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PASSIM – an open source software system for managing information in biomedical studies

Juris Viksna1, Edgars Celms1, Martins Opmanis1, Karlis Podnieks1, Peteris Rucevskis1, Andris Zarins1, Amy Barrett3, Sudeshna Guha Neogi2, Maria Krestyaninova2*, Mark I McCarthy3, Alvis Brazma2 and Ugis Sarkans2*

Author Affiliations

1 Institute of Mathematics and Computer Science, Riga, University of Latvia, Latvia

2 European Bioinformatics Institute, EMBL-EBI, Hinxton, UK

3 Oxford Centre for Diabetes, Endocrinology and Metabolism, Churchill Hospital, Old Road, Headington, Oxford, OX3 7LJ, UK

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BMC Bioinformatics 2007, 8:52  doi:10.1186/1471-2105-8-52

Published: 9 February 2007



One of the crucial aspects of day-to-day laboratory information management is collection, storage and retrieval of information about research subjects and biomedical samples. An efficient link between sample data and experiment results is absolutely imperative for a successful outcome of a biomedical study. Currently available software solutions are largely limited to large-scale, expensive commercial Laboratory Information Management Systems (LIMS). Acquiring such LIMS indeed can bring laboratory information management to a higher level, but often implies sufficient investment of time, effort and funds, which are not always available. There is a clear need for lightweight open source systems for patient and sample information management.


We present a web-based tool for submission, management and retrieval of sample and research subject data. The system secures confidentiality by separating anonymized sample information from individuals' records. It is simple and generic, and can be customised for various biomedical studies. Information can be both entered and accessed using the same web interface. User groups and their privileges can be defined. The system is open-source and is supplied with an on-line tutorial and necessary documentation. It has proven to be successful in a large international collaborative project.


The presented system closes the gap between the need and the availability of lightweight software solutions for managing information in biomedical studies involving human research subjects.