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.
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.
RTLab is an RTLinux/RTAI-based data acquisition and control application. It is designed to help experimenters design and implement their hard realtime control experiements using higher abstractions than the services offered by RTAI or RTLinux. It is split into two parts. One is a user-space series of C++ classes (written for Qt) which implement a reference application called DAQSystem which is designed to acquire analog input voltage data and display it on the screen. DAQSystem communicates with rtlab.o, the realtime kernel module which is the second part of RTLab. The rtlab.o realtime kernel part is a kernel module that loads into RTLinux or RTAI and is responsible for driving COMEDI hardware for the purposes of data acquisition and realtime control. The module is extensible and features a 'plugin' architecture so that scientists who are savvy C programmers can easily leverage the existing framework for their own custom experiment logic. Experiment logic is specified by writing a kernel modules that gets called back for each scan rtlab.o acquires from the COMEDI hardware. In addition, data visualization and storage facilities exist in user space so that experimenters can instantly see graphical plots of their analog input data as it comes in from the hardware.
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.
Trans (short for Transmuter Programming Language) is an extremely dynamic, biologically-inspired prototyping language providing a framework for experimenting with naturally evolving systems of objects over the net, and for exploring new ideas about recombinant software, code morphing, and evolutionary programming. Trans is also a very capable general-purpose programming language. It's fast, flexible, compact, object-oriented, highly extensible, and easy-to-learn. It can be used for rapid prototyping, or as a scripting language, an embedded language, a network server or client, a system of cooperating network nodes, a real-time control and monitoring system, and more.
gfit analyzes data using models. gfit lets the user create a model for virtually any type of system using a minimal amount of computer code. It is particularly useful for studying various systems in biophysics, biochemistry, and cell biology. The interface for gfit models specifies relationships between input and output variables in a rule-based fashion. It provides flexibility and allows the user to reuse same models for many related problems.