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< SIGs‎ | SciTech

(→‎Chemistry: added kalzium)
(Added Molsketch to the list of chemistry packages)
 
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= List of scientific/engineering packages =
= List of scientific and engineering packages =
 
This is quite incomplete.


== 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://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://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://www.cbcb.umd.edu/software/glimmer glimmer] || System for finding genes in microbial DNA
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|-
|-
| [http://lagan.stanford.edu lagan] || Local, global, and multiple alignment of DNA sequences
| [http://lagan.stanford.edu lagan] || Local, global, and multiple alignment of DNA sequences
|-
| [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
|-
|-
| [http://www.bioperl.org/ perl-bioperl] || A collection of tools for bioinformatics in Perl
| [http://www.bioperl.org/ perl-bioperl] || A collection of tools for bioinformatics in Perl
|-
|-
| [http://www.biopython.org/ perl-biopython] || A collection of tools for bioinformatics in Python
| [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
|-
| [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.csb.pitt.edu/ProDy ProDy] || Application for protein structure, dynamics and sequence analysis
|-
| [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.
|-
|-
| [http://pbil.univ-lyon1.fr/software/seaview.html seaview] || Graphical multiple sequence alignment editor
| [http://pbil.univ-lyon1.fr/software/seaview.html seaview] || Graphical multiple sequence alignment editor
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| [http://sibsim4.sourceforge.net SIBsim4] || Align expressed RNA sequences on a DNA template
| [http://sibsim4.sourceforge.net SIBsim4] || Align expressed RNA sequences on a DNA template
|-
|-
| [http://ygingras.net/bioinfo pipviewer] || Visualizer for multiple alignments of genomic sequences
| [http://ugene.unipro.ru/ ugene] || Genome analysis suite
|-
|-
| [http://ygingras.net/bioinfo vhybridize] || Virtual Hybridization command line tools  
| [http://ygingras.net/bioinfo vhybridize] || Virtual Hybridization command line tools  
|-
| [http://ugene.unipro.ru/ ugene] || Genome analysis suite
|}
|}
See also: [[SIGs/SciTech/BioinformaticsWishList|Bioinformatics WishList]]


== Chemistry ==
== Chemistry ==
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|-
|-
| [http://avogadro.openmolecules.net/wiki/Main_Page Avogadro] || An advanced molecular editor for chemical purposes
| [http://avogadro.openmolecules.net/wiki/Main_Page Avogadro] || An advanced molecular editor for chemical purposes
|-
| [http://www.cp2k.org/ cp2k] || Ab Initio Molecular Dynamics
|-
|-
| [http://www.nongnu.org/gchemutils/ GChemistry]  || Gnome Chemistry Utils incl. periodic table of the elements, molecular structure viewer and chemical calculator
| [http://www.nongnu.org/gchemutils/ GChemistry]  || Gnome Chemistry Utils incl. periodic table of the elements, molecular structure viewer and chemical calculator
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|-
|-
| [http://jmol.sourceforge.net/ jmol] || An open-source Java viewer for chemical structures in 3D
| [http://jmol.sourceforge.net/ jmol] || An open-source Java viewer for chemical structures in 3D
|-
| [https://sourceforge.net/projects/molsketch/ Molsketch] || A 2D molecular structures editor
|-
|-
| [http://openbabel.sourceforge.net/ openbabel] || Chemistry software file format converter
| [http://openbabel.sourceforge.net/ openbabel] || Chemistry software file format converter
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|-
|-
| [http://edu.kde.org/kalzium/index.php Kalzium] || Period table, chemsitry calculator, etc.
| [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
|-
| [https://cantera.org/ Cantera] || Libraries and tools for problems involving chemical kinetics, thermodynamics, and transport processes
|}
== Computer science ==
{|
|-
!'''Package Name'''||'''Description'''
|-
|  [http://www.nsnam.org/ ns-3] || ns-3 Network Simulator ([[Features/Ns3]])
|}
|}


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|}
|}


== Geoscience/Geographic Information Systems ==


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


== Mathematics ==
== Mathematics ==
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|-
|-
| [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.
| [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.
|-
| [http://www.gap-system.org/ GAP] || Computational discrete algebra
|-
|-
| kpolynome ||KPolynome is a program to calculate mathematical polynomes based on given data coordinates.
| kpolynome ||KPolynome is a program to calculate mathematical polynomes based on given data coordinates.
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|-
|-
| [http://www.octave.org Octave] || Octave is a Matlab-Clone
| [http://www.octave.org Octave] || Octave is a Matlab-Clone
|-
| [http://www.jmodelica.org/assimulo python-assimulo] || Ordinary differential and differential algebraic equations solver
|-
|-
| [http://www.r-project.org R] || R is a software environment for statistical computing and graphics
| [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
| [http://scigraphica.sourceforge.net scigraphica] || Scientific application for data analysis and technical graphics
|-
| [http://www.scilab.org scilab] || GUI based numerical analysis system
|}
|}


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


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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''
|}
 
== Social Sciences ==
 
* Please check out the separate [[SIGs/SocialScience#Social_Scientists'_diverse_software_needs|Social Science page]].
 
 
 
 
= 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.geneinfinity.org/rastop/ RasTop] - Molecular Visualization Software
* [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].
* [https://www.freecadweb.org/ FreeCAD] - FreeCAD is a program for computer aided design in three dimensions
 
= 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"
|-
! '''Name''' || '''Description''' || '''Why it won't be packaged'''
|-
| [http://www.cpmd.org/ CPMD] || Plane wave/pseudopotential implementation of DFT || Non-Free license (non-redistributable)
|-
| [http://www-c.inria.fr/gamma/cdrom/www/emc2/eng.htm EMC2] || Mesh generation utility || Non-Free license (verified by fedora-legal)
|-
|-
| [http://jmol.sourceforge.net/ jmol] || An open-source Java viewer for chemical structures in 3D
| [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://openbabel.sourceforge.net/ openbabel] || Chemistry software file format converter
| [http://www.cmbi.ru.nl/molden/ MOLDEN] || A package for displaying Molecular Density from Ab Initio and Semi-Empirical packages || Non-Free license
|-
|-
| [http://www.pymol.org pymol] || PyMOL Molecular Viewer
| foo || bar app || patented
|}
|}




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

Latest revision as of 22:12, 4 July 2024

List of scientific and engineering packages

This is quite incomplete.

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)
ProDy Application for protein structure, dynamics and sequence analysis
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
Molsketch A 2D molecular structures editor
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
Cantera Libraries and tools for problems involving chemical kinetics, thermodynamics, and transport processes

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.
GAP Computational discrete algebra
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
python-assimulo Ordinary differential and differential algebraic equations solver
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)

Medicine

Package Name Description
InsightToolkit Medical imaging processing library

Physics

Package Name Description
Add package name here Add package description here

Social Sciences



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
  • RasTop - Molecular Visualization Software
  • 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.
  • FreeCAD - FreeCAD is a program for computer aided design in three dimensions

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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