Protein Information Management System

Mission and Scope

What problem does this project address?

High-throughput automated techniques have revolutionized DNA sequencing techniques over the last 10 years, allowing the study of minute samples on highly parallel instruments. Synchrotrons are also becoming increasingly automated and beginning to offer data collection services with unattended automatic sample changers. The high-throughput approach of automation, miniaturization and parallelization is increasingly being applied to the techniques of protein sample production. Laboratory methods are changing as these technologies become standard, but information tracking software has not managed to keep pace.

What is the goal of this project?

The advent of structural genomics in the UK with the MRC funding of the Oxford Protein Production Facility (OPPF) three years ago and the newly established BBSRC SPoRT consortia demonstrates a growing need for a sophisticated LIMS suitable for academic environments. This proposal offers a mechanism for the incremental development and deployment of such a system by drawing all the interested parties across the UK (and ties across Europe) to pool resources and to work together under a single management framework which is committed to meeting the needs of the two SPoRT consortia funded by the BBSRC. The deliverable of the project is a Protein Information Management System (PIMS) both for deployment at the SPoRT consortia, the OPPF and York University and to be made freely available to all academic laboratories.

What is the scope of this project?

A Laboratory Information Management System for protein sample preparation from selection, cloning, expression, purification, characterisation and, where applicable, crystallisation and automated data deposition in the PDB. Privilege-controlled password-protected security for the system.

The PIMS design will emphasize user-configurability and offers client/server capabilities that will permit easy adaptation to new laboratory processes without reprogramming. Toolkits for workflow and protocol creation will include editing facilities allowing modifications, revisions and updates to workflows and protocols. Exchange of workflows and templates within and between consortia will be a mechanism for standardization. Intra-consortia sample exchange tracking will be through a seamless data import/export functionality making use of the e-HTPX (BBSRC) interchange XML messaging system. Wireless computing capabilities will be implemented for barcode generation/reading and a number of machine interfaces will be produced which will gather data and allow machine scheduling. Data manipulation, visualisation and data mining tools will be constructed to report laboratory data in user defined summary tables and graphs.

As requirements are detailed, and the development team becomes able to give time estimates, the scope of the whole project will be reviewed. The first review will be after 12 months. PIMS will be delivered in a series of increments, and the scope of each release will be decided by discussions between the customers and the development team.

What development methodology is being used?

See our software development methodology document.

Where should a new team member start?

For more information, see the project proposal.

The application for funding has been submitted.

The project is at Feasibility stage in the CCLRC.