SIGs/SciTech/PackageList

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= List of scientific/engineering packages =
+
= List of scientific and engineering packages =
  
 
== Astronomy ==
 
== Astronomy ==
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* Please check out the separate [[SIGs/Astronomy/Packages| page]].
 
* Please check out the separate [[SIGs/Astronomy/Packages| page]].
  
== Biology / Bioinformatics Software ==
+
== Biology and bioinformatics software ==
  
 
{|
 
{|
 
|-
 
|-
 
!'''Package Name'''||'''Description'''
 
!'''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://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])
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|-
 
|-
 
| [http://emboss.sourceforge.net/ EMBOSS] || Hundreds of useful, well documented applications for molecular sequence and other analyses.
 
| [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://www.cbcb.umd.edu/software/glimmer glimmer] || System for finding genes in microbial DNA
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|-
 
|-
 
| [http://ugene.unipro.ru/ ugene] || Genome analysis suite  
 
| [http://ugene.unipro.ru/ ugene] || Genome analysis suite  
 +
|-
 +
| [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://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])
 
|}
 
|}
 +
 +
See also: [[SIGs/SciTech/BioinformaticsWishList|Bioinformatics WishList]]
  
 
== Chemistry ==
 
== Chemistry ==
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|-
 
|-
 
| [http://www.scl.ameslab.gov/~brett/MacMolPlt/ wxmacmolplt] || A graphics program for plotting 3-D molecular structures and normal modes
 
| [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]])
 
|}
 
|}
  
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! '''Package Name'''||'''Description'''
 
! '''Package Name'''||'''Description'''
 
|-
 
|-
| [http://www.gromacs.org gromacs] || Gromacs - Fast, Free and Flexible MD
+
| ''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"
 
|-
 
|-
| [http://jmol.sourceforge.net/ jmol] || An open-source Java viewer for chemical structures in 3D
+
! '''Name''' || '''Description''' || '''Why it won't be packaged'''
 
|-
 
|-
| [http://openbabel.sourceforge.net/ openbabel] || Chemistry software file format converter
+
| [http://www-c.inria.fr/gamma/cdrom/www/emc2/eng.htm EMC2] || Mesh generation utility || Non-Free license (verified by fedora-legal)
 
|-
 
|-
| [http://www.pymol.org pymol] || PyMOL Molecular Viewer
+
| [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
 +
|-
 +
| [http://www.cmbi.ru.nl/molden/ MOLDEN] || A package for displaying Molecular Density from Ab Initio and Semi-Empirical packages || Non-Free license
 +
|-
 +
| foo || bar app || patented
 
|}
 
|}
 +
  
  
 
[[Category:SciTech SIG|Packages list]]
 
[[Category:SciTech SIG|Packages list]]
 
[[Category:Packages|SciTech]]
 
[[Category:Packages|SciTech]]

Revision as of 22:37, 21 July 2012

Contents

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