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THIS IS NO LONGER THE HOME FOR SEURAT. PLEASE GO TO https://sites.google.com/site/seuratsomatic/ --- Seurat is an sequence analysis program for somatic mutation and allelic imbalance discovery in paired tumor and normal genome and transcriptome data.

Based on the not-so-successful Pysimony (https://sourceforge.net/projects/pysimony/), the same determined student takes another go at the phylogenetic problem. Javamony is invoked as follows: java -jar Javamony.jar [input.fasta] [random / stepwise (starting tree)] [# of bootstraps] [outgroup taxon #1] [outgroup taxon #2] ... Not meant as a competitive phylogenetic inference program, Javamony is an opportunity for me to acquire the Java language while learning to address and solve fundamental problems in phylogenetics. ...

Modern MATLAB-based modelling software for 13C metabolic flux analysis (MFA). Support available in Google group (https://groups.google.com/d/forum/13cmfa-openflux).

The source code for SAMSN can be found in github at https://github.com/miquelrojascherto/samsn

...Phenex saves ontology annotations alongside traditional character matrix data using the NeXML format standard for evolutionary data. Current Phenex development is taking place at GitHub: https://github.com/phenoscape/Phenex

...It is a Java/JSF/Hibernate/Spring web application that is actively being developed and used at Harvard Medical School. Note: The Screensaver project has moved to GitHub at https://github.com/hmsiccbl/screensaver.

This is a Java-based project for complex event extraction from text and co-reference resolution. Currently the code can read BioNLP shared task format (http://2011.bionlp-st.org/) and i2b2 Natural Language Processing for Clinical Data shared task format (https://www.i2b2.org/NLP/DataSets/Main.php). Event extraction includes finding events and the parameters for an event in a text. The method is based on SVM but other ML algorithms can be adopted. The method details are explained in the following paper: Ehsan Emadzadeh, Azadeh Nikfarjam, and Graciela Gonzalez. 2011. Double Layered Learning for Biological Event Extraction from Text. ...

iso2l (ˈaisəutuːl, spoken isotool) is a software to calculate the isotopic distribution of a chemical formula or a amino acid chain. The development has been MOVED TO https://github.com/binfalse/iso2l

...Maldonado E, Dutheil JY, da Fonseca RR, Vasconcelos V, Antunes A (2011) IMPACT: Integrated Multiprogram Platform for Analyses in ConTest. Journal of Heredity, 102 (3): 366-369. doi: https://doi.org/10.1093/jhered/esr003

Adjusting PKL-Files derived from MS-experiments. The development of the project has been MOVED TO https://github.com/binfalse/adjustpkl

Repository for the UCLA Laboratory of Neuro Imaging (LONI) Pipeline Globus Plugin Development

CyReposition is an open source Cytoscape Plugin for the reuse of existing Cytoscape network layouts in new Cytoscape projects. This project migrated to github https://github.com/matthiaskoenig/cy2reposition

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.

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).

This Project moved to https://sourceforge.net/projects/synbiowave/ because the name GeneWave is a registered trademark... Please do not use this project anymore.

The JChemPaint Applet and Swing Application are Java programs for drawing 2D chemical structures like those found in most chemistry textbooks. It is based on the Chemistry Development Kit (cdk.sf.net). Downloads, tracker, and source code repository can be found on https://jchempaint.github.io

Chemical Entities of Biological Interest (ChEBI) is a freely available database of chemical compounds and other small molecular entities. WE HAVE MIGRATED TO GITHUB. To create new issues/comments, please use the following link: https://github.com/ebi-chebi/ChEBI/issues