The system consists of two components—Sample Information Management System (SIMS) and Assay data and Information Management System (AIMS) (). As the names suggest, SIMS is designed to collect phenotypical, environmental and technical information about samples, while AIMS handles the experimental data from high-throughput assays. SIMS provides a simple solution for data anonymization by creating identifiers linked to person's information in a separate module. SIMS extends a previously published system (PASSIM; Viksna et al.
). The main new features include customizability and compatibility with data formats MAGE-TAB and ISA-TAB. While, PASSIM was designed to manage patient and sample data, it did not have any means for linking it to data from high-throughput assays.
High level class diagram of SIMS and AIMS.
AIMS is a new system filling this gap, designed for adoptability for any technological platform, and for easy extraction of captured data for analysis. It is linked to SIMS through a three-level hierarchy: a person can be linked to one or more samples, a sample can have one or more aliquots. Each aliquot can have one or more assays performed on it, and each assay can be linked to one or more data files. Assays are grouped in experiments and studies, each of which can have one or more data files attached. For instance, raw microarray data files would be normally linked to individual assays, while normalized gene expression matrices to experiments. Assays are technology-specific; the current AIMS configurations include genotyping, sequencing, proteomics and metabonomics.
The two systems can be installed and used independently, or jointly—if a laboratory already has a local informatics system for sample or assay data, it can be used jointly with AIMS or SIMS, respectively.
SIMBioMS run in Apache Tomcat servlet containers, or other application servers. The data are stored in PostgreSQL databases, but other popular database management systems have been tested and can be used with minimal changes. The systems are platform independent, and have been tested on several MS Windows and Linux. Several preconfigured versions, including ones for type 2 diabetes, metabolic syndrome and autoimmune diseases are packed into .war web-application archives. AIMS/SIMS can be installed either as local (e.g. on a laptop) or as centralized databases. Installation for local use is a simple two-step procedure that does not require special database software (java light database h2 is used). Filtering functionality is customizable, for enumerated value fields a drop-down list can be provided, fields are defined as parameters.