SIGs/SciTech/PackageList

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
perl-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

• 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.
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
• 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)

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