Sdsc Biology Workbench

DBEdit is a plugin for the Eclipse Workbench. It can be used to explore databases, edit tables directly with a spreadsheet like editor, edit SQL und more.

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

The HSQLDB Plug-in embebs a HSQLDB pure-java database server into the Eclipse workbench for use as a data repository for Java applications developed using the IDE or for extending HSQLDB itself


Platforms: Windows, Mac, Linux

hypKNOWsys aims at developing a Java-based workbench for knowledge discovery and knowledge management. Currently, hypKNOWsys has released two intermediate tools: DIAsDEM Workbench (text mining for semantic tagging) and WUMprep (Web mining pre-processing)


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

A Java workbench and toolkit for developing, evaluating, and playing with classical and state-of-the-art optimization algorithms on standard benchmark problem domains; including reference algorithm implementations, graphing, visualizations and much more.


Platforms: Windows, Mac, Linux

This Java software implements Profile Hidden Markov Models (PHMMs) for protein classification for the WEKA workbench. Standard PHMMs and newly introduced binary PHMMs are used. In addition the software allows propositionalisation of PHMMs.


Platforms: Windows, Mac, 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

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

GeneticsLab is an excellent utility for those ones who are learning Biology, Genetics or any related studies. GeneticsLab automates some operations based on the genetic code, so you won't need to do them manually anymore! These are some of the operations


Platforms: Mac

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