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.
MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. This package provides an efficient suffix tree library, seed-and-extend alignment, SNP detection, repeat detection, and visualization tools.
AMOS is a collection of tools for genome assembly
AMOS is a collection of tools and class interfaces for the assembly of DNA reads. The package includes a robust infrastructure, modular assembly pipelines, and tools for overlapping, consensus generation, contigging, and assembly manipulation.
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.
The Yap Prolog System is a ISO-compatible high-performance Prolog compiler. Yap is widely considered one of the fastest available Prolog systems. Yap supports coroutining, CLP(QR), CHR, and depth-bound search. Tabling and parallelism are in development.
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.
DAGchainer identifies chains of gene pairs sharing conserved order between genomic regions, by identifying paths through a directed acyclic graph (DAG).
Oww (One-Wire Weather) is a server and client for Dallas Semiconductor / AAG 1-wire weather station kits.
TransposonPSI is an analysis tool to identify protein or nucleic acid sequence homology to proteins encoded by diverse families of transposable elements.
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.
Project Cogito is a artificial intelligence infrastructure to aid the development of thinking machines. It will provide the ability to create virtual worlds with loadable objects that brains can interact with. Administrative interfaces will be provided.
Ergatis is a web-based utility used to create, run, and monitor reusable computational analysis pipelines, utilizing the Workflow engine. It contains pre-built components for common bioinformatics analysis tasks.
SPM surfrend toolbox is a suite of scripts that add surface-based rendering capabilities to SPM99/2 generated statistical maps.
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.
** 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.
EVidenceModeler (aka EVM) combines ab initio gene predictions and spliced protein and transcript alignments into weighted consensus gene structure predictions.
Ramugen is a music application which assists in / automates composition along stochastic/indeterminate lines. Comes as a Win32 desktop application and a Borland Delphi component-package. Open Source : full source-code and documentation provided. Very fle
Voltage Drop Calculator for EE, supports multiple segments, 1 and 3 phase.
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 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
iROS is a meta-operating system for technology-rich "interactive rooms". The core components (Event Heap, DataHeap, iCrafter) provide communication, data storage, and service management for an iRoom.
sparse linear algebra library, with emphasis on preconditioned Krylov subspace methods for the solution of linear systems of equations
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".