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PhyloPattern is a Java/Prolog API, helpful to simulate human reading of phylogenetic trees. Bioinformatician can: annotate trees, apply complex patterns to a tree to search specific architectures or extract information, compare trees with dynamically gen
Biodiversity Information Group develops software tools and data standards that enable herbaria and museums to create dynamic distributed queries of their online databases. See http://bit.ly/bfirSh and http://bit.ly/bwpnSY for latest developments.
SLEDRIDE: Simplified Learning about Expression Data Running in a Desktop Environment. To provide a general workbench for pipe-lining microarray gene expression data from supervised learning results into unsupervised learning methods.
QSAR is a project that aims to build a GUI that enables people to build quantitative structure activity (or property) relationship models. It will use parts of CDK (cdk.sf.net), JOELib (joelib.sf.net), R (www.r-project.org) and other projects.
A software tool enabling the user to browse through an image stack created by a confocal microscope. Points can be plotted through the stack, producing a digital 3D representation, which can be viewed in 3D and compared with other plots.
AnnaF is an automatic gene annotation framework, that is used to do some automatic annotation for C. higginsianum. It was also tested on F. graminearum and should work well for fungi in general.
AnnaF was build upon the pipeline framework Anna.
Taverna is *no longer* hosted on SourceForge, but has moved to the Apache Software Foundation: https://taverna.apache.org
These pages and mailing list archives are provided for *archival purposes* for older Taverna 1.x releases.
See https://taverna.apache.org/download/ for the latest releases from Apache Taverna.
OmicBrowse, developed with Flash and Java, is a highly evaluated genome browser integrating omics knowledge ranging from genomes to phenomes and is especially appropriate for positional-cloning purposes.
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JAMBLAST: Java Application Manager for the ncbi BLAST results. It is a graphic application that allow the user to display, filter, sort, import/export, store/manage BLAST results produced with the NOBLAST (https://sourceforge.net/projects/noblast).
Quantitative Evalution of Blush: a program to assess myocardial reperfusion on coronary angiograms. This program calculates a value that can be used for risk classification of STEMI patients or as a surrogate endpoint in clinical trials.
A repository linking to eight Bioinformatics Resource Centers (BRCs) sponsored by the NIAID. The BRCs are providing web-based resources to scientific community conducting basic and applied research on organisms considered potential agents of bioterrorism
JRasterCreator allows you to easily & visually build a raster file for the mass spectrometry instrument Bruker Daltonics MS ultraflex II by clicking on various spots/locations.
The Antigen Variability ANAlyzer (AVANA) tool uses information entropy to measure variability in protein sequence alignments. It also compares alignments using mutual information, identifying the mutations that characterize specific sequence sets.
CILib is a framework for developing Computational Intelligence software in swarm intelligence, evolutionary computing, neural networks, artificial immune systems, fuzzy logic and robotics.
Ever got confused while remembering all the various physical properties of all the standard 20 amino acids? Then use Amino Acid Finder!!
It has a built-in database and contains information about all the physical properties and lets you to search them
This Project moved to https://sourceforge.net/projects/synbiowave/ because the name GeneWave is a registered trademark... Please do not use this project anymore.
ARTADE (ARabidopsis Tiling-Array-based Detection of Exons) is a standard tool for the automatic annotation of genome-wide tiling-array data in Arabidopsis. ARTADE is a program originally written by Dr. Tetsuro Toyoda, RIKEN, Japan.
jSim for Gromacs is a Graphical User Interface for the Molecular Dynamics Package Gromacs. It has a project style interface to organize your md simulations. It is also possible to start md simulations on remote computers with ssh.
JOELib/JOELib2 is a cheminformatics library which supports SMARTS substructure search, descriptor calculation, processing/filtering pipes, conversion of file formats, 100% pure Java, and interfaces to external programs (e.g. Ghemical) are available.