From Fedora Project Wiki
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 |
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 |