Perspective: standard Protein information Management System.

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



Outline of talk

■ Why use a LIMS?■ Use of PiMS for real projects■ PiMS concepts■ xtalPiMS for crystallization■ Future work



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



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”



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



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"



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, ...



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



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



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



How it all links together



Target: sequences and annotations



Construct: starting point for experiments, links to target



Sample: has type, owner, location



Experiment: samples in, samples out



Protocol: template for experiment



A workflow derived from PIMS



Experiments can read/write data



Simple reports of how samples are made



Interface being

reworked for

next release

of PiMS

Graphical interface for plate experiments



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



Boxes show

latest updates

for projects

that you have

access to

The xtalPiMS home page



Fast, web-

based access

to images

including

time courses



Fast, web-

based access

to images

including

time courses



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



Future work: Design adoption path

■ Booking instruments ■ Freezer index■ Reagent stocks■ Archive of files■ Protocols■ Experiments

“Outlook for structural biology”



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 -> ?



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



Supplementary material



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



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



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



Dissemination of new technology

■ The greatest credibility gap is from visionaries (~5%) to pragmatists (~33%)

■ This is the stage that PiMS is at.



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.



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



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



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



Diagnosis?

■ Adopting PiMS is like swallowing a cow■ Could be a bite at a time



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”



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

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Perspective: standard Protein information Management System.

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