Download Prediction of Natively Disordered Regions in Proteins Using

PiMS overview:
version 0.3 & beyond
Robert Esnouf, PiMS Project Sponsor, Oxford
PiMS mission statement…
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“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…
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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
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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
Major feature
requests
Project Steering
Board
Major feature
requests
Line Man.
Line Man.
Robert E
Progress and
issues
Strategy and
priorities
Local issues and
requirements;
daily management
Chris M
Developer Developer Developer
Developer
Tasks, coordination
progress monitoring
Developer
Components of PiMS (1)
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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)
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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?
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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
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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
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Module to cover management
of crystallization trials
 Shared development with
BioXHIT allowing external
resources to contribute to
PiMS goals
 A self contained and well
understood module
 One of most demanding in
terms of database use and
user interface performance
 Of immediate use to
several PiMS sites
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Four-way grouping: OPPF, NKI,
EMBL Grenoble, Paris-Sud
PiMS and eHTPX hub/portal
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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