5672
Comment:
|
5775
|
Deletions are marked like this. | Additions are marked like this. |
Line 19: | Line 19: |
* [http://www.gnuplot.info/ gnuplot] is a ''non-free'' package - it is ''not'' a GNU package - ( ''Permission to modify the software is granted, but not the right to distribute the complete modified source code'' ) for quick and for paper quality plots once you get used to it. CLI only. | * [http://www.gnuplot.info/ gnuplot] is good for quick and for paper quality plots once you get used to it. CLI only. It is a ''free'' package but ''not'' a GNU package as it has a weird licence ( ''Permission to modify the software is granted, but not the right to distribute the complete modified source code. Modifications are to be distributed as patches to the released version. ...'' ) |
The goal for this page is to collect material around the ideas discussed at [Helen Faulkner's talk http://dc5video.debian.net/2005-07-17/Using_Debian_for_science_research-Helen_Faulkner.mpeg] at [wiki:?DebConf5Talks Debconf5].
Some ideas emerging from Helen's talk
(please complete)
The dedicated mailing list [http://lists.debian.org/debian-science/ debian-science] has been created [http://lists.debian.org/debian-science/2005/07/msg00000.html thanks to Pascal Hakim] ([http://murphy.debian.org/lists/debian-science/details.html mailing list statistics]). And if you wonder why the mailing-list reply-to is set to the author instead of the list itself, [http://www.unicom.com/pw/reply-to-harmful.html here] are some explanations.
DebianScience could also be a [wiki:CustomDebian CDD project].
It could also be turned into a ["LiveCD"]. [http://dirk.eddelbuettel.com/quantian/ Quantian] already does much of this.
- Development frameworks (should be painless):
- kdevelop for KDE
- Anjuta for Gnome
[wiki:DebianScienceOctave Is Octave really usable]? The main differences or missing features with respect to Matlab should be documented.
- Easy and simple tools to plot data (possibly separate by scriptable and/or gui, plotting for papers vs for 'exploring' data)
[http://www.gnu.org/software/plotutils/ plotutils] is a GPL package good for quick and paper quality plots either from the command line (e.g. pipe a text file into graph ) or as a library
[http://www.gnuplot.info/ gnuplot] is good for quick and for paper quality plots once you get used to it. CLI only. It is a free package but not a GNU package as it has a weird licence ( Permission to modify the software is granted, but not the right to distribute the complete modified source code. Modifications are to be distributed as patches to the released version. ... )
- python is good at that
- labplot is a nice gui plotter that handles 3D data
- openoffice.org calc can be used to plot 2D data
[http://plasma-gate.weizmann.ac.il/Grace/ xmgrace] (from xmgr/ace) seems popular here for 2D publication-quality plotting
[wiki:?DebianScienceR GNU R] is a free implementation of the S programming language for statistical analysis. It is very useful for data visualization and other computational science tasks.
[["OpenDX"] http://www.opendx.org/] is very powerful (for 3D data) but cannot be started intuitivly (aside from import quirks, it is once you understand the idea, though)
[http://mayavi.sourceforge.net/ ?MayaVi] is a data visualizer written in Python based on [http://public.kitware.com/VTK/ vtk]; its available as debian package "mayavi"
[http://www.paraview.org/ ?ParaView] is a parallel visualization application based on [http://public.kitware.com/VTK/ vtk]
[http://soft.proindependent.com/qtiplot.html ?QtiPlot] (GPL, no debian package yet) young promising [http://www.originlab.com/ Origin] clone
Necessity of a [wiki:DebianScienceFortran good Fortran integration]
- Requires also libs (e.g. for FFT) which are often present in add-ons for commercial compilers (FFTW connection in Fortran working now?)
- Useful tools for writing papers - word processing and !LaTeX
- kile (KDE late editor)
- openoffice.org (office suite - good but not 100% !["MSOffice"] filters)
- Useful mathematical libraries
[wiki:DebianScienceFftw FFTW and ["FFTW3"]] (Fast Fourier Transforms)
[wiki:?DebianScienceBlas ATLAS and LAPACK] (Linear Algebra)
[wiki:?["DebianScienceGSL"] GSL] (special functions, pseudorandom numbers, optimizers, solvers, etc. etc.) - ATLAS and LAPACK and BLAS will be installed by default dependencies if you install GSL in debian sarge
- ["GLPK"] (linear, integer and mixed programming library)
Links already inside Debian project
?DebianScienceDebianLinks
Outside links related to science or scientific projects
?DebianScienceOtherLinks
Efforts that could be undertaken
Thematic links
?DebianScienceAstronomy
?DebianScienceBiology
?DebianScienceChemistry
?DebianScienceConferenceTools
?DebianScienceDataFormats
?DebianScienceDataPlotting
?DebianScienceElectronics
?DebianScienceGeography
?DebianScienceHardware
?DebianScienceMathematics
?DebianSciencePhysics
?DebianScienceProgramming
?DebianSciencePublishing
(many still missing)
Unfilled needs
[http://lists.debian.org/debian-science/2005/08/msg00002.html good free software to work with tomographic datasets]
[http://dirk.eddelbuettel.com/quantian/todo.html Quantian TODO list]
Other contributions
(some thoughts added by smoe):
Independent from Helen's presentations that I cannot access at the moment there is
- A technical side of things
- Open Hardware for data aquisition
- Linux Lab Project
- Huge amount of software
Take a little trouble to make your software package [http://www.princeton.edu/~kmccarty/physics-software-rant.html packageable]
- End user applications
- Kstars / general astronomy
- K12 / Education
- Debian-Junior
- Things working in the background
- Parallel computing
- Cluster software (Sun Gridware, Torque, Condor, LSF)
Grid software (Globus, [http://www.nordugrid.org wiki:?NorduGrid])
- ["Boinc"] (see also {alioth:pkg-boinc})
- MPI / PVM
- Statistics
- Maple/Octave
- Parallel computing
- A community side of things
- This wiki page
- Debian at large
- Others
- This