CellProfiler is a system for analyzing cell images. It is designed for biologists without training in computer vision or programming to make quantitative measurements of cells in thousands of images automatically. It is implemented using Matlab, but compiled standalone versions are available.
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).
Blossoc is a linkage disequilibrium association mapping tool that attempts to build (perfect) genealogies for each site in the input, score these according to non-random clustering of affected individuals, and judge high-scoring areas as likely candidates for containing disease affecting variation. Building the local genealogy trees is based on a number of heuristics that are not guaranteed to build true trees, but have the advantage over more sophisticated methods of being extremely fast. Blossoc can therefore handle much larger data sets than more sophisticated tools, but at the cost of sacrificing some accuracy.
Xholon is a flexible tool for multi-paradigm (UML 2, ABM, SBML, NN, GP, PSys, CA, etc.) modeling, simulation, design, execution, and transformation. It is based on generic Java and XML building blocks, and optionally packaged as an Eclipse plugin for UML/SysML/FSM simulation. The Xholon project explores the idea of software as systems of linked nodes, organized hierarchically. The Xholon toolkit supports this back-to-basics approach, and demonstrates practical benefits through examples from numerous domains.
Mauve constructs global multiple alignments of rearranged genome sequences. It also provides an interactive display of multi-species sequence conservation and any annotated features in those genomes. It can be applied for sequence comparison of both finished or incomplete genomes in multiple contigs. The resulting display is useful for identifying functional chromosomal regions under selective pressure and for performing ortholog assignment based on conserved gene order. Mauve writes global alignments in eXtended Multi-FastA (XMFA) format, a phylogenetic guide tree in Newick format, and the location of genomic islands. It identifies the breakpoints of genomic rearrangement and can provide a reduction of the genomes to a signed permutation matrix suitable for inference of rearrangement history.