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…