Computational Biology

Vigyaan is an electronic workbench for bioinformatics, computational biology and computational chemistry. It has been designed to meet the needs of both beginners and experts. VigyaanCD is a live Linux CD containing all the required software to boot the computer with ready to use modeling... Platforms: *nix

The project aims to extend the PHP scripting language to enable PHP developers to write bioinformatics applications more rapidly than if they had to start from scratch using 'vanilla php'. Platforms: Windows, Mac, Linux

Platform for parallel computation in the Amazon cloud, including machine learning ensembles written in R for computational biology and other areas of scientific research. Home to MR-Tandem, a hadoop-enabled fork of X!Tandem peptide search engine. Platforms: Windows, Mac, Linux

MGWT: Identification of protein coding regions using the ModifiedGabor-wavelet transform.Sequence of test:F56F11.4.fasta (included into the zip file)http://www.ncbi.nlm.nih.gov/entrez/viewer....de&val=AF099922http://www.vision.ime.usp.br/~jmena/projec...ome_results/F5/References:[1] J. P.... Platforms: Matlab

ToBiX is a Morphix-based Linux live CD containing a range of specialist applications for bioinformatics. With this distrubution you just boot from the CD and you have a fully functional LINUX OS distribution with open source applications. Besides using some RAM, ToBiX doesnt touch the host... Platforms: *nix

This package is the mRMR (minimum-redundancy maximum-relevancy) feature selection method in (Peng et al, 2005 and Ding & Peng, 2005, 2003), whose better performance over the conventional top-ranking method has been demonstrated on a number of data sets in recent publications. This version uses... Platforms: Matlab

The Systems Biology Markup Language (SBML) is an XML-based description language for representing computational models in systems biology. Visit the project web site to learn more. Platforms: Windows, Mac, Linux

StrBio is a set of Java classes and libraries useful for development of software for computational structural biology research. They are licenced under the LGPL. he strbio.org classes are the basis for several published research projects, including the Pred2ary secondary structure prediction... Platforms: *nix

This is the first example of Computational Physics, Modeling and Simulating a Physical SystemsEx1: Kepler's Laws Platforms: Matlab

Researchers in quantitative systems biology make use of a large number of different software packages for modeling, analysis, visualization, and general data manipulation. The Systems Biology Workbench (SBW), is a software framework that allows heterogeneous application components-written in... Platforms: Windows

SBSI or Systems Biology Software Infrastructure is a handy suite of software tools specially designed for systems biology. It includes parallelized numerical algorithms, and a client application for visualizing results, running simulations, and integrating SBML based plugins. SBSI is a suite of... Platforms: Windows

CILib is a framework for developing Computational Intelligence software in swarm intelligence, evolutionary computing, neural networks, artificial immune systems, fuzzy logic and robotics. Platforms: Windows, Mac, Linux

The Systems Biology Workbench(SBW) is a simple framework for application intercommunications. It uses a broker-based, distributed, message-passing architecture, supports many languages including Java, C++, Perl & Python, and runs under Linux,OSX & Win32. Platforms: Windows, Mac, BSD, Linux

Synthetic Biology Software Suite (SynBioSS) is composed of a wiki for biochemical kinetic constants, a graphical interface for simulating synthetic biological pathways, and a simulator that runs on either a desktop or supercomputer. Platforms: Windows, Mac, BSD, Linux

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. Platforms: Windows, Mac, Linux

The Biomolecule Toolkit is a library for modeling biological macromolecules such as proteins, DNA and RNA. It provides a C++ interface for common tasks in computational structural biology to facilitate and standardize the development of molecular modeling, design and analysis tools. Platforms: *nix

ByoDyn (http://cbbl.imim.es/ByoDyn) is a software tool for the study of biochemical networks within the framework of systems biology. SBML compatible, ByoDyn is a group effort of the Computational Biochemistry and Biophysics Lab. Platforms: *nix

Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. This project offers a flexible rendering engine and a powerful plugin architecture. The main concept behind Avogadro... Platforms: *nix

CILib comes from Computational Intelligence Library. CILib is a collaborative research framework for developing Computational Intelligence algorithms in the fields of swarm intelligence, evolutionary computing, neural networks, artificial immune systems, and fuzzy logic. Whats New in This... Platforms: *nix

Perceptual Image Diff is an image comparison utility that makes use of a computational model of the human visual system to compare two images. Its useful for running automated regression testing on images that are perceptually identical but have minor pixel noise from different random number... Platforms: *nix