System for Information Management in BioMedical Studies (SIMBIOMS)

The System for Information Management in BioMedical Studies is a system for annotation and storage of data, associated with the collection of samples in biomedical studies. Standardisation of sample collection, processing and storage, as well as recoding the relevant information are vital for the proper and accurate reporting on the results of biomedical studies. The SIMBIOMS system not only allows to trace the information on protocols, sample location, transportation and storage conditions, but also solves the data confidentiality issues by mapping sample data to the anonymous patient identifiers. The system is generic, and can be used for annotating any samples, not only human ones. The prototype of SIMBIOMS has been proved to be successful within the MolPAGE project (Molecular Phenotyping to Accelerate Genomic Epidemiology), an integrated EU project, and a broader scientific community could benefit from the use of it in their biomedical projects.

An open source project of this software is available also on website.

Motif search in protein structures (TOPStructure)

TOPS motifs are fragments of TOPS diagrams that are shared by several proteins (domains) believed to have some biological relationship together with some biological annotaion. Appearance of such motif in unfamiliar protein can suggest its similarity to the other proteins that share the same motif. The trustworthiness of such conclusion may vary, however, it may be quite high if the motif that has been found has few or none "false" matches among the familiar proteins. The current motif database is based upon CATH classification, i.e. as biologically similar are considered proteins that share e same CATH number prefix. Hence the motifs can be used as a tool of fast prediction of CATH number.