Biology

CySBGN adds support to Cytoscape to import, visualize and analyse System Biology Graphical Notation (SBGN) maps.

EcoloSim is a Simulation Framework for simple spatial models in biology and ecology, in Java.Typical problems are behavior of a herd of cattle, growth of microbe cells and other populations.

A command-line biochemical network compiler for systems biology.


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

This software is to help the those connected with Biology,Biotechnology,Bio Informatics.The user can select from the choices of proteins, nucleotides,etc(All those found on NCBI's website)and search for the specific results


Platforms: Windows, Mac, BSD, Linux

'Plasmidb' is a database management system (RDMS) used to manipulate, view and store molecular biology information rapidly and easily. Editable information includes: constructed plasmids, clones, standard vectors, primers, antibiotics, enzymes and more


Platforms: Windows, Mac, Linux

The Systems Biology Results Markup Language is a language describing data. Unlike flat data formats, SBRML allows describing the origin of the data as well. This project hosts a library and tools for using SBRML.


Platforms: Windows, Mac, Linux

Create, check, annotate, merge, diff, split SBML (System Biology Markup Lanugage) documents. The latest version of semanticSBML is webbased with a RESTful interface.


Platforms: Windows, Mac, Linux

Java class libraries for structural biology development: includes protein format conversion tool, printf-based text formatting, Pred2ary secondary structure prediction, neural net library, Hooke-Jeeves global optimizer, and misc. math & statistics.


Platforms: Windows, Mac, Linux

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


Platforms: Windows, Mac, BSD, Linux

Wattos is a collection of mostly Java programs for Structural Biology and NMR Spectroscopy. It's programs analyze, annotate, parse, archive, and disseminate experimental NMR data deposited by authors world wide into the PDB and BMRB.


Platforms: Windows, Mac, Linux

The performance of the level set segmentation is subject to appropriate initialization and optimal configuration of controlling parameters, which require substantial manual intervention. A new fuzzy level set algorithm is proposed in this paper to facilitate medical image segmentation. It is able...


Platforms: Matlab

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

This program presents the solution to an ode model of the circadian clock, published by Locke et al (2005) 'http://www.nature.com/msb/journal/v1/n1/full/msb4100018.html', in two different ways.A moving plot can show either time series or a limit cycle in 2D or 3D mode, with the user able to...


Platforms: Matlab

Bio link contains solutions to some topics in biology and bioinformatics. The solutions will be made available as soon as they are developed. Therefore they may contain bugs. Please let me know if you encounter a bug so that it can be fixed asap. Most tools will be in JAVA. The jar files can be...


Platforms: Matlab

Dynamic Bayesian networks (DBN) are widely applied in modeling various biological networks, including the gene regulatory network. Due to several NP-hardness results on learning static Bayesian network, most methods for learning DBN are heuristic, that employ either local search such as greedy...


Platforms: Matlab

Biomatters was founded on the principle of creating software that can be used by all researchers in their daily work. Our technology converts raw data into meaningful, visual information, simplifying research and ultimately improving efficiency. Biomatters???*a*? flagship software packages are:...


Platforms: *nix

ESBTL (Easy Structural Biology Template Library) is a lightweight C++ library that allows the handling of PDB data and provides a data structure suitable for geometric analysis and advanced constructions.


Platforms: *nix

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