-lims.org
Why PiMS?
Chris Morris
STFC Daresbury Laboratory…
Perspective: standard
…and the PIMS development team
St Andrews University 18/01/2011
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
Protein information Management System
Perspective: standard
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
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
Perspective: standard
■ 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”
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
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!”
Perspective: standard
■ 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"
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
■
■
■
■
Perspective: standard
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, ...
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
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:
Perspective: standard
■ Private to you
■ Or readable by your supervisor
■ Or shared with colleagues
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
Perspective: standard
■ 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
Protein information Management System
www.pims-lims.org
How it all links together
Perspective: standard
Protein information Management System
www.pims-lims.org
Target: sequences and annotations
Perspective: standard
Protein information Management System
www.pims-lims.org
Construct: starting point for
experiments, links to target
Perspective: standard
Protein information Management System
www.pims-lims.org
Sample: has type, owner, location
Perspective: standard
Protein information Management System
www.pims-lims.org
Experiment: samples in, samples out
Perspective: standard
Protein information Management System
www.pims-lims.org
Protocol: template for experiment
Perspective: standard
Protein information Management System
www.pims-lims.org
A workflow derived from PIMS
Perspective: standard
Protein information Management System
www.pims-lims.org
Experiments can read/write data
Perspective: standard
Protein information Management System
www.pims-lims.org
Simple reports of how samples are made
Perspective: standard
Protein information Management System
www.pims-lims.org
Graphical interface for plate experiments
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:
Perspective: standard
■ Private to you
■ Or readable by your supervisor
■ Or shared with colleagues
Protein information Management System
www.pims-lims.org
The xtalPiMS home page
Perspective: standard
Protein information Management System
www.pims-lims.org
Perspective: standard
Protein information Management System
www.pims-lims.org
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
Perspective: standard
CM funded by CCP4 to July 2013
have to say “no” to some requests
Also part of “BioMedBridges” FP7 application
Protein information Management System
www.pims-lims.org
Future work: Design adoption path
■
■
■
■
■
■
Booking instruments
Freezer index
Reagent stocks
Archive of files
Protocols
Experiments
Perspective: standard
“Outlook for structural biology”
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
Perspective: standard
? -> PiMS -> xtalPiMS
-> ISPYB -> Xia -> CCP4 -> ?
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
Perspective: standard
■ xtalPiMS people
■ Ian Berry
■ PiMS and xtalPiMS users
Protein information Management System
www.pims-lims.org
Supplementary material
Perspective: standard
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
Perspective: standard
Need for collaborative knowledge
management solutions
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
Perspective: standard
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
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
Perspective: standard
Funding bodies will not
tell scientists to use PiMS
Protein information Management System
www.pims-lims.org
Dissemination of new technology
Perspective: standard
■ The greatest credibility gap is from visionaries
(~5%) to pragmatists (~33%)
■ This is the stage that PiMS is at.
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.
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
Perspective: standard
Protein information Management System
www.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
Perspective: standard
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
Perspective: standard
■ 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
Protein information Management System
www.pims-lims.org
Diagnosis?
Perspective: standard
■ Adopting PiMS is like swallowing a cow
■ Could be a bite at a time
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
Perspective: standard
“Outlook for structural biology”
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
Perspective: standard
Protein information Management System
www.pims-lims.org