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31 Ιαν 2013 (πριν από 4 χρόνια και 2 μήνες)

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PIMS: The Problems of

Project Management

Robert Esnouf, Scientific Sponsor for PIMS

OPPF/STRUBI, University of Oxford



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

Research processes rapidly evolve (need
configuration rather than customization)

No two laboratories have the same working

Potential targets / bioinformatics annotation

Target selection and construct design

Project planning and progress

Experiments and protocols (templates)

plate: expression, purification, “traditional” work

based: PCR, cloning, crystallization

QA: gels, mass spectroscopy, sequencing, DLS

Samples and sample descriptions (


Holders and locations

Stocks, reagents and reference data

Health and safety information

Users, roles, access / sharing and security

Databases and external references

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


An interface for recovering / analyzing data

An interface for project management

Administration (configuration and management roles)

Interface to external software (

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

in support of

other SPoRT

award holders (SSPF and MPSI) with heavy

involvement of CCP4 (2 FTE), OPPF and others

PIMS effectively started 4/2005 (one post 2/2006)

Management structure re
investigated late 2005

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
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…






Chris M

Line Man.

Line Man.

Project Steering


Strategy &



& issues

Major feature


Major feature


Local issues and


daily management

Tasks, coordination

progress monitoring

Robert E

term / long
term issues…

Meeting the needs of SPoRT consortia / OPPF / YSBL

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

Data model

Current interaction with CCPN…

PIMS model

Business Logic

User Interface


‘Hibernate’ API

Persistence Layer

PostgreSQL DB




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

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
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 gels

and 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…