pims: the problems of project management robert esnouf, scientific sponsor for pims oppf/strubi,...
TRANSCRIPT
PIMS: The Problems ofProject Management
Robert Esnouf, Scientific Sponsor for PIMS
OPPF/STRUBI, University of Oxford
strubi.ox.ac.uk
PIMS “mission statement”… “To produce a commercial-quality freely
available laboratory information management system (LIMS) suitable for use in structural biology research 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
Potential targets / bioinformatics annotation Target selection and construct design Project planning and progress Experiments and protocols (templates)
Non-plate: expression, purification, “traditional” work Plate-based: PCR, cloning, crystallization QA: gels, mass spectroscopy, sequencing, DLS
Samples and sample descriptions (e.g. sequences) Holders and locations Stocks, reagents and reference data Health and safety information Users, roles, access / sharing and security Databases and external references X-ray diffraction / structure solution
Information to be managed…
Functionality required… An interface for entering data
Simple to use, intuitive Minimal client software
Secure storage of well defined data (database) An interface for recovering / analyzing data An interface for project management Administration (configuration and management roles) Interface to external software (e.g. web services) Integration of robotic platforms
parsing output files producing run sequence files direct robotic control
Scientific goals for PIMS…Recording laboratory information
A lot of data recording 10,000s of experiments 1,000,000s of samples
Data interchange and interoperation Collaboration in protein production Share data between stages and sites Data transfer to beam line or NMR operations
Data mining and reporting Analysis of positive and negative results Data deposition Scientific publications
The story of PIMS so far… PIMS started as a loose consortium involving labs
in the UK, France and elsewhere PIMS BBSRC SPoRT grant (3.62 FTE)
in collaboration with and in support of other SPoRTaward holders (SSPF and MPSI) with heavyinvolvement of CCP4 (2 FTE), OPPF and others
PIMS effectively started 4/2005 (one post 2/2006) Management structure re-investigated late 2005
Part-time ‘Scientific Sponsor’ (Robert E)who works with ‘Project Manager’ (Chris M)
Version 1.0 released 15/1/2007 Version 1.1 due 17/4/2007
PIMS version 1.0: January 2007… Improved performance
Adequate for small-to-medium scale Barely adequate for scale of OPPF target data
10,000 targets, 4,000 constructs imported, 3 genomes
Support for plate-based experiments Simplified user interface
“Generic” interface became “Expert” interface Development guided by end-user feedback
First sample tracking to link experiments together Create a pipeline of data
Workshop to introduce users to PIMS Now focusing on SPoRT/OPPF use
PIMS management structure…
Developer DeveloperDeveloperDeveloperDeveloper
Chris M
Line Man. Line Man.
Project SteeringBoard
Strategy &priorities
Progress& issues
Major featurerequests
Major featurerequests
Local issues andrequirements;daily management
Tasks, coordinationprogress monitoring
Robert E
Short-term / long-term issues… Meeting the needs of SPoRT consortia / OPPF / YSBL etc.
Implementations of established experimental procedures Interfacing existing software Each lab gets a custom interface
Developing a truly generic LIMS for end of project Balancing competing interests One size fits all/no one Model is comprehensive/cumbersome Interface is complex Lack of early user input
Shared goals Common way of representing data underneath Contributed software Extensible application
Object Domain
Complete Data model
Current interaction with CCPN…
PIMS model Business Logic
User Interface
PIMS API
‘Hibernate’ API
Hibernate Persistence Layer
PostgreSQL DB
PIMS/CCPNAutogeneration
SoftwareHibernate Mapping Files
• Review of data model/data base• ObjectDomain has ceased trading
Problems of distributed projects… Isolated developers
Need good support Face contradictory demands
Developers not near experimentalists Relevance of developments Usability of developments
Focus is provided by real use Needs “big picture” vision to get to “real use” stage First experience of users can be brutal
Need developers to spend time together Code camps / teleconferencing Email is poor communication
Problems of distributed projects… Management by a distributed PSB
Requires consent/indulgence of collaborating groups Hard to get PSB together for meetings Interaction between PSB and developers Need for clear minutes/actions Scientific sponsor could easily be full time role
Assessment by BBSRC Review not by computer scientists (not bad!) Original review process contained no demo (very bad!) Visiting group assessed PIMS in November ‘Mid-term’ review will consist of demo at BBSRC
PIMS non-plate experiments…
PIMS plate-based experiments…
Oxford Protein Production Facility… Example follows 96 constructs through PCR, Gateway
cloning and expression screening with two cell lines and two protocols:
Top shows plate usage Bottom shows the number of 96-lane agarose gels, 24-well
colony-plate images and 26-lane SDS–PAGE gels 96 constructs uses 34 96-well plates and 36 24-well plates… …generates 480 images of colony wells,
1536 lanes on agarose gelsand 416 lanes on SDS–PAGE gels
Target annotation (largely covered in PIMS 0.4) Target selection (not planned for PIMS) Construct design (using VectorNTI) Obtain/store source strain genomic DNA Describe selected genes Describe primers, link to VectorNTI output Describe entry clones as plasmids Describe expression constructs Describe high-throughput expression trials Describe solubilization trials…
Working with MPSI to increase use…
Solubilization trials (Leeds)… Solubilization trials performed in 96-well format Perform 24-trials per target, therefore four targets per set
Det 1
Det 2
Det 3
Det 4
Det 1
Det 2
Det 3
Det 4
Target 1
Target 3
Target 2
Target 4
Detergent concentration gradients…