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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. | ||
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| [http://www.scl.ameslab.gov/~brett/MacMolPlt/ wxmacmolplt] || A graphics program for plotting 3-D molecular structures and normal modes | |||
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Revision as of 15:35, 9 December 2010
List of scientific/engineering packages
Astronomy
- Please check out the separate page.
Biology / Bioinformatics Software
Package Name | Description |
---|---|
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. |
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 |
Chemistry
Package Name | Description |
---|---|
Avogadro | An advanced molecular editor for chemical purposes |
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 |
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 |
---|---|
gromacs | Gromacs - Fast, Free and Flexible MD |
jmol | An open-source Java viewer for chemical structures in 3D |
openbabel | Chemistry software file format converter |
pymol | PyMOL Molecular Viewer |