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.
COPASI is a software application for modeling and simulation of biochemical networks. The software package has a GUI that lets users define biochemical network models by entering chemical reactions and kinetic equations. A powerful simulation engine can then perform simulations of the dynamics of the networks and carry out many different computational analyses. COPASI can simulate dynamics using either an ODE approach or a stochastic chemical kinetics approach (Gillespie-type algorithms).
ParseGenBank is a minimalistic, incremental, event-driven GenBank Flat File Format parser. It aims to efficiently produce events for keywords, features, qualifiers, and coding data. It does not attempt to parse the contents of feature or qualifier data, but provides a framework on which such a system can be built.
Wandora is a general purpose data extraction, management, and publishing application based on Topic Maps and Java. Wandora has a graphical user interface, layered presentation of knowledge, several data storage options, rich data extraction, import and export capabilities, and an embedded HTTP server that enables dynamic publication of Topic Maps. Wandora is well suited for rapid ontology construction and knowledge mashups.
EPoS is a modular software framework for phylogenetic analysis and visualization. EPoS combines a powerful graphical user interface with a plugin system that allows simple integration of new algorithms, visualizations, and data structures. EPoS currently supports distance based tree construction from multiple sequence alignments and distance matrices as well as different algorithms to create consensus trees and supertrees. EPoS also integrates a tree visualization module that can be used to compare two trees and export visualizations.