Biology Workbench

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

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.

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

A collection of plug-in algorithms for the WEKA machine learning workbench including artificial neural network (ANN) algorithms, and artificial immune system (AIS) algorithms.


Platforms: Windows, Mac, Linux

YARI is a comprehensive tool suite to debug (layouts), spy, spider, inspect and navigate SWT and Eclipse based application GUIs (Workbench or RCP) at runtime.


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

PriorsEditor is a general workbench for regulatory region analysis and transcription factor binding site discovery. The program emphasizes the use of positional priors to focus the search for binding sites towards portions of DNA sequences that are considered more likely to contain true...


Platforms: Mac

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

CUDASW++ software is a public open source software for Smith-Waterman protein database searches on Graphics Processing Units with CUDA. This software have been added to the NVIDIA Tesla Bio Workbench (http://www.nvidia.com/object/swplusplus_on_tesla.html


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

SBSI (Systems Biology Software Infrastructure) is a suite of tools for systems biology, such as parallelized numerical algorithms, and a Java, Eclipse RCP based client for visualizing results, running simulations, and integrating SBML based plugins.


Platforms: *nix

Vrapper is an eclipse plugin which acts as a wrapper for eclipse text editors to provide a Vim-like input scheme for moving around and editing text. Unlike other plugins which embed Vim in Eclipse, Vrapper imitates the behaviour of Vim while still using whatever editor you have opened in the...


Platforms: *nix

A small download that times the reactions of the user and displays the results onscreen. Can be used for biology or health physics. All uses have no cost attached. No limitations. Best reaction times can be submitted to the developer's website at http://www.reaction-timer.co.nr/


Platforms: Windows