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Open Engine Dynamics. Library for simulation of rigid bodies dynamics.

ODE is an open source, high performance library for simulating rigid body dynamics. It is fully featured, stable, mature and platform independent with an easy to use C/C++ API. It has advanced joint types and integrated collision detection with friction. ODE is useful for simulating vehicles, objects in virtual reality environments and virtual creatures. It is currently used in many computer games, 3D authoring tools and simulation tools. This library is free software.

GeoNetwork, spatial references resource based in standarts

GeoNetwork is a standards based, Free and Open Source catalog application to manage spatially referenced resources through the web. It provides powerful metadata editing and search functions as well as an embedded interactive web map viewer.

Technical Specification

GeoNetwork opensource implements both the Portal component and the Catalog database of a Spatial Data Infrastructure (SDI) defined in the OGC Reference Architecture. It provides tools for managing and publishing metadata on spatial data and related services. GeoNetwork opensource allows a distributed search providing access to a huge volume of metadata that come from different Clearinghouses and also provides a web-based interactive map viewer that allows people to composite maps picking layers from distributed servers on the internet

ORBITER flight simulator The big toy for engineers.

ORBITER is a free flight simulator that goes beyond the confines of Earth’s atmosphere. Launch the Space Shuttle from Kennedy Space Center to deploy a satellite, rendezvous with the International Space Station or take the futuristic Delta-glider for a tour through the solar system – the choice is yours.
But make no mistake – ORBITER is not a space shooter. The emphasis is firmly on realism, and the learning curve can be steep. Be prepared to invest some time and effort to brush up on your orbital mechanics background. Good starting points are JPL’s Basics of Space Flight, and R. Braeunig’s Rocket & Space Technology.

SBML, System Biological Markup Language

The Systems Biology Markup Language (SBML) is a machine-readable language, based on XML, for representing models of biological processes. SBML can represent metabolic networks, cell-signaling pathways, regulatory networks, and many other kinds of systems.

SBML has three main purposes:

enabling the use of multiple software tools without rewriting models for each tool;
enabling models to be shared and published in a form other researchers can use even in a different software environment;
ensuring the survival of models beyond the lifetime of the software used to create them.

SBML is not an attempt to define a universal language for quantitative models. SBML’s purpose is to serve as a lingua franca—an exchange format used by different present-day software tools to communicate the essential aspects of a computational model

Jmol, viewer for chemical structures in 3D

Jmol is a molecule viewer. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems. The JmolApplet is a web browser applet that can be integrated into web pages, the Jmol application is a standalone Java application that runs on the desktop and the JmolViewer is a development tool kit that can be integrated into other Java applications.

Features

Free, open-source software licensed under the GNU Lesser General Public License

Applet, Application, and Systems Integration Component

Multi-language

Cross-platform

Supports all major web browsers…

High-performance 3D rendering with no hardware requirements

File formats (see also file formats section within Jmol Wiki):

CIF/mmCIF – Crystallographic Information File and Macromolecular Crystallographic Information File, the standards from the International Union of Crystallography

CML – Chemical Markup Language

CSF – Fujitsu CAChe chemical structure, now Fujitsu Sygress

CTFile – Elsevier MDL chemical table

GAMESS – General Atomic and Molecular Electronic Structure System output, Gordon Research Group, Iowa State University

Gaussian 94/98/03 output – Gaussian, Inc.

Ghemical

HIN – HyperChem from Hypercube, Inc.

Jaguar – Schrodinger, LLC

MM1GP – Ghemical molecular mechanics

MOL – Elsevier MDL structure

MOLPRO – Molpro output

MOPAC – MOPAC 93/97/2002 output (public domain)
- MOPAC 2007 (v.7.101) graphf output (.mgf files) (public domain)

NWCHEM – NWChem output, Pacific Northwest National Laboratory

odydata – Odyssey data, WaveFunction, Inc.

PDB – Protein Data Bank, Research Collaboratory for Structural Bioinformatics

QOUT – Q-Chem, Inc.

SDF – Elsevier MDL structure

SHELX – Structural Chemistry Department, University of Göttingen (Germany)

SMOL – Spartan data, Wavefunction, Inc.

spinput – Spartan data, Wavefunction, Inc.

xodydata – Odyssey XML data, WaveFunction, Inc.

XYZ – Minnesota Supercomputer Institute XMol file

XYZ+vib – XYZ format files with added vibrational vector information

XYZ-FAH – Folding@home XYZ file

Animations

Vibrations

Basic support for unit cell and symmetry operations

Schematic shapes for secondary structures in biomolecules

Measurements

Support for RasMol/Chime scripting language

JavaScript support library

Exports to .jpg, .png, .ppm, .pdf, and PovRay

For more details, see the history of development.

Manual:

MathGL, library for scientific graphics

MathGL is:

a library for making high-quality scientific graphics under Linux and Windows;
a library for the fast data plotting and handling of large data arrays;
a library for working in window and console modes and for easy embedding into other programs;
a library with large and growing set of graphics.

Stelarium, a Planetarium through your computer

Stellarium is a free open source planetarium for your computer. It shows a realistic sky in 3D, just like what you see with the naked eye, binoculars or a telescope.It is being used in planetarium projectors. Just set your coordinates and go.

Main features:

sky

default catalogue of over 600,000 stars
extra catalogues with more than 210 million stars
asterisms and illustrations of the constellations
constellations for twelve different cultures
images of nebulae (full Messier catalogue)
realistic Milky Way
very realistic atmosphere, sunrise and sunset
the planets and their satellites

interface

a powerful zoom
time control
multilingual interface
fisheye projection for planetarium domes
spheric mirror projection for your own low-cost dome
all new graphical interface and extensive keyboard control
telescope control

visualisation

equatorial and azimuthal grids
star twinkling
shooting stars
eclipse simulation
skinnable landscapes, now with spheric panorama projection

Avogadro, advanced molecular designer

Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible rendering and a powerful plugin architecture.

* Cross-Platform: Molecular builder/editor for Windows, Linux, and Mac OS X.
* Free (of Freedom): Easy to install and all source code is available under the GNU GPL.
* International: Translations into Chinese, French, German, Italian, Russian, and Spanish, with more languages to come.
* Intuitive: Built to work easily for students and advanced researchers both.
* Fast: Supports multi-threaded rendering and computation.
* Extensible: Plugin architecture for developers, including rendering, interactive tools, commands, and Python scripts.
* Flexible: Features include Open Babel import of chemical files, input generation for multiple computational chemistry packages, crystallography, and biomolecules.
* Find out more or contact us

“R” for Statistical Computing

R is a programming language and software environment for statistical computing and graphics. The R language has become a de facto standard among statisticians for the development of statistical software,^[4]^[5] and is widely used for statistical software development and data analysis.^[5]

R provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, …) and graphical techniques, and is highly extensible. The S language is often the vehicle of choice for research in statistical methodology, and R provides an Open Source route to participation in that activity.

Software introduction in PDF (here). Example Sesion in page 78.

GNU Octave, “matlab” GNU version.

GNU Octave is a high-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments using a language that is mostly compatible with Matlab. It may also be used as a batch-oriented language.

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Open Engine Dynamics. Library for simulation of rigid bodies dynamics.

GeoNetwork, spatial references resource based in standarts

Technical Specification

ORBITER flight simulator The big toy for engineers.

SBML, System Biological Markup Language

Jmol, viewer for chemical structures in 3D

Features

MathGL, library for scientific graphics

MathGL is:

Stelarium, a Planetarium through your computer

Main features:

sky

interface

visualisation

Avogadro, advanced molecular designer

“R” for Statistical Computing

GNU Octave, “matlab” GNU version.

Distros GNU/Linux

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