- A generic and fairly complete cellular automata simulation engine. CAGE is a fairy generic and complete cellular automaton simulation engine in Python. It supports both 1D and 2D automata, a variety of prepackaged rules, and the concept of "agents" which can move about independently on the map for implementing agent behavior. CAGE comes with numerous examples of fully-functional CA systems, including Conway's Game of Life, Langton's self-reproducing automaton, Langton's "vants," and 1D automata rule explorers. It also comes with simple displayers (including a curses interface for 2D automata). Also included is a unique implementation of a finite state machine (ant.py).
- CT Sim
- Computed Tomography is the technique of estimating the interior of objects from the measurements of radiation projected through the object. That radiation can be transmitted through the object such as in X-ray computed tomography or emitted from internal radiation sources as in nuclear medicine scans. CTSim simulates the transmission of X-rays through phantom objects. These X-ray data are called projections; CTSim reconstructs the original phantom image from the projections using a variety of algorithms. The program also has a wide array of image analysis and image processing functions.
- 'CoaSim' is a tool for simulating the coalescent process with recombination and gene conversion under the assumption of exponential population growth. It constructs the ancestral recombination graph for a given number of individuals and uses this to simulate samples of SNP and micro-satellite haplotypes/genotypes. The generated sample can afterwards be separated in cases and controls, depending on states of selected individual markers. The tool can accordingly also be used to construct cases and control data sets for association studies.
- 'CoaSim-gui' is a graphical use interface for the coalescence process simulator CoaSIm.
- 'cvEyeTracker' is a toolkit for low-cost real-time eye tracking. It is intended to provide a hardware design and a set of software tools useful for the analysis of eye movement data collection using inexpensive, off-the-shelf hardware. Available tools include algorithms to measure eye movements from digital videos, techniques to calibrate the eye tracking system, and example software to facilitate real-time eye-tracking application development.
- DataMelt (DMelt) is an environment for numeric computation, statistical analysis, data mining, and graphical data visualization on the Java platform. This Java multiplatform program is integrated with a number of scripting languages: Jython (Python), Groovy, JRuby, BeanShell. DMelt can be used to plot functions and data in 2D and 3D, perform statistical tests, data mining, numeric computations, function minimization, linear algebra, solving systems of linear and differential equations. Linear, non-linear and symbolic regression are also available. Neural networks and various data-manipulation methods are integrated using powerful Java API. Elements of symbolic computations using Octave/Matlab scripting are supported.
- DataStatix is a free software for GNU/Linux and Windows useful to manage data of every kind (although it has been written to manage biomedical data), to create descriptive statistics and graphs and to export items easily to R environment or to other statistic softwares. In order to handle properly big amount of data and many concurrent users, DataStatix works with MySql database and it has been developed and tested with MySql community edition 5.5. Some features of the software are: users management (create, delete, modify password) within the software; different users levels of data access (administrator, default, read only); user defined templates (models) of data, to create new databases easily; importation and esportation of data in CSV format (used also by Calc and Excel); updating of existing data from a CSV file created with DataStatix; descriptive statistics from every data (some more kind of statistics to come); graphs from every data.
- Datamash is a command-line program which performs basic numeric, textual and statistical operations on input textual data files. Datamash is designed to be portable and reliable, and aid researchers to easily automate analysis pipelines, without writing code or even short scripts.
- E-CELL Simulation Environment
- 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.
- Lightweight, super fast C/C++ library for sequence alignment using edit distance.
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