- AceDB
- Genome database system developed to provide a custom database kernel and a nonstandard data model for the flexible of scientific data.
- Biochemical Algorithms Library (BALL)
- C++ application framework specifically designed to reduce development times in the field of computational molecular biology and molecular modeling.
- BioPHP
- Open source project aimed at providing a scripting language for the bioinformatics field.
- Biopython
- Project initiated by an international association of software developers. Aims to build freely available Python tools for computational molecular biology.
- BioQuery
- Bioinformatics program developed to help formulate strategies in organizing biomedical databases.
- BioRuby
- Project aimed at implementing an integrated environment for bioinformatics with the Ruby language.
- BioWarehouse
- Open-source software environment developed to enable the integration of a set of biological databases into a single physical database management system.
- Cell Electrophysiology Simulation Environment (CESE)
- Comprehensive framework intended for the performance of computational electrophysiological simulations.
- EST2uni
- Parallel tool for database creation and automated EST analysis. Features a data mining web interface.
- InterMine
- Open source data warehouse system. Enables the creation of databases of biological data accessible with sophisticated web query tools.
- NeoBio
- Library of Java-implemented bioinformatics algorithms. Relies on the SMAWK algorithm and makes use of Lempel-Ziv compression.
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