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JUNG provides a common and extendible language for the modeling, analysis, and visualization of data that can be represented as a graph or network.
New version now available on GitHub: https://github.com/jrtom/jung/releases/tag/jung-2.1
HOT is a package of Matlab and Octave compatible functions that manage thermodynamic data for a wide range of species. Functions calculate almost all the most common thermodynamic quantities of mixtures.
Python users may also want to look at PYroMat at https://chmarti1.github.io/PYroMat/index.html
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.
RADAR stands for Rapid Automatic Detection and Alignment of Repeats in protein sequences. RADAR identifies gapped approximate repeats and complex repeat architectures involving many different types of repeats.
Radar has moved to github (https://github.com/AndreasHeger/radar)
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>>> MIA has been moved to GitHub! <<<
Please use the new Location:
https://github.com/udo-stenzel/mapping-iterative-assembler
=========================================================
This project is no longer hosted on sourceforge, please go to https://github.com/jodersky/sims instead.
A library for rigid body simulation written in Scala. This project was created under the terms of a one-year project at school (Gymnase de Burier). Another program for testing and visualizing SiMS, Graphyx, is included.
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).
* Note: The Google Maps V2 API used by this module has been deprecated. *
For V3, consider pygeocoder: https://pypi.python.org/pypi/pygeocoder
Easy-to-use Python wrapper for the Google Maps V2 and Local Search APIs. Provides geocoding, reverse geocoding, directions, and local search.
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This Project moved to https://sourceforge.net/projects/synbiowave/ because the name GeneWave is a registered trademark... Please do not use this project anymore.
A project to help students calculate symbolic derivatives and integrals. Plus, a Java expression tree library for developers who may need to do such things in their programs.
The project has moved to github: https://github.com/generalpenguin89/calchelper
A novel stochastic simulation environment for biochemical modeling
UPDATE(2017-07-24) This repository has moved to BitBucket: https://bitbucket.org/parkinsonlab/cell-2017
Cell++ is a novel stochastic simulation environment which is capable of modeling diverse biochemical phenomena including signal transduction pathways, metabolic pathways and intracellular calcium signaling.
See https://github.com/arcanericky/thermorbios953w
Project at https://github.com/arcanericky/thermorbios953w Developers are encouraged to fork and request pulls as my personal weather station has seen better days.
Thermor / BIOS BW953 and BW976 Weather Station daemon for Linux.
CC2430 Flash programmer and simple debug interface with NoICE support. It uses USB interface to communicate with the target CC2430 over debug interface. To install on linux do: svn co https://ccflasher.svn.sourceforge.net/svnroot/ccflasher/trunk ccfl
Netlist database and manipulation API with interfaces to Java and Ruby. Verilog netlist inputs are supported.
Project branch continues to evolve: https://github.com/gburdell/nldb
including addition of tclsh UI.
NOTE: labrad development has moved to github. You can find up-to-date versions of labrad servers at https://github.com/martinisgroup/servers
This project contains a number of LabRAD Modules that provide out-of-the-box basic functions like hardware interfacing (GPIB, HID, RS232, IEEE802.3, ...), instrument control (Wiimote ;)), data storage, on-the-fly data plotting and analysis, etc.
EXPR is a software package for the recording and analysis of animal behaviour. Recording is done by pressing particular keyboard keys on the computer. The software then saves the sequence and timing of behaviours. Note that the DOS (1995: https://sourceforge.net/projects/expr/files/expr/fb-port-expr-00-1995/EXPR-binary-DOS-0.0.1995.tar.gz/download) version is currently the only fully functional and is recommended for use. On modern computers, DOS software can run in DOSBOX (https://www.dosbox.com/).
TaxonX is an XML schema for encoding taxonomic treatments to: create open, persistent full digital surrogates of treatments; identify treatments and their major structures; identify textual data such as names, localities, characters, and citations
Maintenance of TaxonX has moved to: https://github.com/tcatapano/TaxonX
GtkPlot is a graphical front-end for Gnuplot, based on gtk+. Features: 2D/3D plotting (parametric as well), labelling, axes management, and much more... Please consider shifting to the pyGtkPlot project: https://launchpad.net/pygtkplot
Main source code is moved at https://github.com/jpahullo/planetsim. We recommend authors of contributions sections to move your code to github. Since then, contributions remain here for your use at will.
PlanetSim is an object oriented simulation framework for overlay networks and services. This framework presents a layered and modular architecture with well defined hotspots documented using classical design patterns.
MOVED TO GITHUB!! https://github.com/cmwslw/nxt-plus-plus
NXT++ is an interface written in C++ that allows the control LEGO MINDSTORMS NXT robots directly through a USB or Bluetooth connection. The interface is intended to be simple and easy to use. The interface can be used in any C++ program.
ScapeToad is an easy to use application for the cartogram creation. Cartograms are deformed maps where the polygon size is proportional to a given statistical value. ScapeToad reads and writes Shapefiles.
See <https://github.com/christiankaiser/ScapeToad> for the latest version of the code.