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BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics.
Framework for text mining, data integration and data analysis. Keywords: ontology and graph alignment, relation mining, warehouse, semantic database integration, bioinformatics, systems biology, microarray, Java.
coreboot is aimed at replacing the proprietary BIOS (firmware) found in most computers. coreboot performs a little bit of hardware initialization and then executes additional boot logic, called a payload. coreboot can scale from specialized applications that run directly from firmware, run operating systems in flash, load custom bootloaders, or implement firmware standards, like PC BIOS services or UEFI.
Synthetic Biology Software Suite (SynBioSS) is composed of a wiki for biochemical kinetic constants, a graphical interface for simulating synthetic biological pathways, and a simulator that runs on either a desktop or supercomputer.
Bowtie, an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers. Please cite: Langmead B, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25.
GNU Octave is a high-level interpreted language, primarily intended for numerical computations. It provides capabilities for the numerical solution of linear and nonlinear problems, and for performing other numerical experiments. It also provides extensive graphics capabilities for data visualization and manipulation. Octave Forge is a place for development of its packages; from bioinformatics and fuzzy logic to mechanics and instrument control.
The Hidden Markov Model Toolkit (HTK) is a portable toolkit for building and manipulating hidden Markov models. HTK is primarily used for speech recognition research although it has been used for numerous other applications including research into speech synthesis, character recognition and DNA sequencing. HTK is in use at hundreds of sites worldwide.
NHibernate is a mature, open source object-relational mapper for the .NET framework. NHibernate is a port of Hibernate Core for Java to the .NET Framework. It handles persisting plain .NET objects to and from an underlying relational database.
ITK is an open-source, cross-platform system that provides developers with an extensive suite of software tools for image analysis. Developed through extreme programming methodologies, ITK employs leading-edge algorithms for registering and segmenting multidimensional data.
The Biomolecule Toolkit is a library for modeling biological macromolecules such as proteins, DNA and RNA. It provides a C++ interface for common tasks in structural biology to facilitate the development of molecular modeling, design and analysis tools.