PiMS overview: version 0.3 & beyond

Robert Esnouf, PiMS Project Sponsor, Oxford

PiMS mission statement… “To produce a commercial-quality freely available

laboratory information management system (LIMS) suitable for use in structural biology 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

The story of PiMS so far… PiMS is a loose consortium involving labs in UK, France

and elsewhere PiMS is also the name of a BBSRC SPoRT grant in the

UK and is heavily supported by CCP4 PiMS SPoRT grant required reapplication supported by

other SPoRT award holders (SSPF and MPSI) PiMS effectively started Apr 2005, Bill Lin Feb 2006 Management structure re-investigated late 2005 Created part-time ‘Project Sponsor’ role late Jan 2006 Version 0.3 released ~25 February 2006 Developer meeting to start new structure 17 March

PiMS (and associated) staff Supported directly by PiMS grant

Ed Daniel (Daresbury), Anne Pajon (EBI), Katya Pilicheva (OPPF), Susy Griffiths (York – not full time)

Supported by CCP4 Chris Morris (Daresbury – project manager), Bill Lin

(Daresbury) Supported by BBSRC at SSPF, MPSI and OPPF

Jo van Niekerk (Dundee), Petr Troshin (Daresbury), Jon Diprose (OPPF)

Not available full-time to PiMS Supported by MRC

Robert Esnouf (OPPF – part time)

Diagram of new PiMS structure

Robert E

Developer DeveloperDeveloperDeveloperDeveloper

Chris M

Line Man. Line Man.

Project SteeringBoard

Strategy andpriorities

Progress andissues

Major featurerequests

Major featurerequests

Local issues andrequirements;daily management

Tasks, coordinationprogress monitoring

Components of PiMS (1) Standardized, consistent user interface Multiple views onto database

Detailed view of experiments (processes) Tracking of ‘target’ / ‘construct’ progress Simplified view of project / laboratory progress Views based on samples / users / locations / activities

Administration (configuration and management roles) Security / authorization module / access control / roles Interface for multiple databases and web services Locations / people / groups / projects Sample and reagent description / tracking Integration of robotic platforms

run sequence files output files

Components of PiMS (2) Potential target collection / annotation Target selection and construct design Project progress / target tracking Non-plate experiments

Expression, purification, custom experiments Plate experiments

PCR, cloning, crystallization QA experiments

Gels, mass spectroscopy, sequencing, DLS Reporting / virtual lab book Crystallization setup and imaging (eHTPX and BioXHIT) Links to x-ray data collection (eHTPX) Reagent management … more sophisticated features …

Where is PiMS currently? PiMS version 0.3 ‘released’ 25 February 2006

Logging on Target tracking Reagent management A basic, but generic, user interface (Ability to record experimental information) (Definition of work required for crystallization) MPSI target data from Leeds have been entered

PiMS releases 2006 PiMS version 0.4, 24 May 2006

Provide DB support for SPoT Beginnings of consistent user interface / better web site Target progress / tracking

PiMS version 0.5, 2 October 2006 Major upgrade of database machinery Consistent user interface throughout Experiments and protocols

PiMS version 1.0, 4 December 2006 Plate experiments Crystallization interface (work with BioXHIT) … Crystal shipping (draw on eHTPX) …

PiMS crystallization module Module to cover management

of crystallization trials Shared development with

BioXHIT allowing externalresources to contribute toPiMS goals

A self contained and well understood module

One of most demanding interms of database use anduser interface performance

Of immediate use to several PiMS sites

Four-way grouping: OPPF, NKI, EMBL Grenoble, Paris-Sud

PiMS primarily intended to cover protein production Molecular biology, protein expression, purification

This is only part of the whole process Target annotation precedes production Crystallization follows production (for most PiMS sites) Both parts should eventually be integrated into PiMS to

give extended framework Structure solution / refinement / deposition

eHTPX hub/portal covers getting crystals to beam lines Cryo-treatment of crystals Links back to crystallization data Links forward to x-ray experiment data Beam line logs

PiMS and eHTPX hub/portal