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= List of scientific/engineering packages =
= List of scientific and engineering packages =


== Astronomy ==


* Please check out the separate [[SIGs/Astronomy/Packages| page]].


== Mathematics ==
== Biology and bioinformatics software ==


{|
{|
|-
|-
! '''Package Name'''||'''Description'''  || '''Link'''
!'''Package Name'''||'''Description'''
|-
| [http://bowtie-bio.sourceforge.net/index.shtml bowtie] || Memory-efficient short-sequence read aligner
|-
| [http://bio-bwa.sourceforge.net/ bwa] || Burrows-Wheeler Alignment Tool for efficient short read alignment ([https://bugzilla.redhat.com/show_bug.cgi?id=597315 original Review Request])
|-
| [http://www.cbcb.umd.edu/software/ELPH/ elph] || Tool to find motifs in a set of DNA or protein sequences
|-
| [http://emboss.sourceforge.net/ EMBOSS] || Hundreds of useful, well documented applications for molecular sequence and other analyses.
|-
| [http://hannonlab.cshl.edu/fastx_toolkit/index.html FASTX-Toolkit] || Command line tools for Short-Reads FASTA/FASTQ files preprocessing ([https://bugzilla.redhat.com/show_bug.cgi?id=597307 original Review Request])
|-
| [http://www.cbcb.umd.edu/software/glimmer glimmer] || System for finding genes in microbial DNA
|-
| [http://hmmer.wustl.edu hmmer] || Profile HMM software for protein sequence analysis
|-
| [http://lagan.stanford.edu lagan] || Local, global, and multiple alignment of DNA sequences
|-
|-
| kpolynome ||KPolynome is a program to calculate mathematical polynomes based on given data coordinates. ||
| [http://www.bioperl.org/ perl-bioperl] || A collection of tools for bioinformatics in Perl
|-
|-
| R || R is a software environment for statistical computing and graphics || http://www.r-project.org
| [http://www.biopython.org/ perl-biopython] || A collection of tools for bioinformatics in Python
|-
|-
| octave || Octave is a Matlab-Clone || http://www.octave.org
| [http://samtools.sourceforge.net/ SAMtools] || SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. Tools for sorting, merging etc. sam format files.
|-
|-
| scigraphica || Scientific application for data analysis and technical graphics || http://scigraphica.sourceforge.net
| [http://pbil.univ-lyon1.fr/software/seaview.html seaview] || Graphical multiple sequence alignment editor
|-
|-
| calc || Calc is an arbitrary precision C-like arithmetic system that is a calculator, an  algorithm-prototyper, and a mathematical research tool.  || http://isthe.com/chongo/tech/comp/calc/
| [http://sibsim4.sourceforge.net SIBsim4] || Align expressed RNA sequences on a DNA template
|-
|-
| blitz || Blitz++ is a C++ class library for matrix scientific computing || http://www.oonumerics.org/blitz
| [http://ygingras.net/bioinfo pipviewer] || Visualizer for multiple alignments of genomic sequences
|}
|-
 
| [http://www.pypop.org/ PyPop] || Software for analyzing population genomics data
 
== Mechanical engineering ==
 
{|
|-
|-
!'''Package Name'''||'''Description'''  ||'''Link'''
| [http://ygingras.net/bioinfo vhybridize] || Virtual Hybridization command line tools
|-
|-
| Qcad ||QCad is an application for computer aided drafting in two dimensions (2d) || http://www.qcad.org/qcad.html
| [http://ugene.unipro.ru/ ugene] || Genome analysis suite
|-
|-
| FreeFEM || Free<code></code>Fem++ is an implementation of a language dedicated to the finite element method. It enables you to solve Partial Differential Equations (PDE) easily. || http://www.freefem.org/ff++/index.htm
| [http://pngu.mgh.harvard.edu/~purcell/plink/ plink] || Whole genome association analysis toolset ([https://bugzilla.redhat.com/show_bug.cgi?id=841266 Original Review Request])
|-
|-
| Scilab || Scilab is a [http://www.gnu.org/licenses/license-list.html non-Free] numerical computational package developed by INRIA and ENPC in France. As Scilab is '''not''' Free Software, it cannot be included in Fedora. || http://www.scilab.org/
| [http://cufflinks.cbcb.umd.edu/ cufflinks] || Transcript assembly, differential expression, and differential regulation for RNA-Seq ([https://bugzilla.redhat.com/show_bug.cgi?id=694998 Original Review Request])
|}
|}


== Electrical engineering ==
See also: [[SIGs/SciTech/BioinformaticsWishList|Bioinformatics WishList]]
 
== Chemistry ==


{|
{|
|-
|-
!'''Package Name'''||'''Description''' || '''Link'''
! '''Package Name'''||'''Description'''
|-
| [http://avogadro.openmolecules.net/wiki/Main_Page Avogadro] || An advanced molecular editor for chemical purposes
|-
| [http://cp2k.berlios.de/ cp2k] || A molecular dynamics engine capable of classical and Car-Parrinello simulations
|-
|-
| The Geda Suite || The complete suite for Electrical schematic and simulation || -
| [http://www.nongnu.org/gchemutils/ GChemistry]  || Gnome Chemistry Utils incl. periodic table of the elements, molecular structure viewer and chemical calculator
|-
|-
| geda-docs<BR>geda-examples<BR>geda-gattrib<BR>geda-gnetlist<BR>geda-gschem<BR>geda-gsymcheck <BR>geda-symbols<BR>geda-utils||Documentation for gEDA <BR>Circuit examples for gEDA<BR>Attribute editor for gEDA<BR>Netlister for the gEDA project<BR>Electronics schematics editor<BR>Symbol checker for electronics schematics editor<BR>A bunch of symbols of electronic devices used by gschem.<BR>Utilities for gEDA|| -
| [http://www.gromacs.org gromacs] || Gromacs - Fast, Free and Flexible MD
|-
|-
| gresistor || To allow for identification, resistors are usually marked with colored bands. Often refereed to as color codes, these markings are indicative of their resistance, tolerance and temperature coefficient. || -
| [http://www.iupac.org/inchi/ inchi] || The IUPAC International Chemical Identifier library
|-
|-
| gnucap || GNU Circuit Analysis Package||-
| [http://jmol.sourceforge.net/ jmol] || An open-source Java viewer for chemical structures in 3D
|-
|-
| ktechlab || Development and simulation of microcontrollers and electronic circuits || -
| [http://openbabel.sourceforge.net/ openbabel] || Chemistry software file format converter
|-
|-
| Ngspice || A mixed level/signal circuit simulator ||-
| [http://www.pymol.org pymol] || PyMOL Molecular Viewer
|-
|-
| pcb || PCB is an interactive printed circuit board editor for the X window system.|| -
| [http://pyquante.sourceforge.net/ PyQuante] || Python Quantum Chemistry
|-
|-
| toped || IC Layout Editor || -
| [http://xdrawchem.sourceforge.net/ xdrawchem] || 2D chemical structures drawing tool
|-
|-
| xcircuit || Xcircuit is a general-purpose drawing program and also a specific-purpose CAD program for circuit schematic drawing and schematic capture. || -
| [http://bkchem.zirael.org/ BKChem] || chemical drawing program
|-
|-
| qucs || Qucs is a circuit simulator with graphical user interface.  The software aims to support all kinds of circuit simulation types, e.g. DC, AC, S-parameter and harmonic balance analysis.  || http://qucs.sourceforge.net/
| [http://edu.kde.org/kalzium/index.php Kalzium] || Period table, chemsitry calculator, etc.
|-
|-
| freehdl || A project to develop a free, open source, GPL'ed VHDL simulator for Linux.  || http://www.freehdl.seul.org/
| [http://www.scl.ameslab.gov/~brett/MacMolPlt/ wxmacmolplt] || A graphics program for plotting 3-D molecular structures and normal modes
|}
|}


== Computer science ==


{|
|-
!'''Package Name'''||'''Description'''
|-
|  [http://www.nsnam.org/ ns-3] || ns-3 Network Simulator ([[Features/Ns3]])
|}


== Chemistry ==
== Electrical engineering ==


{|
{|
|-
|-
! '''Package Name'''||'''Description''' || '''Link'''
!'''Package Name'''||'''Description'''
|-
| The Geda Suite || The complete suite for Electrical schematic and simulation
|-
| geda-docs<BR>geda-examples<BR>geda-gattrib<BR>geda-gnetlist<BR>geda-gschem<BR>geda-gsymcheck <BR>geda-symbols<BR>geda-utils||Documentation for gEDA <BR>Circuit examples for gEDA<BR>Attribute editor for gEDA<BR>Netlister for the gEDA project<BR>Electronics schematics editor<BR>Symbol checker for electronics schematics editor<BR>A bunch of symbols of electronic devices used by gschem.<BR>Utilities for gEDA
|-
| gresistor || To allow for identification, resistors are usually marked with colored bands. Often refereed to as color codes, these markings are indicative of their resistance, tolerance and temperature coefficient.
|-
| gnucap || GNU Circuit Analysis Package
|-
| ktechlab || Development and simulation of microcontrollers and electronic circuits
|-
| Ngspice || A mixed level/signal circuit simulator
|-
| pcb || PCB is an interactive printed circuit board editor for the X window system.
|-
|-
| GChemistry  || Gnome Chemistry Utils incl. periodic table of the elements, molecular structure viewer and chemical calculator || http://www.nongnu.org/gchemutils/
| toped || IC Layout Editor
|-
|-
| inchi || The IUPAC International Chemical Identifier library || http://www.iupac.org/inchi/
| xcircuit || Xcircuit is a general-purpose drawing program and also a specific-purpose CAD program for circuit schematic drawing and schematic capture.
|-
|-
| openbabel || Chemistry software file format converter || http://openbabel.sourceforge.net/
| [http://qucs.sourceforge.net/ qucs] || Qucs is a circuit simulator with graphical user interface.  The software aims to support all kinds of circuit simulation types, e.g. DC, AC, S-parameter and harmonic balance analysis.
|-
|-
| xdrawchem || 2D chemical structures drawing tool || http://xdrawchem.sourceforge.net/
| [http://www.freehdl.seul.org/ freehdl] || A project to develop a free, open source, GPL'ed VHDL simulator for Linux.
|}
|}




== Astronomy ==
 
== Mathematics ==


{|
{|
|-
|-
! '''Package Name'''||'''Description'''  || '''Link'''
! '''Package Name'''||'''Description'''
|-
|-
| sextractor || A program that builds a catalogue of objects from an astronomical image. || http://terapix.iap.fr/rubrique.php?id_rubrique=91/
| [http://arma.sourceforge.net Armadillo] || fast C++ matrix library with interfaces to LAPACK and ATLAS
|-
|-
| wcstools || Software utilities to display and manipulate the WCS of a FITS image. || http://tdc-www.harvard.edu/software/wcstools/
| [http://www.oonumerics.org/blitz blitz] || Blitz++ is a C++ class library for matrix scientific computing
|-
|-
| stellarium || 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. || http://www.stellarium.org/
| [http://isthe.com/chongo/tech/comp/calc/ calc] || Calc is an arbitrary precision C-like arithmetic system that is a calculator, an  algorithm-prototyper, and a mathematical research tool.
|-
|-
| funtools || Minimal FITS library and utilities || http://hea-www.harvard.edu/RD/funtools/
| kpolynome ||KPolynome is a program to calculate mathematical polynomes based on given data coordinates.
|-
|-
| qfits || A stand-alone general purpose FITS library || http://www.eso.org/projects/aot/qfits/
| [http://www.brics.dk/mona/ mona] || Mona is a decision procedure for the WS1S and WS2S logics
|-
|-
| cpl || ESO library for automated astronomical data-reduction  || http://www.eso.org/sci/data-processing/software/cpl/
| [http://www.octave.org Octave] || Octave is a Matlab-Clone
|-
| [http://www.r-project.org R] || R is a software environment for statistical computing and graphics
|-
| [http://scigraphica.sourceforge.net scigraphica] || Scientific application for data analysis and technical graphics
|}
|}


 
== Mechanical engineering ==
== Biology ==


{|
{|
|-
|-
!'''Package Name'''||'''Description'''  ||'''Link'''
!'''Package Name'''||'''Description'''
|-
|-
| elph || Tool to find motifs in a set of DNA or protein sequences || http://www.cbcb.umd.edu/software/ELPH/
| [http://www.freefem.org/ff++/index.htm FreeFEM] || Free<Fem++ is an implementation of a language dedicated to the finite element method. It enables you to solve Partial Differential Equations (PDE) easily.
|-
|-
| glimmer || System for finding genes in microbial DNA || http://www.cbcb.umd.edu/software/glimmer
| [http://www.qcad.org/qcad.html Qcad] ||QCad is an application for computer aided drafting in two dimensions (2d)
|}
 
== Physics ==
 
{|
|-
|-
| hmmer || Profile HMM software for protein sequence analysis || http://hmmer.wustl.edu
! '''Package Name'''||'''Description'''
|-
| ''Add package name here'' || ''Add package description here''
|}
 
= Potential Packages =
 
* [[Asana Math font]]
* [http://ambermd.org/#AmberTools AmberTools] - A set of tools for Assisted Model Building with Energy Refinement (AMBER). [[User:Rathann|Dominik Mierzejewski]] is working on the package, contact him if you are interested or want to help.
* [http://lammps.sandia.gov/] LAMMPS Molecular Dynamics Simulator
* [http://mgltools.scripps.edu/ MGLTools]  - Includes AutoDockTools (docking of molecules), Python Molecular Viewer and Vision (python visual programming). Packaged for debian : http://mgltools.scripps.edu/News/mgltools-available-for-debian
* [http://nanodesigner.sourceforge.net/ Nanodesigner] - Example design 1 The Nanodesigner project is an attempt to create a software platform for research on nanometer sized objects. By objects is meant everything that consists of atoms: molecular motors, biomolecules, a crystal slab
* [http://nebc.nox.ac.uk/tools/bio-linux/package-list Ideas of packages for bioinformatics base on bio-linux].
* [http://www.creatis.insa-lyon.fr/rio/vv VV] - Fast and simple image viewer, designed for visualization of spatio-temporal images: 2D, 2D+t, 3D and 3D+t (or 4D) - There are already binary rpms [http://www.creatis.insa-lyon.fr/rio/vv#Download_VV available]
* [http://www.gap-system.org/ GAP] - Computer algebra system - JasonTibbitts [http://www.math.uh.edu/~tibbs/rpms/gap has a working and up-to-date GAP package], but it needs significant cleanup before it has a chance of passing review.
* [http://www.geneinfinity.org/rastop/ RasTop] - Molecular Visualization Software
* [http://www.itk.org/ ITK]  - Insight Segmentation and Registration Toolkit - software system to support the [http://www.nlm.nih.gov/research/visible/visible_human.html Visible Human Project] - Under review [https://bugzilla.redhat.com/show_bug.cgi?id=539387 InsightToolkit]
* [http://www.math.pitt.edu/~bard/xpp/xpp.html XPP] - A tool for solving differential equations - Jason Tibbitts has a working package, but the program has such a poor interface that it may not be worth adding to the distro
* [http://www.neuron.yale.edu/neuron/ Neuron] - A simulator of neurons and networks, useful for computational biology.  Packages are available upstream; shouldn't be terribly hard to package properly but requires a truly ancient user interface toolkit.
* [http://www.sagemath.org SAGE] Mathematica-like open source mathematics software ([[SIGs/SciTech/SAGE|SAGE packaging discussion]])
* [http://www.scilab.org Scilab] GUI based numerical analysis system ([[SIGs/SciTech/Scilab|details on current status]])
 
= List of applications we will NOT package =
 
* Non-commercial clauses in applications licenses render them invalid for inclusion into Fedora Package Collection. Such apps are not Free and open source software and violates Clause 6 of the [http://opensource.org/docs/definition.php OSI definition]. See an example of such clause:
 
<pre>
This software may be copied and distributed for educational, research, and not
for profit purposes provided that this copyright and statement are included in
all such copies. Other copyrights may also apply.
</pre>
 
{| border="1"
|-
|-
| lagan || Local, global, and multiple alignment of DNA sequences || http://lagan.stanford.edu
! '''Name''' || '''Description''' || '''Why it won't be packaged'''
|-
|-
| perl-bioperl || A collection of tools for bioinformatics in Perl || http://www.bioperl.org/
| [http://www-c.inria.fr/gamma/cdrom/www/emc2/eng.htm EMC2] || Mesh generation utility || Non-Free license (verified by fedora-legal)
|-
|-
| perl-biopython || A collection of tools for bioinformatics in Python || http://www.biopython.org/
| [http://www.ks.uiuc.edu/Research/vmd/ VMD] || Molecular Visualization and Analysis Package || Non-Free license
|-  
| [http://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml fasta2 and fasta3] || The FASTA programs find regions of local or global (new) similarity between Protein or DNA sequences || [http://faculty.virginia.edu/wrpearson/fasta/COPYRIGHT License] contains non-commercial clause
|-
|-
| seaview || Graphical multiple sequence alignment editor || http://pbil.univ-lyon1.fr/software/seaview.html
| [http://www.cmbi.ru.nl/molden/ MOLDEN] || A package for displaying Molecular Density from Ab Initio and Semi-Empirical packages || Non-Free license
|-
|-
| SIBsim4 || Align expressed RNA sequences on a DNA template || http://sibsim4.sourceforge.net
| foo || bar app || patented
|}
|}


[[Category:SIG]]
 
 
[[Category:SciTech SIG|Packages list]]
[[Category:Packages|SciTech]]

Revision as of 22:37, 21 July 2012

List of scientific and engineering packages

Astronomy

  • Please check out the separate page.

Biology and bioinformatics software

Package Name Description
bowtie Memory-efficient short-sequence read aligner
bwa Burrows-Wheeler Alignment Tool for efficient short read alignment (original Review Request)
elph Tool to find motifs in a set of DNA or protein sequences
EMBOSS Hundreds of useful, well documented applications for molecular sequence and other analyses.
FASTX-Toolkit Command line tools for Short-Reads FASTA/FASTQ files preprocessing (original Review Request)
glimmer System for finding genes in microbial DNA
hmmer Profile HMM software for protein sequence analysis
lagan Local, global, and multiple alignment of DNA sequences
perl-bioperl A collection of tools for bioinformatics in Perl
perl-biopython A collection of tools for bioinformatics in Python
SAMtools SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. Tools for sorting, merging etc. sam format files.
seaview Graphical multiple sequence alignment editor
SIBsim4 Align expressed RNA sequences on a DNA template
pipviewer Visualizer for multiple alignments of genomic sequences
PyPop Software for analyzing population genomics data
vhybridize Virtual Hybridization command line tools
ugene Genome analysis suite
plink Whole genome association analysis toolset (Original Review Request)
cufflinks Transcript assembly, differential expression, and differential regulation for RNA-Seq (Original Review Request)

See also: Bioinformatics WishList

Chemistry

Package Name Description
Avogadro An advanced molecular editor for chemical purposes
cp2k A molecular dynamics engine capable of classical and Car-Parrinello simulations
GChemistry Gnome Chemistry Utils incl. periodic table of the elements, molecular structure viewer and chemical calculator
gromacs Gromacs - Fast, Free and Flexible MD
inchi The IUPAC International Chemical Identifier library
jmol An open-source Java viewer for chemical structures in 3D
openbabel Chemistry software file format converter
pymol PyMOL Molecular Viewer
PyQuante Python Quantum Chemistry
xdrawchem 2D chemical structures drawing tool
BKChem chemical drawing program
Kalzium Period table, chemsitry calculator, etc.
wxmacmolplt A graphics program for plotting 3-D molecular structures and normal modes

Computer science

Package Name Description
ns-3 ns-3 Network Simulator (Features/Ns3)

Electrical engineering

Package Name Description
The Geda Suite The complete suite for Electrical schematic and simulation
geda-docs
geda-examples
geda-gattrib
geda-gnetlist
geda-gschem
geda-gsymcheck
geda-symbols
geda-utils		 Documentation for gEDA
Circuit examples for gEDA
Attribute editor for gEDA
Netlister for the gEDA project
Electronics schematics editor
Symbol checker for electronics schematics editor
A bunch of symbols of electronic devices used by gschem.
Utilities for gEDA
gresistor To allow for identification, resistors are usually marked with colored bands. Often refereed to as color codes, these markings are indicative of their resistance, tolerance and temperature coefficient.
gnucap GNU Circuit Analysis Package
ktechlab Development and simulation of microcontrollers and electronic circuits
Ngspice A mixed level/signal circuit simulator
pcb PCB is an interactive printed circuit board editor for the X window system.
toped IC Layout Editor
xcircuit Xcircuit is a general-purpose drawing program and also a specific-purpose CAD program for circuit schematic drawing and schematic capture.
qucs Qucs is a circuit simulator with graphical user interface. The software aims to support all kinds of circuit simulation types, e.g. DC, AC, S-parameter and harmonic balance analysis.
freehdl A project to develop a free, open source, GPL'ed VHDL simulator for Linux.


Mathematics

Package Name Description
Armadillo fast C++ matrix library with interfaces to LAPACK and ATLAS
blitz Blitz++ is a C++ class library for matrix scientific computing
calc Calc is an arbitrary precision C-like arithmetic system that is a calculator, an algorithm-prototyper, and a mathematical research tool.
kpolynome KPolynome is a program to calculate mathematical polynomes based on given data coordinates.
mona Mona is a decision procedure for the WS1S and WS2S logics
Octave Octave is a Matlab-Clone
R R is a software environment for statistical computing and graphics
scigraphica Scientific application for data analysis and technical graphics

Mechanical engineering

Package Name Description
FreeFEM Free<Fem++ is an implementation of a language dedicated to the finite element method. It enables you to solve Partial Differential Equations (PDE) easily.
Qcad QCad is an application for computer aided drafting in two dimensions (2d)

Physics

Package Name Description
Add package name here Add package description here

Potential Packages

  • Asana Math font
  • AmberTools - A set of tools for Assisted Model Building with Energy Refinement (AMBER). Dominik Mierzejewski is working on the package, contact him if you are interested or want to help.
  • [1] LAMMPS Molecular Dynamics Simulator
  • MGLTools - Includes AutoDockTools (docking of molecules), Python Molecular Viewer and Vision (python visual programming). Packaged for debian : http://mgltools.scripps.edu/News/mgltools-available-for-debian
  • Nanodesigner - Example design 1 The Nanodesigner project is an attempt to create a software platform for research on nanometer sized objects. By objects is meant everything that consists of atoms: molecular motors, biomolecules, a crystal slab
  • Ideas of packages for bioinformatics base on bio-linux.
  • VV - Fast and simple image viewer, designed for visualization of spatio-temporal images: 2D, 2D+t, 3D and 3D+t (or 4D) - There are already binary rpms available
  • GAP - Computer algebra system - JasonTibbitts has a working and up-to-date GAP package, but it needs significant cleanup before it has a chance of passing review.
  • RasTop - Molecular Visualization Software
  • ITK - Insight Segmentation and Registration Toolkit - software system to support the Visible Human Project - Under review InsightToolkit
  • XPP - A tool for solving differential equations - Jason Tibbitts has a working package, but the program has such a poor interface that it may not be worth adding to the distro
  • Neuron - A simulator of neurons and networks, useful for computational biology. Packages are available upstream; shouldn't be terribly hard to package properly but requires a truly ancient user interface toolkit.
  • SAGE Mathematica-like open source mathematics software (SAGE packaging discussion)
  • Scilab GUI based numerical analysis system (details on current status)

List of applications we will NOT package

  • Non-commercial clauses in applications licenses render them invalid for inclusion into Fedora Package Collection. Such apps are not Free and open source software and violates Clause 6 of the OSI definition. See an example of such clause:
This software may be copied and distributed for educational, research, and not
for profit purposes provided that this copyright and statement are included in
all such copies.  Other copyrights may also apply.
Name Description Why it won't be packaged
EMC2 Mesh generation utility Non-Free license (verified by fedora-legal)
VMD Molecular Visualization and Analysis Package Non-Free license
fasta2 and fasta3 The FASTA programs find regions of local or global (new) similarity between Protein or DNA sequences License contains non-commercial clause
MOLDEN A package for displaying Molecular Density from Ab Initio and Semi-Empirical packages Non-Free license
foo bar app patented
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