Open Source C Data Visualization Software

The SourceForge OpenRasMol project is an adjunct to the RasMol and OpenrasMol project at http://rasmol.org. It is hoped that the SourceForge OpenRasMol project will provide a convenient focal point for active collaborative contributions.

RasTop is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules based on the popular Rasmol software. The program is aimed at the rapid visualization and analysis of molecules.

The project has moved to GitHub: https://github.com/pixmeo/osirix

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

TinkerCell is a software for synthetic biology. The visual interface allows users to design networks using various biological "parts". Models can include modules and multiple cells. Users can program new functions using C or Python. www.tinkercell.

This site hosts the source code for C++ version of the Broker for SBW, NOM module, advanced simulation suite, analysis applications and model editors.

CQRlib is an ANSI C implementation of a utility library for quaternion arithmetic and quaternion rotation math.

A base for programs. Includes algorythms for Q-learning and SOM's etc. too. Examples: Hamron: Simulates evolution, uses the 2D-renderer. DriveUnit: created for school, for a robotic arm, uses the 3D-renderer. Hlearn: http://www.sagenb.org/home/pub/8

Acre calculates growing-space or stand-density of trees and creats pictures of it. It can also be used to calculate weighted Voronoi-Diagrams (splits up an area to the neares point or to the point with the greatest influence at a certain place).

CoactivationMap is a graphic user interface to browse through a map of functional co-activations of the human brain. Click on a region, and observe which other regions are likely to be connected

CompLearn is a general-purpose compression-based machine learning system that uses data compression to learn or data mine patterns in arbitrary data.

CompuCell3D is a software framework for multimodel simulations of biocomplexity problems. It has been developed as an ongoing project for the Interdisciplinary Center for the Study of Biocomplexity at the university of Notre Dame.

Flow Investigation using N-Dimensions (FIND) is a program designed for analysis and visualization of Flow Cytometry data. FIND focuses specifically on automated population discovery (clustering) methods. The project targets both users and developers.

This is a generalized rack widget written using the Gnome Canvas, which is specifically targeted for scientific operations (including Chemistry/Biology). The main purpose of the widget would to visualize standardized containers such as microtiter plates.

The project is for developing libraries for visualizing biological sequence data on the web. The libraries are written in C and currently use a language (lex/yacc) based front end for presenting features on genomes, contigs, or any type of sequence.

PANorama is a Linux-compatible, open-source software package for panicle image acquisition, processing, and phenotyping. PANorama 2.0 contains new phenotype measurements and is available for download within the "Files" tab listed above. Installation and user instructions are located within the "Wiki" tab. How to videos are available for streaming at the link below, or for download in the "Files" tab above. Information regarding the project and funding can be found at http://ricediversity.org, and within the corresponding publications and how-to videos: How to videos: http://vimeo.com/cornellricelab PANorama1.0 (Crowell et al. 2014): http://www.plantphysiol.org/content/165/2/479.short PANorama2.0 (Crowell et al. 2016): (http://goo.gl/vQux5Z)

Simple static viewer of abnormal read pairs in second-generation alignment data.

ProgPorts is an administrative and easy user interface to hundreds of proteomics, molecular dynamics, and protein crystallography programs. It is a hybrid of the prog/setup system, developed at Johns Hopkins University, and GNU-Darwin ports system.

This is a sophisticated & integrated simulation and analysis environment for dynamical systems models of physical systems (ODEs, DAEs, maps, and hybrid systems). It supports symbolic math, optimization, continuation, data analysis, biological apps...

RNAfdl is a highly flexible tool for drawing RNA secondary structures. Secondary structures can be visualized as classical secondary structure plot, circle plot, linear plot or mountain plot. RNAfdl allows manual editing and several drawing styles, as well as a fully automated conjugate gradients minimization approach to draw more complex structures without user interaction. In addition, RNAfdl allows you to incorporate non-canonical base pairs into drawings.

SBEVSL is a collaborative project between Dowling and RIT on the development of a Structural Biology Extensible Visualization Scripting Language, so that users can move freely among various molecular graphics tools, such as rasmol, pymol, raster3d, etc.

ViNSS View is a highly flexible tool for drawing RNA secondary structures. Secondary structures can be visualized as classical secondary structure plot, circle plot, linear plot or mountain plot. ViNSS View allows manual editing and several drawing styles, as well as a fully automated conjugate gradients minimization approach to draw more complex structures without user interaction. In addition, ViNSS View allows you to incorporate non-canonical base pairs into your drawing.

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.

cdfread is a program for people wirking with mass spectrometry datasets. cdfread implements the routines to read mass spectra and mass chromatograms from data files in netCDF ("Andi-MS") format. Centroid and profile data are supported.