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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://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])
|-
| [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.
|-
|-
| kpolynome ||KPolynome is a program to calculate mathematical polynomes based on given data coordinates. ||
| [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])
|-
|-
| R || R is a software environment for statistical computing and graphics || http://www.r-project.org
| [http://www.cbcb.umd.edu/software/glimmer glimmer] || System for finding genes in microbial DNA
|-
|-
| octave || Octave is a Matlab-Clone || http://www.octave.org
| [http://hmmer.wustl.edu hmmer] || Profile HMM software for protein sequence analysis
|-
|-
| scigraphica || Scientific application for data analysis and technical graphics || http://scigraphica.sourceforge.net
| [http://lagan.stanford.edu lagan] || Local, global, and multiple alignment of DNA sequences
|-
|-
| 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://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download ncbi-blast+] || NCBI BLAST+ finds regions of similarity between biological sequences
|-
|-
| blitz || Blitz++ is a C++ class library for matrix scientific computing || http://www.oonumerics.org/blitz
| [http://www.bioperl.org/ perl-bioperl] || A collection of tools for bioinformatics in Perl
|-
|-
| mona || Mona is a decision procedure for the WS1S and WS2S logics || http://www.brics.dk/mona/
| [http://www.biopython.org/ python-biopython] || A collection of tools for bioinformatics in Python
|}
|-
 
| [http://ygingras.net/bioinfo pipviewer] || Visualizer for multiple alignments of genomic sequences
== Mechanical engineering ==
|-
 
| [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])
{|
|-
| [http://www.pypop.org/ PyPop] || Software for analyzing population genomics data
|-
| [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.
|-
|-
!'''Package Name'''||'''Description'''  ||'''Link'''
| [http://pbil.univ-lyon1.fr/software/seaview.html seaview] || Graphical multiple sequence alignment editor
|-
|-
| Qcad ||QCad is an application for computer aided drafting in two dimensions (2d) || http://www.qcad.org/qcad.html
| [http://sibsim4.sourceforge.net SIBsim4] || Align expressed RNA sequences on a DNA template
|-
|-
| 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://ugene.unipro.ru/ ugene] || Genome analysis suite
|-
|-
| 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://ygingras.net/bioinfo vhybridize] || Virtual Hybridization command line tools
|}
|}


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


{|
{|
|-
|-
!'''Package Name'''||'''Description'''  || '''Link'''
! '''Package Name'''||'''Description'''
|-
|-
| The Geda Suite || The complete suite for Electrical schematic and simulation || -
| [http://avogadro.openmolecules.net/wiki/Main_Page Avogadro] || An advanced molecular editor for chemical purposes
|-
|-
| 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.cp2k.org/ cp2k] || Ab Initio Molecular Dynamics
|-
|-
| 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.nongnu.org/gchemutils/ GChemistry]  || Gnome Chemistry Utils incl. periodic table of the elements, molecular structure viewer and chemical calculator
|-
|-
| gnucap || GNU Circuit Analysis Package||-
| [http://www.gromacs.org gromacs] || Gromacs - Fast, Free and Flexible MD
|-
|-
| ktechlab || Development and simulation of microcontrollers and electronic circuits || -
| [http://www.iupac.org/inchi/ inchi] || The IUPAC International Chemical Identifier library
|-
|-
| Ngspice || A mixed level/signal circuit simulator ||-
| [http://jmol.sourceforge.net/ jmol] || An open-source Java viewer for chemical structures in 3D
|-
|-
| pcb || PCB is an interactive printed circuit board editor for the X window system.|| -
| [http://openbabel.sourceforge.net/ openbabel] || Chemistry software file format converter
|-
|-
| toped || IC Layout Editor || -
| [http://www.pymol.org pymol] || PyMOL Molecular Viewer
|-
|-
| xcircuit ||  Xcircuit is a general-purpose drawing program and also a specific-purpose CAD program for circuit schematic drawing and schematic capture. || -
| [http://pyquante.sourceforge.net/ PyQuante] || Python Quantum Chemistry
|-
|-
| 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://xdrawchem.sourceforge.net/ xdrawchem] || 2D chemical structures drawing tool
|-
|-
| freehdl || A project to develop a free, open source, GPL'ed VHDL simulator for Linux. || http://www.freehdl.seul.org/
| [http://bkchem.zirael.org/ BKChem] || chemical drawing program
|-
| [http://edu.kde.org/kalzium/index.php Kalzium] || Period table, chemsitry calculator, etc.
|-
| [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'''
|-
|-
| GChemistry  || Gnome Chemistry Utils incl. periodic table of the elements, molecular structure viewer and chemical calculator || http://www.nongnu.org/gchemutils/
| The Geda Suite || The complete suite for Electrical schematic and simulation
|-
|-
| inchi || The IUPAC International Chemical Identifier library || http://www.iupac.org/inchi/
| 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
|-
|-
| openbabel || Chemistry software file format converter || http://openbabel.sourceforge.net/
| 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.
|-
|-
| xdrawchem || 2D chemical structures drawing tool || http://xdrawchem.sourceforge.net/
| 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.
|-
| [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.
|-
| [http://www.freehdl.seul.org/ freehdl] || A project to develop a free, open source, GPL'ed VHDL simulator for Linux.
|}
|}


== Geoscience/Geographic Information Systems ==


== Astronomy ==
* Please check out the separate [[GIS| GIS page]].
 
== Mathematics ==


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


== Mechanical engineering ==
{|
|-
!'''Package Name'''||'''Description'''
|-
| [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.
|-
| [http://www.qcad.org/qcad.html Qcad] ||QCad is an application for computer aided drafting in two dimensions (2d)
|}


== Biology ==
== Physics ==


{|
{|
|-
|-
!'''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/
| ''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://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.salome-platform.org/ Salome] - Open source integration platform for numerical simulation. Ongoing packaging effort can be found [https://github.com/fedora-scientific/fedora-salome here].
 
= 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"
|-
|-
| glimmer || System for finding genes in microbial DNA || http://www.cbcb.umd.edu/software/glimmer
! '''Name''' || '''Description''' || '''Why it won't be packaged'''
|-
|-
| hmmer || Profile HMM software for protein sequence analysis || http://hmmer.wustl.edu
| [http://www.cpmd.org/ CPMD] || Plane wave/pseudopotential implementation of DFT || Non-Free license (non-redistributable)
|-
|-
| lagan || Local, global, and multiple alignment of DNA sequences || http://lagan.stanford.edu
| [http://www-c.inria.fr/gamma/cdrom/www/emc2/eng.htm EMC2] || Mesh generation utility || Non-Free license (verified by fedora-legal)
|-
|-
| perl-bioperl || A collection of tools for bioinformatics in Perl || http://www.bioperl.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
|-
|-
| perl-biopython || A collection of tools for bioinformatics in Python || http://www.biopython.org/
| [http://www.cmbi.ru.nl/molden/ MOLDEN] || A package for displaying Molecular Density from Ab Initio and Semi-Empirical packages || Non-Free license
|-
|-
| seaview || Graphical multiple sequence alignment editor || http://pbil.univ-lyon1.fr/software/seaview.html
| foo || bar app || patented
|-
| SIBsim4 || Align expressed RNA sequences on a DNA template || http://sibsim4.sourceforge.net
|}
|}


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

Revision as of 11:53, 21 May 2015

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)
cufflinks Transcript assembly, differential expression, and differential regulation for RNA-Seq (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
ncbi-blast+ NCBI BLAST+ finds regions of similarity between biological sequences
perl-bioperl A collection of tools for bioinformatics in Perl
python-biopython A collection of tools for bioinformatics in Python
pipviewer Visualizer for multiple alignments of genomic sequences
plink Whole genome association analysis toolset (Original Review Request)
PyPop Software for analyzing population genomics data
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
ugene Genome analysis suite
vhybridize Virtual Hybridization command line tools

See also: Bioinformatics WishList

Chemistry

Package Name Description
Avogadro An advanced molecular editor for chemical purposes
cp2k Ab Initio Molecular Dynamics
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.

Geoscience/Geographic Information Systems

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
scilab GUI based numerical analysis system

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
  • 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.
  • Salome - Open source integration platform for numerical simulation. Ongoing packaging effort can be found here.

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
CPMD Plane wave/pseudopotential implementation of DFT Non-Free license (non-redistributable)
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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