Viksna J, Celms E, Opmanis M, Podnieks K, Rucevskis P, Zarins A, Barrett A, Neogi SG, Krestyaninova M, McCarthy MI, Brazma A, Sarkans U. PASSIM - an open source software system for managing information in biomedical studies. BMC Bioinformatics. 2007 Feb 9;8:52.
Brazma A, Krestyaninova M, Sarkans U. Standards for systems biology. Nat Rev Genet. 2006 Aug; 7(8):593-605. Review.
PASSIM for BioMedical Studies
The Patient and Sample System for Information Management (
Submission and retrieval of information about patients and biomedical samples
Easy to customize for various needs of biomedical projects
Secures patient confidentiality by separating de-identified information from private record
Web-based with role-defined user access rights
Successful in a large international collaborative project- MolPAGE
Assay and Data Management System (AIMS)
Overview of PASSIM
The data submission form is brief, thus making the system simple to use and customize for any biomedical study easily. When used for a particular study, many of the original PASSIM parameters can be reused.
The PASSIM consists of the two parts:
1. Stand-alone Person Management Tool (PMT), used on-site by staff collecting the samples
PMT is intended for registering and searching through confidential information about the patients from which samples have been taken. The system assigns a unique anonymous identifier to each of the patients, which is then used for patient identification in Sample Management Database. Each sample collection site hosts their local copy of the PMT and a local database of the corresponding data. The use of PMT is optional and Sample Management Database can be configured either to accept PMT generated patient identifiers, to accept any identifiers, or to generate identifiers automatically.
2. Sample Management Database accessible through the web-based interface
Sample Management Database can be accessed online through a web-based interface and contains non-confidential information about samples. It allows the registration of samples and aliquots as well as subsequent tracing of aliquot locations
Download of Sample Management Database and PMT
Sample Management Database:
And Sample System for Information Management (version 2.1).
Stand-alone Person Management Tool (PMT):
Person Management Tool (.zip file containing Windows executable, .xml database file and installation description in README file).
There are two counterparts of the PASSIM: Sample Management Database - an open source project downloadable from http://sourceforge.net/, and Person Management Tool - a Windows executable available from http://bioinf.mii.lu.lv/passim/.
Installation of the PASSIM modules
1. Stand-alone Person Management Tool (PMT):
Person Management Tool
.zip file containing Windows executable,
.xml database file and installation description in README file.
2. Sample Management Database (SIMS):
Easy 3-step installation:
Download and install the
latest version of Java Download and install
Apache Tomcat Download the
SIMS.war and deploy it on the server
Email: passim pie sourceforge punkts net
Institute of Mathematics and Computer Science
Raina bulvaris 29 Riga, LV-1459, LATVIA
European Bioinformatics Institute
European Bioinformatics Institute
Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD, UK
+44 (0)1223 494 444
+44 (0)1223 494 468