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Some links I find from time to time about interesting programs

To be sorted : http://wiki.eagle-usb.org/wakka.php?wiki=LogicielsScientifiques existing packages are described (I miss the snapshots)
once a program is chosen see CompilePrograms to add compilation / tests / screenshots... see PresentationScientificPackaging to see how to contribute and get numerous other scientific programs included in public distributions.

===science-related GNU/Linux distributions===
http://www.caelinux.com/CMS/index.php?option=com_simpleboard&Itemid=43&func=view&id=232&catid=2 [en] many suggestions of programs, being sorted
http://www.caelinux.com/CMS/index.php?option=com_simpleboard&Itemid=43&func=view&id=218&catid=2 [en] some have been included
see CAELinuxSuggestions

https://www.scientificlinux.org/ distribution for scientific use, based on RHEL4
https://www.scientificlinux.org/distributions/4x/40/sl.release.note.40.i386 not much added :/ (openafs, mp3, ...) at least it permit to have a standard base

http://www.paipix.org/tikiwiki/tiki-read_article.php?articleId=47 AIPIX scientific live-DVD (based on Debian)
http://itmanagement.earthweb.com/entdev/article.php/3701421 The 7 Most Influential GNU/Linux Distribution Guide

===presentation of products===
http://archimedes.iv.org.br/portal/project/archimedes-project/ - [[http://archimedes.iv.org.br/portal/screenshots-2 screenshots]] computer-aided design software focused on architecture
http://ceu.fi.udc.es/SAL/index.shtml SAL (Scientific Applications on Linux) is a collection of information and links to software that will be of interest to scientists and engineers. The broad coverage of Linux applications will also benefit the whole Linux/Unix community. There are currently 2,965 entries in SAL
http://ceu.fi.udc.es/SAL/B/index.shtml [en] list of Numerical Analysis programs
http://ceu.fi.udc.es/SAL/Z/2/index.shtml [en] list of chemical/biological software
http://sal.jyu.fi/index.shtml [en] a mirror just in case other sites are down for SAL
http://franck.fresnel.free.fr/ATNT/Presentation.php (GPL) Acquisition et traitement numérique (java)
http://adullact.net/projects/atn/
http://www.libres-apps.org/index.php?tags=scientifique [fr] annuaire logiciels scientifiques

http://sourceforge.net/projects/octaviz/ (GPL) [ [[http://octaviz.sourceforge.net/index.php?page=screen screenshots]] ] ""Octaviz is a visualization system for Octave. It is a wrapper that makes all VTK classes accessible from within Octave using the same object-oriented syntax as in C++ or Python. Octaviz also provides high-level functions for 2D and 3D visualization. Using those functions, most common visualization tasks (3D surface plots, contour plots, meshes etc) can be accomplished without any knowledge about VTK.""

http://ab-initio.mit.edu/wiki/index.php/Meep (GPL) free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems, along with our MPB eigenmode package

http://people.web.psi.ch/geus/pyfemax/index.html [ [[http://people.web.psi.ch/geus/pyfemax/screenshots.html screenshots]] ] PySparse extends the Python interpreter by a set of sparse matrix types holding double precision values. PyFemax is a set of Python modules which allow to compute eigensolutions of the time-harmonic Maxwell equations
~-http://sourceforge.net/projects/pysparse/ (BSD) A Sparse Matrix Library for Python

http://freshmeat.net/projects/radarfdtd/ (GPL) a program to simulate electromagnetic waves propagating through various materials (the author used it mainly for Ground Penetrating Radar (GPR) applications, but it is not limited to this). Using generalized perfectly matched layers (GPML) as an absorbing boundary condition

http://alioth.debian.org/projects/tessa/ (GPL) Tessa is a three-dimensional simulation software for optical systems, based on the FDTD method. It is believed to be terribly efficient. Tessa was developed in the LEOM laboratory, École centrale de Lyon: http://leom.ec-lyon.fr/

http://savannah.fzk.de/ a german forge with scientific software (using grid)

http://www.gnu.org/software/gsl/ to be checked : programs based on gnu scientific library (maybe not all are packaged ?)

http://wiki.debian.org/DebianScience programs in debian (or not)

http://zaimi.free.fr/informatique/ [fr] list of many programs
http://82.231.148.189/dokuwiki/doku.php?id=doc:veille:ingenierie [fr]
http://www-math.univ-fcomte.fr/pp_Annu/DCALUGARU/liens.php [fr]

http://ubunpingoo.tuxfamily.org/doku.php?id=installation_rapide_de_logiciels_utilisables_en_milieu_educatif [fr] many programs for science

http://www.aiaa-houston.org/newsletter/jan06/jan06.pdf [en] review of astronautics with octave, maxima, flight gear, ""IT++"", ode, openscenegraph

http://www.archilinux.org/archi-cao/archi-cao.html [fr] some programs either free or non-free for CAD, import autocad files in blender

http://www.tech-edv.co.at/lunix/CADlinks.html [en] table identifying CAD software for Linux with license type / source code provided / binary packages
http://www.tech-edv.co.at/lunix/UTILlinks.html [en] CAD/3d Utilities Links
http://www.tech-edv.co.at/lunix/MODlinks.html [en] Linux Modelers Links

http://www.evl.uic.edu/cavern/sage/applications.php Scalable Adaptive Graphics Environment (to be checked)

http://www.librecours.org/cgi-bin/main?callback=presentation [fr]

https://lipforge.ens-lyon.fr/softwaremap/trove_list.php

http://gforge.inria.fr/softwaremap/trove_list.php
http://www.inria.fr/valorisation/logiciels/calcul.fr.html

http://norma.mas.ecp.fr/wikimas/ScientificComputingSoftware [en] lots of sofware, some with a F/OSS license

http://www.loria.fr/software/tous?license=free&theme=all&search_string= [fr] list of sofware with free license

http://www.csc.fi/suomi/hakemisto/sovelluslista/ohjelmistot.html.en [en] Application software and databases at CSC (check what is free)
http://sw-tools.pdb.org/apps/MAXIT/index.html maxit Program Suite was developed by the PDB (Protein Data Bank) and NDB (Nucleic Acid Database) to assist in the processing and curation of macromolecular structure data

http://gersoo.free.fr/calsci/calsci1.html [fr] long list of products (either free software or sometimes not)

http://techer.pascal.free.fr/postgis/ [fr] geographic information systems (postgres with spatial options)

http://freshmeat.net/projects/aisee/ Free for non-commercial use graph browser which supports 15 layout algorithms, recursive graph nesting and easy printing
http://freshmeat.net/projects/siptoolbox/ scigraphica
http://luke.no-ip.org/code/ [en] many programs, some about fractals or open GL...
http://luke.no-ip.org/code/kueye/

http://g3d-cpp.sourceforge.net/ commercial-grade 3D Engine available as Open Source (BSD License). It is used in games, tech demos, research papers, military simulators, and university courses. It can support real-time rendering, off-line rendering, back-end game server management of 3D worlds, and use of graphics hardware for general purpose computing.
http://freshmeat.net/browse/97/
http://freshmeat.net/projects/ghemical/ A molecular modelling package with GUI and 3D-visualization tools.
http://freshmeat.net/projects/gmsh/ A 3D finite element mesh generator with built-in CAD engine and post-processor.
http://freshmeat.net/projects/visit/ Software for scientific visualization and analysis.

http://www.mathtools.net/ [en] many programs, most of them proprietary after a quick glance :-(

http://sourceforge.net/projects/elisa an open ""C++"" library for constraint programming and constraint solving techniques (requires gaol)
http://sourceforge.net/projects/gaol ""C++"" library for interval arithmetic (RPMs are available - requires IBM mathlib)

===List of existing packages or programs===
Those are lists of programs for GNU/Linux, which may be already packaged.

http://club.mandriva.com/xwiki/bin/KB/SciApps
http://rpms.mandrivaclub.com/rpms/Groups.html see http://rpms.mandrivaclub.com/rpms/Sciences_Mathematics.html and others in Sciences/you name it...

http://packages.ubuntu.com/breezy/math/

http://www.freshports.org/math/ ports for ""FreeBSD""

http://www.biolinux.org/soft.html rpm packages for biology => verify whether they are in plf or contrib

http://www.usinglinux.org/science/

http://www.jesuislibre.org/applications/Scientifique_et_Technique/ [fr] many programs to verify

http://repos.opensuse.org/science/SUSE_Factory/repodata/ a repository dedicated to Software for Scientists and Engineers (SUSE_Factory)

http://www.eso.org/science/scisoft/ packaging of astronomical software
http://www.eso.org/science/scisoft/rpm2html/Applications_Scientific.html

http://fr.wikipedia.org/wiki/Programmes_GNU-Linux_d'astronomie

===Programs with packages available===
Those programs could be included either in main or in contrib, only need a maintainer and adaptation of spec file

http://calculix.de/ (GPL) Three-Dimensional Structural Finite Element Program
http://www.dhondt.de/ to download calculix
http://www.colorfullife.com/~manfred/ccx/ rpm are available
see TestCalculix

http://sourceforge.net/projects/apbs - [ [[http://sourceforge.net/project/screenshots.php?group_id=148472 screenshots]] ] (GPL) software package for the numerical solution of the Poisson-Boltzmann equation, a popular continuum model for describing electrostatic interactions between molecular solutes over a wide range of length scales
http://sourceforge.net/project/showfiles.php?group_id=148472 rpm are available
see CompileApbs

verify if this is obsoleted by what provides apbs...
http://www.fetk.org/ ""The Finite Element ToolKit (FEtk)"" is an evolving collection of parallel adaptive multilevel finite element software libraries and tools for solving coupled systems of partial differential equations (PDE) and integral equations (IE)
http://cam.ucsd.edu/~mholst/codes/maloc/index.html (GPL) MALOC (Minimal Abstraction Layer for Object-oriented C) is a small, portable, abstract C environment library for object-oriented C programming
http://cam.ucsd.edu/~mholst/codes/maloc/index.html#download rpm are available
http://cam.ucsd.edu/~mholst/codes/mc/index.html hum missing the downloading links :-(
http://cam.ucsd.edu/~mholst/codes/sg/index.html (GPL) SG is an unstructured simplex mesh OpenGL display and manipulation tool for use with the finite element research codes MC and PLTMG
http://cam.ucsd.edu/~mholst/codes/sg/index.html#download rpm are available
verify if this is obsoleted by what provides apbs...

http://www-fourier.ujf-grenoble.fr/~parisse/giac_fr.html (GPL) ""calcul formel, de la géométrie dynamique, du tableur et de la programmation. Xcas est une interface de Giac, une bibliothèque C++ de calcul formel libre (licence GPL). Giac dispose d'un mode de compatibilité avec les logiciels Maple et MuPAD et les calculatrices TI89/TI92/Voyage 200""
http://www-fourier.ujf-grenoble.fr/~parisse/giac_fr.html#packages debian packages available

http://www.math.u-bordeaux.fr/~belabas/pari/ PARI/GP computer algebra system designed for fast computations in number theory (factorizations, algebraic number theory, elliptic curves...)
http://modular.fas.harvard.edu/SAGE/ a graphical interface

===Programs not yet packaged===
Have a look at those programs, check license and whether packages (deb, rpm, ...) would be available

http://gcalc.net/ (GPL) [ [[http://gcalc.net/screenshots.php screenshots]] ] set of graphing functionality for algebra, pre-calculus, calculus and beyond. (Java)

http://www2.enel.ucalgary.ca/~vigmond/flounder/ - Flounder is a quick way to visualize regularly spaced 4D data, i.e., a data set that is a function of x, y, z, and time.

http://cocoa.dima.unige.it/ (public domain) Computations in Commutative Algebra

http://www.gap-system.org (GPL) GAP is a system for computational discrete algebra, with particular emphasis on Computational Group Theory.

http://home.gna.org/mipisti/ (GPL) ""MicroscopePictureStitching (MiPiSti)"" arrange charts to one overall picture
https://gna.org/projects/mipisti project page

https://gna.org/projects/mini3d/ (GPL) mini3d is a set of basic tools for exporting/importing 3d mesh. This lib provide read/write 3d mesh in 3ds ascii format (.asc)

https://gna.org/projects/micromodel/ (GPL) ""This MicroModel library is about modeling low polycount 3d models. A visual mouse driven modeler is featured to help building models.""
http://cvs.gna.org/cvsweb/?cvsroot=micromodel cvs

https://gna.org/projects/metafract/ (GPL) Metafract is an all-purpose fractal generator using GTK+2.
http://svn.gna.org/viewcvs/metafract/trunk/ svn


http://www.decade-dynamics.org/ (GPL) Decade is an acronym for Dynamic Engine for Computer Aided DEsign software. It aims to provide a full dynamic engine for simulating rigid body. Decade can work as a standalone tool, as well as an extension for CATIA V5 and SolidWorks CAD softwares.
https://gna.org/projects/decade/ project page
http://download.gna.org/decade/ download

https://gna.org/projects/haplo/ (GPL) a finite element program
http://download.gna.org/haplo/debian/ debian packages

http://www.swox.com/gmp/ (LGPL) GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers. There is no practical limit to the precision except the ones implied by the available memory in the machine GMP runs on. GMP has a rich set of functions, and the functions have a regular interface.

http://www.opencfd.co.uk/ (GPL) computational fluid dynamics (CFD) Open FOAM (Open Field Operation and Manipulation) CFD Toolbox can simulate anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics, electromagnetics and the pricing of financial options
http://freshmeat.net/projects/openfoam/ license : GPL

http://gfs.sourceforge.net/ - [ [[http://gfs.sourceforge.net/gallery.html screenshots]] ] (GPL) library for the solution of the partial differential equations describing fluid flow

http://www.geuz.org/getdp/ (GPL) ""GetDP"" has been initially developed in the field of computational electromagnetics, general finite element solver using mixed elements to discretize de Rham-type complexes in one, two and three dimensions
http://www.geuz.org/gmsh/ - [ [[http://www.geuz.org/gmsh/#Screenshots screenshots]] ] (GPL) Gmsh is a three-dimensional finite element mesh generator with built-in pre- and post-processing facilities

http://www.hpfem.jku.at/netgen/index.html - [ [[http://www.hpfem.jku.at/netgen/index.html?/netgen/screenshots.html screenshots]] ] (LGPL) Netgen is an automatic 3d tetrahedral mesh generator
http://www.hpfem.jku.at/ngsolve/index.html (LGPL) NGSolve is a general purpose 3D finite element solver. Version 1.x supports scalar (heat flow), elasticity and magnetic field problems.
http://www.opencascade.org/ - [ [[http://www.opencascade.org/showroom/screenshots/ screenshots]] ] ([[http://www.opencascade.org/occ/license/ LGPL-like]]) Open CASCADE is a powerful CAD/CAM/CAE kernel and development platform for 3D modeling applications

http://www.mit.edu/~ibaran/kseg.html [en] GPL Geometry
http://www.stat.umn.edu/macanova/macanova.home.html [en] GPL interactive statistical analysis program
http://socnetv.sourceforge.net/ [en] GPL comprehensive Social Networks Analysis and Visualisation
http://eye.jimbomania.com/eyefract.html [en] maybe-GPL
http://jimbomania.com/glfract.html [en] GPL loads fractal {Mandelbrot, Julia} sets from file as specified by David Eyerman's Eyefract v0.6.0 and displays them in 3D space with ""OpenGL/Glut""
http://spike.sandia.gov/Trilinos/about.html Project Trilinos effort to develop and implement robust parallel algorithms using modern object-oriented software design, while still leveraging the value of established numerical libraries such as PETSc, Aztec, the BLAS and LAPACK.
http://www.ap-i.net/skychart/modules.php?op=modload&name=PagEd&file=index&page_id=18 [fr] cartes du ciel (skychart), compiles with lazarus free pascal
http://www.wings3d.com/index.php [en] Wings 3D is a subdivision modeler BSD, developed in erlang :-(

http://home.fnal.gov/~gnedin/IFRIT/ - [ [[http://home.fnal.gov/~gnedin/IFRIT/intro_shots.html screenshots]] ] (Public Domain) powerful tool that can be used to visualize 3-dimensional data sets

http://www.ncnr.nist.gov/xtal/software/gsas.html (BSD-like) GSAS (General Structure Analysis System) is a comprehensive system for the refinement of structural models to both x-ray and neutron diffraction data. The GSAS package can be used with both single-crystal and powder diffraction data (Rietveld analysis) -- TagScara
http://www.ncnr.nist.gov/programs/crystallography/software/expgui/expgui.html Public Domain tcl/tk EXPGUI is a GUI for GSAS

http://jsynoptic.sourceforge.net/ (LGPL) JSynoptic renders information graphically. It can be used as a simple graph plotter, or as a complex run-time monitoring environment
http://jsynoptic.sourceforge.net/screenshots.html
http://sourceforge.net/projects/jsynoptic/ Java

http://jcae.sourceforge.net/ (LGPL) # simple volumes modeler # finite elements mesher # portable on platforms which support Java and Opencascade
http://jcae.sourceforge.net/screenshots.html
http://www.sourceforge.net/projects/jcae Java

http://consult.cern.ch/writeup/garfield/files/ (no license found) Garfield is a computer program for the detailed simulation of two- and three-dimensional drift chambers.


===software that seems not free===
to be looked at later... even though they seem open source (OSI) approved. Non-commercial is a severe restriction :-(
http://femm.foster-miller.net/index.html A Windows finite element solver for 2D and axisymmetric magnetic and electrostatic problems with graphical pre- and post-processors.
http://femm.foster-miller.net/Archives/license.htm not a free license (cannot charge)
http://femm.foster-miller.net/Archives/linux/readme.htm runs in wine :-(

http://www.dealii.org/ - [[http://www.dealii.org/developer/license.html QPL licensing]] The main aim of deal.II is to enable development of modern finite element algorithms, using among other aspects sophisticated error estimators and adaptive meshes.
http://www.informatik.tu-darmstadt.de/TI/LiDIA/ - [[ftp://ftp.informatik.tu-darmstadt.de/pub/TI/systems/LiDIA/current/COPYING non-commercial license]] A ""C++"" Library For Computational Number Theory

http://www.ill.fr/pages/science/IGroups/diff/Soft/fp/index.html - [[ license to be found]] ""a set of crystallographic programs (FullProf, WinPLOTR, EdPCR, GFourier, etc...) mainly developed for Rietveld analysis (structure profile refinement) of neutron (constant wavelength, time of flight, nuclear and magnetic scattering) or X-ray powder diffraction data collected at constant or variable step in scattering angle 2theta."" -- TagScara
http://www-llb.cea.fr/fullweb/fp2k/fp2k_intro_whatis.htm brief presentation
http://www.ill.fr/pages/science/IGroups/diff/Soft/fp/php/downloads.html (last version when checked : June 2006)
http://www-llb.cea.fr/fullweb/fp2k/fp2k.htm (dates back to january 2003 ?)
http://www-llb.cea.fr/fullweb/others/jfullprof.htm jfullprof (java interface)

===Compilations of programs===
for programs that have not yet been packaged and that I try to get compiled see CompilePrograms
CompileElmer GPL tool using finite element method for multi-physics problems (compiles with g95 fortran ""gcc-c++"" ...)
TestCalculix GPL tool
TestScilab non-free license (non-commercial) tool for many scientific problems

===For Scara===
http://openscientist.lal.in2p3.fr/
http://wikiomics.org/wiki/Main_Page
http://www.openscience.org/links/index.php?section=21
http://pgopher.chm.bris.ac.uk/
http://www.steletch.org/spip.php?rubrique4
http://fsffrance.org/science/chimie.fr.html
http://www.alchem.org/
http://www.alchem.org/list.php3?id_rubrique=2 [fr] list of software


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