An intuitive molecular editor and visualization tool
Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science and related areas. It offers a flexible rendering framework and a powerful plugin architecture.
Bowtie, an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers. Please cite: Langmead B, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25.
The PDL module gives standard perl the ability to COMPACTLY store and SPEEDILY manipulate the large N-dimensional data sets that are the bread and butter of scientific computing.
GMOD is a set of interoperable open source software components for visualizing, annotating, and managing biological data. See http://gmod.org for more.
The home of the Gene Ontology project on SourceForge, including ontology requests, software downloads, bug trackers, and much, much more.
Webtunnel is an HTTP tunnel with some unique features: it runs in the context of a web server; it uses simple requests/responses for proxy traversal; and it is multi-threaded to allow many parallel connections to many destinations simultaneously.
Oww (One-Wire Weather) is a server and client for Dallas Semiconductor / AAG 1-wire weather station kits.
A Python interface to the Wordnet database of word meanings and lexical relationships. allows the user to type expressions such as N['dog'], hyponyms(N['dog']), and closure(ADJ['red'], SYNONYM) to query the database for lexical relationships.
slclust: a utility that performs single-linkage clustering with the option of applying a Jaccard similarity coefficient to break weakly bound clusters into distinct clusters. The slclust utility is written in ANSI C++.
PerlMol is a collection of Perl modules for chemoinformatics and computational chemistry with the philosophy that "simple things should be simple". It should be possible to write one-liners that use this toolkit to do meaningful "molecular munging".
A software solution for clustering large EST/mRNAs datasets.
Statistics modules in Perl Data Language, with a quick-start guide for non-PDL people. They make the PDL shell work like R, but with PDL threading (fast automatic iteration) of procedures including t-test, linear regression, and k-means clustering.
Spotfinder is an image processing software tool for microarray image analisys. It is written on C++ with QT GUI toolkit and runs on Windows, X11, and Mac OSX.
This project provides a framework for the research and development of software tools for the analysis of highway capacity (asphalt and concrete, not electronic!) Our first focus will be on perl module implementations of the procedures in the Highway Capa
GLEAN is an unsupervised learning system to integrate disparate sources of gene structure evidence (gene model predictions, EST/protein genomic sequence alignments, SAGE/peptide tags, etc) to produce a consensus gene prediction, without prior training.
** Deprecated ** Important! All of the software on this web site has been deprecated, and has not been maintained since 2014. All of this software is now being maintained on Github - and can be obtained from https://github.com/jpaulm . Changes and enhancements are still ongoing, and while older software should still work, newer features described in the literature will not be available in SourceForge. The old license was the Artistic license - the software is now in process of being converted to LGPL. This will gradually take place (on Github) over the next few months (in 2016). JavaFBP is now also on Maven.
CloudBurst is a parallel read-mapping algorithm optimized for mapping next-generation sequence data to the human genome and other reference genomes, for use in a variety of biological analyses including SNP discovery, genotyping, and personal genomics.
This module provides functions for calculating the path to a map tile at OpenStreetMap out of geographic coordinates.
The Introspector enables the programming tools that deal with source code such as the compiler to communicate in a standard and neutral manner reducing the accidental cost of programming. http://github.com/h4ck3rm1k3/
Association de l'asie pacifique et de l'asie mineur : Mention projet \apac (SF.NET) Chancellerie fédérale Palais fédéral ouest 3003 Berne
The project will provide a Cocoa framework to interface OpenGL in a more OO-fashioned style. It is not meant to be the fastest code possible, nor to leverage all the power of OpenGL, but to give developers a easy way to start working in 3D
The Disease Ontology has moved to Github. New project page: https://github.com/DiseaseOntology Disease Ontology is a stuctured controlled vocabulary originally based upon and mapped to medical billing codes. The goal of this ontology is to create a comprehensive hierachical controlled vocabulary to represent subsumptive disease relationships.
The intentions of this project are as follows: 1; Determine the potential interest level in developing a basic interface for creating models in GAMS (General Algebraic Modeling System). 2; To create a sounding board for what should be added to the exist
Open Wound is a free CGI cut-up engine based on the experimental writing and art of Tzara, Burroughs, and Gysin. They meant to rupture the perception of reality by disjointing found text using cut-up newspapers. Open Wound bleeds 1000x faster.
A cross-platform interface for the *.mfj file format.
mobcalPARSER is a command line based PERL frontend/interface for MOBCAL with limited wrapper functionality. "MOBCAL - A Program to Calculate Mobilities" is available from Professor Martin F. Jarrold's webpage http://www.indiana.edu/~nano/software.html.