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SimThyr is a continuous simulation program for the human pituitary-thyroid feedback control system. Applications of this program cover research, including development of hypotheses, and education of students in biology and medicine, nurses and patients.
Tissue Simulation Toolkit is a two-dimensional library for the Cellular Potts Model (Graner and Glazier 1992; Phys. Rev. Lett. 69, 2013), which is increasingly used by computational biologists to study tissue patterning and developmental mechanisms.
XNBC is a graphic application to simulate biologic neural networks.
XNBC is a full featured application for computer naive neuroscientists. It simulates biological neural networks using graphic tools to edit neurons and networks, to run the simulation and to analyze results. Written in C, it runs on Unix and Windows.
Web site : http://ticemed-sa.upmc.fr/xnbc/
All recent versions are on this site.
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Census is a comprehensive cross-platform project manager and integration hub for NONMEM, the gold standard tool for model-based pharmacometric data analysis.
"""
E-Cell's source code repository has moved to GitHub!
https://github.com/ecell
The development of E-Cell now continues on GitHub.
The Subversion repository was abandoned.
"""
E-Cell System is an object-oriented software suite for modeling, 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 in a model.
MASyV (Multi-Agent System Visualization) enables one to write agent-based models/cellular automata, eg. in C, visualize them in real time & capture to movie file with MASyVs GUI & message passing lib. Includes examples: Hello World, ants, viral infection
The Tomographic Image Reconstruction Interface of the Universite de Sherbrooke (TIRIUS) is a Qt-based user-interface software for reconstructing 3D images from data generated by real apparatus or generated by the GATE Monte Carlo simulator.
FM100 is a computer simulation of the Farnsworth-Munsel 100 hue colour (color) vision test. The results of the test can be used to assess the user's colour vision.
Two Dimensional NOesy simulation (TDN) implementents an algorithm that creates a time-domain 2D NOesy spectrum. TDN does not calculated the nOe peak intensities, Therefore, you will need the CORMA (Complete nuclear Overhauser Relaxation Matrices).
http://www.princeton.edu:80/pr/pwb/01/0326/1b.shtml
http://www.cs.princeton.edu/immsim/
Immsim is an immune systemsimulation used by Immunology students and researchers. Currently it is being used at Princeton University.
The Integrative Biology VRE is a web-based graphical user interface and repository that provides an environment where biological simulation experiments can be constructed without the need for any knowledge of unix, cluster computing, or shell scripting.