Cactus is a general, modular, parallel environment for solving systems of partial differential equations. The code has been developed over many years by a large international collaboration of numerical relativity and computational science research groups and can be used to provide a portable platform for solving any system of partial differential equations.
Clarrhmos is a description language and simulator for myocardial structure and electrophysiology. Input to the program is a model file specifying types of cells, action potential shape, refractory period, 3D placement of the cells, relation of parameters to other functions, pacing, electrode placement. Output is a file describing depolarisation and repolarisation of the myocardium and electrograms. A graphic tool for interactive inspection of the output file is also included.
E-Cell System is an object-oriented software suite for modelling, simulation, and analysis of large scale complex systems such as biological cells. It allows many components, driven by multiple algorithms with different timescales, to coexist. The core library is written in C++ with a Python binding, and frontend software uses Python.
EGO is a program to perform molecular dynamics simulations on parallel as well as on sequential computers. Supported parallel machines include the Hitachi SR8000, CRAY-T3E, IBM-SP2, Fujitsu VPP700, Parsytec-CC under PARIX, and inhomogeneous clusters of UNIX workstations under PVM or MPI. EGO also runs sequentially on any decent UNIX workstation, even Windows95/NT PC's (with a GNU-C compiler) can be used.
Genpak is a small set of utilities designated to process DNA, RNA, and protein sequences in a very Un*x-like manner. This way, Genpak programs can be combined using pipes and redirections, as well as easily incorporated into CGI scripts. The utilities include a program for calculating GC content, Tm, translating DNA/RNA sequences into protein sequences, quick sequence retrieval, random sequence generation, and finding promoter sequences using a Hertz matrix.
Ghemical is a molecular modelling software package with some nice 3D visualization tools. It supports methods based on both molecular mechanics and quantum mechanics (using MOPAC7, and MPQC for QM). The geometry optimization (for MM and QM) and molecular dynamics (for MM) algorithms are included. Ghemical is written in C++, and hopefully offers a good framework for a generic freeware molecular modelling tool.
OIO is a Web-based metadata/data management front-end which is built using Zope and works with Postgresql. No programming is required to build and manage Web-forms or to perform data mining/analysis on the collected data. It is in production at the Harbor/UCLA Medical Center for clinical outcomes management and research data. Forms created with OIO and hosted on any OIO server can be downloaded as XML files. Once downloaded from the "Forms library" and imported into an OIO server, the necessary database tables are automatically recreated and the imported forms become immediately available to the users of that OIO server.
PLOTICUS is a command line utility for creating bar, line, pie, boxplot, scatterplot, sweep, heatmap, vector, timeline, Venn diagrams, and other types of charts and plots. ploticus is good for automated or just-in-time graph generation. It handles date, time, and categorical data nicely, and has some basic statistical capabilities. It can output to GIF, PNG, SVG, SWF, JPEG, PostScript, EPS, and X11. You can use convenient preset options or create complex scripts with rich and detailed color and style operations.
R is a language and environment for statistical computing and graphics. It is similar to S, which was developed at Bell Laboratories by John Chambers et al. It provides a wide variety of statistical and graphical techniques (linear and nonlinear modelling, statistical tests, time series analysis, classification, clustering, etc.). R is designed as a true computer language with control-flow constructions for iteration and alternation, and it allows users to add additional functionality by defining new functions. For computationally intensive tasks, Fortran and C code can be linked and called at run time.