PubSearch is a literature curation management system designed to store and manage the available literature for an organism or system of interest. It provides database curators with a powerful literature search capability, stores relevant biological information, creates automatic associations between the biological information and the literature, and provides a user-friendly web interface for manual validation and curation.
SIMS (SIMBioMS) is a web based system that allows researchers to track information related to sample collection, processing, location, transportation and storage conditions etc. The system can be easilly used either for Data submission – entering and editing the information on samples and individuals, or Data access – browsing and querying this information, and generating reports. The organization of data within SIMS is based on three main categories: First level (Persons), Second level (Samples) and Third level (Aliquots), where an arbitrary number of second level records (samples) can be associated with each record from the first level (person) and an arbitrary number of third level records (aliquots) can be associated with each the second level record (sample). It is possible to configure SIMS with other categories’ titles and meta-data (for example, Persons, Vists and Samples or Persons, Characteristics and Samples).
Bioinformatics. 2009 Oct 15;25(20):2768-9. doi: 10.1093/bioinformatics/btp420. Epub 2009 Jul 24. A System for Information Management in BioMedical Studies–SIMBioMS.
Krestyaninova M1, Zarins A, Viksna J, Kurbatova N, Rucevskis P, Neogi SG, Gostev M, Perheentupa T, Knuuttila J, Barrett A, Lappalainen I, Rung J, Podnieks K, Sarkans U, McCarthy MI, Brazma A.
SBEAMS is a framework for collecting, storing, and accessing data produced by a wide variety of experiments. The software provides a customizable framework to meet the needs of modern systems biology research.
SBEAMS – Microarray provides MIAME-compliant Affymetrix GeneChip microarray database functionality under the SBEAMS framework.
SBEAMS-Proteomics is part of the SBEAMS (Systems Biology Experiment Analysis Management System) Project, which is a framework for collecting, storing, and accessing data produced by a variety of different experiments; these experiments can be managed separately but then correlated later under the same framework.
RAMPART is a de novo assembly pipeline that makes use of third party-tools and High Performance Computing resources. It can be used as a single interface to several popular assemblers, and can perform automated comparison and analysis of any generated assemblies.
PiMS (Protein Information Management System) is a Laboratory Information Management System (LIMS) developed to support the unpredictable workflows of Molecular biology and Protein production labs of all sizes.
Labmatica is a Laboratory Information Management System ( LIMS ). With Labmatica you can: manage samples; create sample types from methods & parameters; easily generate reports & certificates; fine tune user rights. Ready made reports and certificates are included in the distribution. You can easily configure these report templates to your corporate identity.
CDK Taverna project based on the “Pipelining Technology” idea tries to address the advantages of software libraries and sophisticated information systems.The project combines two other open-source projects:
The Taverna workbench as a workflow container.
The Chemistry Development Kit (CDK) as a basic chemo-/bioinformatics library.
AIMS is a web based system that serves as the central repository for experimental data produced by different experimental technologies (genomic, transcriptomic, proteomic, metabolomic data etc). The basic structure of AIMS resemples that of SIMS, with data organized around three main categories: Studies, Experiments and Assays. However the system is designed to be extremely flexible reagrding its configuration, since it is intended for one instance of AIMS system to be used for data obtained by several different technologies.