Structural Biology at York Structural Biology Laboratory; Laboratory Information Management Systems for Structural Genomics
Jan Dohnálek
Institute of Macromolecular Chemistry of the Czech
Academy of Science, Heyrovského nám. 2, 16206 Praha 6
The Laboratory of Structural Biology of the University of York has played an important role in development of methods of modern 3D structural analysis of biological macromolecules by means of X-ray crystallography in the last 30 years. Research groups of the Laboratory specialized in different fields form a compact and friendly environment which influenced careers of many scientists also in the Czech and Slovak scientific communities. Current research topics range from industrial applications of knowledge gained from the 3D structural insight into protein structure and protein-ligand interactions through to structural genomics efforts and development of new computational methods in areas of structural analysis, bioinformatics, automation of structure determination process and also development of laboratory information management systems.
Structural genomics projects generate large amounts of experimental data, which are required to be safely recorded and accessible in an organized manner to provide maximum efficiency of information content.
Laboratory Information Management System stands for an ensamble of electronic databases, interfaces and utility programs that enables systematic recording (manual and automatic, i.e. machine produced) of crucial data during research projects at each experimental stage. Such a system should possess several fundamental properties:
1.
Well defined but
still flexible data model.
2.
Ease of data input.
3.
Flexible data
accessibility.
4.
Security.
5.
Hierarchy of
information type.
6.
Compatibility with
other LIMS systems.
Structural genomics centers throughout the world developed different approaches to this problem. LIMS systems developed for the purpose of structural genomics activities can be utilized also in research groups with less ambitious goals as for quantity. Several freely available systems for academics were released in the past few years Xtrack1, CLIMS2, MOLE3, PIMS, eHTPX4, HalX5. These provide variable levels of implementation of the above given criteria and of other capabilities. Ease of installation and use and applicability of several of these systems will be discussed.
Introduction
of LIMS systems is supported by the Czech Ministry of Education, project no.
1K05008.
1.
Harris, M.
and Jones, T.A. (2002) Xtrack - a web-based crystallographic notebook.
Acta Cryst. D58, 1889-1891.
2.
Fulton,
K. F., Forster, R., Jodun, R. Ervine, S., Ly, W., Robilliard, L., Sonsini, J.,
Whelan, D., Whisstock, J. C. & Buckle, A. M. (2004) CLIMS: Crystallography
Laboratory Information Management System. Acta
Cryst. D60 pp 1691-3.
3.
http://www.mole.ac.uk, MOLE - Mining
Organising and Logging Experiments
4.
Allan,
R., Keegan, R., Meredith, D., Winn, M., Winter, G., Diprose, J., Mayo, C.,
Launer, L., Fillon, J., Young, P., (2004) e-HTPX HPC, Grid and Web-Portal Technologies in
High Throughput Protein Crystallography. In: All Hands e-Science 2004,
Nottingham, U.K. 2004.
5.
http://halx.genomics.eu.org/. HalX. A free-source LIMS (Laboratory Information Management
System) for small to large scale structural biology labs.