1. Natural Sciences
|
1.1. Chemistry
1.1.1. General
ASAD - a package for integrating chemical schemes in atmospheric models
BKChem - Chemical drawing program
Bioclipse - Bioclipse is a rich-client platform chemistry and biology workbench. It provides access to many open source bioinformatics and chemoinformatics toolkits and has plugins for the Chemistry Development Kit, JChemPaint, Jmol, and BioJava
CHEMCALC - a calculator that is more oriented towards chemistry
Chemtool - chemical structure editor
CDA - analyze chemical systems which can be described as donor-acceptor complexes
CHEMEQ - translate chemical equations to LaTeX code
CHEMSUITE - molecular 2/3D drawing and chemical reaction simulation software
CHIMP - a generic tool for the modeling of chemical phenomena
CACTVS Tools - a visualization package for chemist
E-CELL Simulation Environment - Software for cellular and biochemical modeling and simulation
EMAN - 3D particle reconstruction package
Easychem - Draw high-quality molecules and 2D chemical formulas
Fityk - Non-linear curve fitting and data analysis
GAMGI - A program to build, view, and analyse atomic structures
Gabedit - is a graphical user interface (GUI) to computational chemistry packages
Gchempaint - 2D chemical structures editor for the GNOME2 desktop
GDC - A utility to calculate compressible flow (Gas Dynamics Calculator)
GDIS - Software to display and manipulate isolated molecules and periodic systems
GenChemLab - Simulates general chemistry laboratory exercises
gElemental - A periodic table viewer
genoAMOVA - is a small program that does the one level Analysis of MOlecular VAriance calculations
Ghemical - Molecular modelling application
GPeriodic - Periodic table application
GROMACS - Simulates molecular dynamics
Gnome Chemistry Utils - The Gnome Chemistry Utils include three utilities: a chemical calculator (computes raw formule, molar weight, mass composition and isotopic pattern), a molecule 3d viewer using OpenGL to display molecular models, a crystal structues viewer and editor and a periodic table of the elements
gdpc - Visualizes molecular simulation
Jmol - Chemical structure editor
Kalzium - chemistry teaching tool for KDE. (KDE stands for K Desktop Environment - which is a powerful Open Source graphical desktop environment for Unix workstations)
Kci - Simulates chemical reactions
Lamprop - Calculates properties of fiber-reinforced composite laminates
MayaChemTools - is a growing collection of Perl scripts to support day-to-day computational discovery needs
Melting - Nearest-neighbor compilation of nucleic acid hybridation
OpenBabel - Translates chemical file formats and data
polyxmass - Mass spectrometric framework for simulation and analysis of mass spectrometric data of (bio-)polymers
PyMOL - An OpenGL Molecular Graphics System written in Python
RasMol - Visualize biological macromolecules
VESTA - is a 3D visualization program for structural models and volumetric data such as electron/nuclear densities
Viewmol - A graphical front end for computational chemistry programs
XDrawChem - Program to draw chemical structures
Xem - Program to calculate Ph balance
Xmakemol - Program for visualizing atomic and molecular systems
1.1.2. Organic Chemistry
Bist - Bist (Bidimensional Structures) is a chemical drawing program focussed on organic chemistry
OSET - OSET (Organic Synthesis Exploration Tool) is a computer-assisted organic synthesis (CAOS) program for the retrosynthetic analysis of target molecules. Intended for educational use, as a tool for learning chemical synthetic design at undergraduate organic chemistry courses
BOSS - biochemical and organic simulation system
1.1.3. Environmental Chemistry
ALOGPS - provides prediction of logP and aqueous solubility of compounds to be used in drug design (ADMET and HTS) and environmental chemistry studies. The ALOGPS program can be also used to predict logD values
1.2. Earth Sciences
1.2.1. Meteorology
Geo::Weather - Retrieves weather.com information
PHP Weather - Shows current weather on a Web page
phpWX - Displays current weather conditions
Snow Path Formation Simulator - Graphically displays the formation of paths in the snow formed by people
StormSiren - Severe weather monitoring tool
WeatherGraph - Generates graphs of weather conditions
WeatherPlotter - Gathers, tracks, and analyzes historical weather data
WeatherSpect - Simulates the current weather in ASCII art
Wmweather+ - Weather application for windowmaker
wxweather - Reference implementation of the Open Weather Project system
1.2.2. Geology
GeoTIFF Viewer - A viewer for GeoTIFF files
iGMT - Visual tool for GMT script mapping
mezoGIS - is a GIS application, a graphical interface to query and analyse spatial data
PrimaGIS - A collaborative Web mapping application for Zope and Plone
Seismic Toolkit - is a tool for processing and displaying seismic signal data in a graphical interface
UDIG - UDIG stands for (User-friendly Desktop Internet GIS) is a spatial data viewer and editor with emphasis on the OpenGIS standards for Internet GIS, the Web Map Server and Web Feature Server standards
wxweather - wxweather' is a reference implementation of the Open Weather System, an open weather monitoring and prediction network
1.2.3. Geography
Appomattox - Create maps and analyze spatial data
DGPS - Lets you get GPS corrections over IP
Earth3D - Visualizes the earth in realtime in a 3D view
GDAL - API for accessing raster geospatial data
GEOS - C++ implementation of the OpenGIS "Simple Features for SQL" specification
Geocanvas - A developer API library to assist in creating geographically referenced canvas applications
GeoRecorder - Record audio files and add geo-tag them automatically
GeoToad - Speeds up choosing a cache and collecting data
gama - Geodetic network adjustment program
GMAP - Gnome Map Application Program, a Gtk# / mono program that lets you view maps without the internet
GMT - Geographic mapping tools that produce EPS illustrations
GPS applet - displays latitude and longitude on panel. Supports NMEA serial GPS receivers
GPSBabel - Converts waypoint data between various formats
Gpsdrive - Map-based navigation system
GPSMan - Graphical manager for GPS data
GPStk - Set of GPS processing algorithms
GRASS - Geographic information system. GRASS stands for Geographic Resources Analysis Support System
Harmonics - Harmonics files for Xtide
Height Map Generator - Terrain map generator
MapServer - Web-enabled mapping application development tool
PostGIS - Adds support for geographic objects to PostgreSQL
Pytrainer - is a tool to log all your sport excursion (e.g journey, ride). It is originally programmer for cyclist geeks :D, but it can be used by another type of sport people.. like runner, swimers, mountain bikers, etc.
QGIS - Geographic Information System
RoadMap - GIS program that displays street maps / A Car Navigation System for Linux and UNIX
Thuban - Interactive GIS viewer
tkgeomap - Tcl/tk commands for manipulating geographic data
Viking - A GPS data viewer/editor and map viewer
XTide - Tide clock and tide predictor
Xrmap - Displays portions of the earth
XYZ2LLA - is a little C program to convert earth-centred earth-fixed (ECEF) cartesien coordinates to latitude, longitude and altitude (LLA in degree)
WW2D - allows you to explore Earth using satellite imagery, topographic maps and image from other data sources
1.2.4. Geostatistics
gstat - Geostatistical modelling, simulation, and prediction
1.3. BioScience / Life Sciences
1.3.1. Biology
Bioinformatics Template Library - Library for life sciences programming
Blossoc - A block-association mapping tool
CTSim - Computed tomography simulator
CoaSim - Coalescence process simulator
CoaSim-gui - GUI for the CoaSim coalescence process simulator
cvEyeTracker - Tools for eye tracking
E-CELL Simulation Environment - Software for cellular and biochemical modelling and simulation
E-Cell System 3 - E-Cell System is an object-oriented software suite for modelling, simulation, and analysis of large scale complex systems such as biological cells
fastDNAml - Phylogenetic analysis software
Folding@Gnome - The Folding@Gnome applet is a GUI that keeps track of the background protein folding progress done by Folding@Home
GENtle - Bioinformatics software for everyday molecular biology tasks
HASAS - Hydro-Acoustic Signal Analysis System
PerlPrimer - Designs primers for standard, bisulphite, and real-time PCR, and sequencing
Phylographer - Visualizes evolutionary relationships
QDist - Computes the quartet distance between unrooted evolutionary trees
RIGEL - Representation-Independant Genetic Engine Library
SigmaPi Neurosimulator - A simulator for recurrent neural networks
Split-Dist - Calculates the number of splits (edges) that differs for two trees
Xmedcon - Medical image conversion utility and library
1.3.2. Biology Genetics
E-CELL Simulation Environment - Software for cellular and biochemical modelling and simulation
GAUL - Library for programming applications using genetic algorithms
GENtle - Bioinformatics software for everyday molecular biology tasks
OpenBeagle - Evolutionary computation framework
1.4. Physics
Atlc - Package for designing and analyzing electrical transmission lines and directional couplers
aITALC - Performs automated perturbative loop calculations of cross sections in high energy physics
Cernlib - A suite of data analysis tools and libraries created for use in physics experiments, but also with applications to other fields such as the chemical and biological sciences
CLHelp - HEP-specific foundation and utility classes
Dimnum - C++ library for storage and conversion of dimensionful values
EPICS - Distributed Process Control Tool Kit Components
Elmer - Elmer is a computational tool for multi-physics problems
Geant321 - A toolkit for the simulation of the passage of particles through matter
libgpiv - Library for Particle Image Velocimetry (PIV)
libquantum - Simulation of a quantum computer
nMod nBody Modelling Toolkit - Particle-particle nbody model
GAMGI - A program to build, view, and analyze atomic structures
GDIS - Software to display and manipulate isolated molecules and periodic systems
GPSimulator (GPS) - Simulates particle behavior
gpiv - GUI for analyzing images obtained by the Particle Image Velocimetry technique (PIV)
gpivtools - Set of tools for the Particle Image Velocimetry technique
Gnome Flow - Calculates and visualizes steady-state fluid flows
Light Speed - Simulates a geometric lattice
MIT Photonic Bands - Computes photonic band structures
McStas - Neutron ray-trace simulation application
Meep - finite-difference time-domain (FDTD) electromagnetic simulations
octopus - Electronic structure based on time-dependent density functional theory
OOF - Calculate macroscopic properties from images of microstructures
OOFEM - Object oriented finite element code
OpenLB - A library for lattice Boltzmann numerics
SpecTcl - Helps analyze nuclear physics event data
SALOME - is a free software that provides a generic platform for Pre and Post-Processing for numerical simulation
Vp7wkp - Simulates radioactive decay
1.4.1. Biophysics
Coot - Superb tool for crystallographers
Pymol - An open source visualization program. Reads many formats, including crystallographic map files
VMD - Another visualization program, this one better suited for reading trajectories from simulations, or generating custom graphics
1.5. Space Sciences
1.5.1. Astronomy
Astro::Catalog - Object-oriented astronomical catalogue
Astroconst - Makes header files that define astrophysical constants
avsomat - Autoschedules and manages astronomical observation data
Celestia - Visual simulation of space
cora - Line fitting tool designed for emission line spectra with low count numbers
EPICS - Distributed Process Control Tool Kit Components
Ephemeris - Reads, writes and interpolates planetary positions using JPL's ephemeris files
EXTREMA - is an interactive program with publication quality graphics and mathematical analysis capabilities
Einstein@GNOME - A GNOME panel applet for the Einstein@Home neutron star search
gcx - Complete set of data-reduction functions for CCD photometry
GNOME Lunar Clock Applet - GNOME Lunar Clock displays the current phase of the Moon as an applet for the gnome panel
gnuskies - Project to create a free version of the xephem program
Gpredict - is a real-time satellite tracking and orbit prediction program
HASAS - HASAS (Hydro-Acoustic Signal Analysis System) is a modular system for passive sonar signal analysis
Hitchhiker 2000 - Astronomy simulation program
Kstars - Desktop planetarium for KDE
LibRadtran - Calculates solar and thermal radiation
libnova - Celestial mechanics and astronomical calculation library
Msetimon - Multi-SETI@home Monitor
nMod nBody Modelling Toolkit - Particle-particle nbody model
Nightfall - Simulate eclipsing binary stars
Planet Finder - Shows the location of planetary bodies
Qastrocam - Video capture program
SImg - Astronomical image processing software
SkyNET - is a mono program which draws a skychart
StarPlot - is a 3-dimensional perspective star map viewer
Stellarium - Renders realistic skies in real time with openGL
Sunclock - Clock for the X Window System
Sunwait - Calculates sunrise, sunset, and civil, nautical, twilight, astronomical twilight
Spacechart - Displays the stars in space in 3D
Xplanet - Draws the earth or other planets
XYZ2LLA - is a little C program to convert earth-centred earth-fixed (ECEF) cartesien coordinates to latitude, longitude and altitude (LLA in degree)