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.
CTSim is a Computed Tomography simulator. It simulates the process of obtaining x-ray data around a phantom object. It then uses various reconstruction algorithms for reconstructing the original image. It supports animation of projection and reconstruction processes, 3-dimensional viewing using OpenGL as well as cross platform support using GTK and Win32.
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.
nut is nutrition software to record what you eat and analyze your meals for nutrient composition. The database included is the latest USDA Nutrient Database for Standard Reference. This database contains values for vitamins, minerals, fats, calories, protein, carbohydrates, fiber, etc., and includes the essential polyunsaturated fats, Omega-3 and Omega-6. Nutrient levels are expressed as a percentage of the Daily Value, the familiar standard of food labeling in the United States, but also can be fully customized. Foods can be added from recipes or food labels, and nutrient intake can be graphed. The program is completely menu-driven and there are no commands to learn.
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.
VMD (Visual Molecular Dynamics) is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer. VMD uses OpenGL and OpenGL Programmable Shading Language for high performance rendering of large structures.
The VP7 Way Kool Project is a GTK application which simulates a laboratory experiment with radioactive nuclei. The user can choose between many predefined radioactive sources or create new ones. The number of decayed nuclei and the activity of the source can be determined with a built-in counter. The beam can be attenuated with shields of paper, aluminium, and/or lead.