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

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

Please check out the separate GIS page.

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

Please check out the separate Social Science page.

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

@@ Line 1: / Line 1: @@
-= List of scientific/engineering packages =
+= List of scientific and engineering packages =
+This is quite incomplete.
 == Astronomy ==
@@ Line 5: / Line 7: @@
 * Please check out the separate [[SIGs/Astronomy/Packages| page]].
-== Biology / Bioinformatics Software ==
+== Biology and bioinformatics software ==
 {|
 |-
 !'''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.
+|-
+| [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
@@ Line 22: / Line 30: @@
 |-
 | [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.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.
@@ Line 33: / Line 51: @@
 | [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://www.pypop.org/ PyPop] || Software for analyzing population genomics data
 |-
 | [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 ==
@@ Line 50: / Line 66: @@
 | [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
+| [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
@@ Line 59: / Line 75: @@
 |-
 | [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
@@ Line 73: / Line 91: @@
 |-
 | [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]])
 |}
@@ Line 104: / Line 133: @@
 |}
+== Geoscience/Geographic Information Systems ==
+* Please check out the separate [[GIS| GIS page]].
 == Mathematics ==
@@ Line 117: / Line 148: @@
 |-
 | [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.
@@ Line 123: / Line 156: @@
 |-
 | [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://scigraphica.sourceforge.net scigraphica] || Scientific application for data analysis and technical graphics
+|-
+| [http://www.scilab.org scilab] || GUI based numerical analysis system
 |}
@@ Line 138: / Line 175: @@
 |-
 | [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
 |}
@@ Line 146: / Line 192: @@
 ! '''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:Packages|SciTech]]

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SIGs/SciTech/PackageList: Difference between revisions

Latest revision as of 22:12, 4 July 2024

Contents

List of scientific and engineering packages

Astronomy

Biology and bioinformatics software

Chemistry

Computer science

Electrical engineering

Geoscience/Geographic Information Systems

Mathematics

Mechanical engineering

Medicine

Physics

Social Sciences

Potential Packages

List of applications we will NOT package