ProActive is a Java library for parallel, distributed, and concurrent computing as well as mobility and security in a uniform framework. It provides a comprehensive API and a graphical interface and is based on an Active Object pattern, a uniform way to encapsulate a remotely accessible object, a thread as an asynchronous activity, an actor with its own script, a server of incoming requests, a mobile and secure agent, and a component with server and client interfaces. It simplifies the programming of applications distributed over a LAN, clusters, an intranet, or Internet GRIDs.
Babase is a baboon data management system. It is designed to facilitate the retrieval, storage, maintenance, and analysis of the following broad data categories: group membership, social status (dominance rank), life events, sexual cycle events (including progeny), sexual cycle day-to-day status, dyadic social interactions, focal animal samples, and multi-party social interactions. Integration of other data is supported. Babase is designed for Web access.
HapCluster++ is a software package for linkage disequilibrium mapping using coalescent theory. It is based on a Bayesian Markov-chain Monte Carlo (MCMC) method for fine-scale linkage-disequilibrium gene mapping using high-density marker maps. HapCluster++ is a C++ implementation of the method described in the paper "Fine Mapping of Disease Genes via Haplotype Clustering" by E.R.B. Waldron, J.C. Whitaker, and D.J. Balding. Genetic Epidemiology. 30: 170–179. (2006).
SNPfile is a library and API for manipulating large SNP data sets with associated meta-data, such as marker names, marker locations, individuals' phenotypes, etc. in an I/O efficient binary file format. In its core, SNPfile assumes very little about the metadata associated with markers and individuals, but leaves this up to application program protocols.
Quick-Join implements a heuristic for speeding up neighbour joining, making neighbour joining feasible for large sets of taxa. The inferred tree is identical to the tree inferred by the traditional neighbour joining method, but the heuristic will (potentially) construct the tree significantly faster.
Cell Electrophysiology Simulation Environment is a framework to perform electrophysiological simulations. It can, for example, simulate cardiac myocyte electrical activity. It is useful for simulations of action potentials, individual ionic currents, and changes in ionic concentrations.
BioMAJ (BIOlogie Mises A Jour) is a workflow engine dedicated to data synchronization and processing. It automates the update cycle and the supervision of the locally mirrored data repository. The application is generalist, but was applied in the bioinformatics field for biological data bank management. The packaging includes workflow and indexing post-processing scripts for most used biological data banks. Developed in Java and Ant, the application is compatible with various Unix-based systems.