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## Auto-converted by kwiki2moinmoin v2005-10-07 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:Self:DebConf5Talks Debconf5]. |
== Goals == * Provide researchers and scientists a better experience using Debian. * Classify, package and distribute free software useful to science and research. * Support any quality efforts around free scientific software. * Manage the efforts dealing with various implementations (MPI, BLAS, LAPACK...). * Maintaining the [[DebianScience/Blend|Debian Science Blend]] == How to use it? == * You can use Debian Science just as you are using Debian because it is a completely internal project and is nothing other than Debian itself. We felt a need to found a team that works as a strike force for scientific software inside Debian. * [[#metapackages]] provide an easy way of installing a range of software appropriate to your particular field. == Related Blends == * [[DebianGis]] * [[DebianMed]] * [[DebianAstro]] |
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== Some ideas emerging from Helen's talk == (please complete) |
<<Anchor(metapackages)>> === metapackages === |
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* 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]). * DebianScience could also be a [wiki:Self: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:Self: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.gnuplot.info/ gnuplot] is nice for quick and for paper quality plots once you get used to it. CLI only. * 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:Self: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/ Microcal Origin] clone * Necessity of a [wiki:Self: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:Self:DebianScienceFftw FFTW and ["FFTW3"]] (Fast Fourier Transforms) * [wiki:Self:DebianScienceBlas ATLAS and LAPACK] (Linear Algebra) * [wiki:Self:["DebianScienceGSL"] GSL] (special functions, pseudorandom numbers, optimizers, solvers, etc. etc.) * ["GLPK"] (linear, integer and mixed programming library) |
The aim of the [[http://blends.debian.org/science/tasks|Debian Science metapackages]] is to provide a useful set of packages for someone working in a specific field of science. |
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== Links already inside Debian project == * DebianScienceDebianLinks |
|| sentinel || Wiki || debtag [1] || ITP/RFP [2] || Bugs [3,4]|| || [[http://blends.debian.org/science/tasks/biology|sentinel]] || [[DebianScience/Biology]] || [[https://debtags.debian.org/search/?q=field::biology|field::biology]] || [[http://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=field..biology;users=debian-science@lists.debian.org|ITP/RFP]] || [[http://blends.debian.org/science/bugs/biology.html|bugs]]|| || [[http://blends.debian.org/science/tasks/chemistry|sentinel]] || [[DebianScience/Chemistry]] || [[https://debtags.debian.org/search/?q=field::chemistry|field::chemistry]] || [[http://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=field..chemistry;users=debian-science@lists.debian.org|ITP/RFP]] || [[http://blends.debian.org/science/bugs/chemistry.html|bugs]]|| || [[http://blends.debian.org/science/tasks/economics|sentinel]] || Economics|| || || [[http://blends.debian.org/science/bugs/economics.html|bugs]]|| || [[http://blends.debian.org/science/tasks/electronics|sentinel]] || [[DebianScience/Electronics]] || [[https://debtags.debian.org/search/?q=field::electronics|field::electronics]] || [[http://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=field..electronics;users=debian-science@lists.debian.org|ITP/RFP]] || [[http://blends.debian.org/science/bugs/electronics.html|bugs]]|| || [[http://blends.debian.org/science/tasks/engineering|sentinel]] || [[DebianScience/Engineering]] || [[https://debtags.debian.org/search/?q=field::engineering|field::engineering]] || [[http://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=field..engineering;users=debian-science@lists.debian.org|ITP/RFP]] || [[http://blends.debian.org/science/bugs/engineering.html|bugs]]|| || [[http://blends.debian.org/science/tasks/engineering-dev|sentinel]] || Engineering-dev|| || || [[http://blends.debian.org/science/bugs/engineering-dev.html|bugs]]|| || [[http://blends.debian.org/science/tasks/geography|sentinel]] || [[DebianScience/Geography]] || [[https://debtags.debian.org/search/?q=field::geography|field::geography]] || [[http://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=field..geography;users=debian-science@lists.debian.org|ITP/RFP]] || [[http://blends.debian.org/science/bugs/geography.html|bugs]]|| || [[http://blends.debian.org/science/tasks/linguistics|sentinel]] || [[DebianScience/Linguistics]] || [[https://debtags.debian.org/search/?q=field::linguistics|field::linguistics]] || [[http://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=field..linguistics;users=debian-science@lists.debian.org|ITP/RFP]] || [[http://blends.debian.org/science/bugs/linguistics.html|bugs]]|| || [[http://blends.debian.org/science/tasks/mathematics|sentinel]] || [[DebianScience/Mathematics]] || [[https://debtags.debian.org/search/?q=field::mathematics|field::mathematics]] || [[http://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=field..mathematics;users=debian-science@lists.debian.org|ITP/RFP]] || [[http://blends.debian.org/science/bugs/mathematics.html|bugs ]]|| || [[http://blends.debian.org/science/tasks/mathematics-dev|sentinel]] || [[DebianScience/MathematicsDev]] || || ||[[http://blends.debian.org/science/bugs/mathematics-dev.html|bugs]]|| || [[http://blends.debian.org/science/tasks/meteorology|sentinel]] || [[DebianScience/Meteorology]] || [[https://debtags.debian.org/search/?q=field::meteorology|field::meteorology]] || [[http://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=field..meteorology;users=debian-science@lists.debian.org|ITP/RFP]] ||[[http://blends.debian.org/science/bugs/meteorology.html|bugs]]|| || [[http://blends.debian.org/science/tasks/meteorology-dev|sentinel]] || Meteorology-dev || || ||[[http://blends.debian.org/science/bugs/meteorology-dev.html|bugs]]|| || [[http://blends.debian.org/science/tasks/nanoscale-physics|sentinel]] || [[DebianScience/NanoscalePhysics]] || [[https://debtags.debian.org/search/?q=field::physics|field::physics]] || [[http://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=field..nanoscale-physics;users=debian-science@lists.debian.org|ITP/RFP]] || [[http://blends.debian.org/science/bugs/nanoscale-physics.html|bugs]]|| || [[http://blends.debian.org/science/tasks/nanoscale-physics-dev|sentinel]] || [[DebianScience/NanoscalePhysicsDev]] || [[https://debtags.debian.org/search/?q=field::physics|field::physics]] || [[http://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=field..nanoscale-physics-dev;users=debian-science@lists.debian.org|ITP/RFP]] || [[http://blends.debian.org/science/bugs/nanoscale-physics-dev.html|bugs]]|| || [[http://blends.debian.org/science/tasks/physics|sentinel]] || [[DebianScience/Physics]] || [[https://debtags.debian.org/search/?q=field::physics|field::physics]] || [[http://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=field..physics;users=debian-science@lists.debian.org|ITP/RFP]] || [[http://blends.debian.org/science/bugs/physics.html|bugs]]|| || [[http://blends.debian.org/science/tasks/robotics|sentinel]] || [[DebianRobot]] || || [[http://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=field..robotics;users=debian-science@lists.debian.org|ITP/RFP]] || [[http://blends.debian.org/science/bugs/robotics.html|bugs]] || || [[http://blends.debian.org/science/tasks/statistics|sentinel]] || [[DebianScience/Statistics]] || [[https://debtags.debian.org/search/?q=field::statistics|field::statistics]] || [[http://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=field..statistics;users=debian-science@lists.debian.org|ITP/RFP]] || [[http://blends.debian.org/science/bugs/statistics.html|bugs]] || || [[http://blends.debian.org/science/tasks/typesetting|sentinel]] || [[DebianScience/Typesetting]] || [[https://debtags.debian.org/search/?q=use::typesetting|use::typesetting]] || [[http://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=use..typesetting;users=debian-science@lists.debian.org|ITP/RFP]] || [[http://blends.debian.org/science/bugs/typesetting.html|bugs]] || || [[http://blends.debian.org/science/tasks/viewing|sentinel]] || [[DebianScience/Viewing]] || [[https://debtags.debian.org/search/?q=use::viewing|use::viewing]] || [[http://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=use..viewing;users=debian-science@lists.debian.org|ITP/RFP]] || [[http://blends.debian.org/science/bugs/viewing.html|bugs]]|| || [[http://blends.debian.org/science/tasks/dataacquisition|sentinel]] || DebianScience/DataAcquisition || || || [[http://blends.debian.org/science/bugs/dataacquisition.html|bugs]] || || [[http://blends.debian.org/science/tasks/dataacquisition-dev|sentinel]] || DebianScience/DataAcquisitionDev || || || [[http://blends.debian.org/science/bugs/dataacquisition-dev.html|bugs]] || || [[http://blends.debian.org/science/tasks/imageanalysis|sentinel]] || Image Analysis || || || [[http://blends.debian.org/science/bugs/imageanalysis.html|bugs]] || || [[http://blends.debian.org/science/tasks/numericalcomputation|sentinel]] || Numerical Computation || || || [[http://blends.debian.org/science/bugs/numericalcomputation.html|bugs]] || || || [[DebianScience/Grid]] || || || || || [[http://blends.debian.org/science/tasks/logic|sentinel]] || [[DebianScience/Logic]] || || || || |
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== Outside links related to science or scientific projects == * DebianScienceOtherLinks |
[1] [[http://debtags.debian.org/|Debtags]] are a means of classifying packages. |
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[2] RFP/ITP - Request for package / Intent to package - these are pseudo bugs that track which packages have been requested and whether someone is working on them. [3] The list of bugs is a work in progress. It is not yet regenerated automatically, so may be out of date. [4] The debian-science QA page at http://qa.debian.org/developer.php?login=debian-science-maintainers@lists.alioth.debian.org&ordering=3 provides additional information. === How to join === * Debian Science has a mailing list [[http://lists.debian.org/debian-science/|debian-science]]. This mailing list should be used for general questions. 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|read this]]. * The packaging team has also [[https://alioth.debian.org/mail/?group_id=100159|two mailing lists]] available on Alioth: debian-science-maintainers for general packaging discussions & debian-science-commits for commit notifications. == Contributing to Debian Science == General advice for helping Debian is available at [[http://www.debian.org/intro/help]] in addition to the DebianScience specific suggestions below. * If you are willing to help: DebianScience/ContributingToDebianScience & [[https://science-team.pages.debian.net/policy/|Debian Science Policy]] Don't let the fact that you aren't a Debian Developer put you off - there are still lots of useful things you can do to improve the scientific software in Debian. A list of [[#efforts]] being undertaken is below. === How Non-Debian Developers can help === * Propose new scientific packages to sponsor. * Test the software and provide informative bug reports. See http://www.chiark.greenend.org.uk/~sgtatham/bugs.html for one view on how to report bugs effectively * Sometimes bugs are difficult to reproduce - you can help by reproducing them and providing test cases. * Send patches that fix bugs to the bug tracking system. * Translations * Add debtags to classify packages. See [[http://debtags.debian.org/]] === How Debian Developers can help === * NMU bug fixes. * Sponsor package uploads. * Package useful software. * Encourage upstream authors to release their software with a free license. DebianScienceSampleLetter may be useful for this. == Resources == * DebianEdu - a Debian project to make the best distribution for educational purposes. * DebianMed - The Debian Med project presents packages that are associated with medicine, pre-clinical research, and life science. Its developments are mostly focused on three areas for the moment: medical practice, imaging and bioinformatics. * DebianGis - Geographic Information Systems (GIS) * DebianAstro - Astronomy related packages * Inside Debian: DebianScience/DebianLinks * Outside resources related to science or scientific projects: DebianScience/OtherLinks * [[Teams/DebianScience]] * DebianScience/ConferenceTools * DebianScience/DataFormats * [[DebianScience/Hardware]] * [[DebianScience/Programming]] * DebianSciencePsychology <<Anchor(efforts)>> |
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* ["DebianScienceCDD"] * ["DebianScienceLiveCD"] * DebianScienceClassification |
* [[DebianScience/Blend]] - There have been efforts to create a Debian Pure Blend for Debian/Science; at the moment no installer is available. * [[DebianScience/Debsci]] - Add autopkgtest to enhance debian-science package QA. * [[DebianScience/LiveCD]] * [[DebianScience/Classification]] * [[DebianScience/Sage]] - Packaging the computer algebra system Sage * [[DebianScience/Sponsoring]] * DebianScience/UnofficialRepository * [[DebianScience/Usertags]] * [[DebianScience/Wallpapers]] * [[DebianScience/References]] - Provide bibliographic references to the software and data we ship. |
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== Thematic links == * DebianScienceBiology * DebianScienceChemistry * DebianScienceConferenceTools * DebianScienceDataPlotting * DebianScienceElectronics * DebianScienceMathematics * DebianSciencePhysics * DebianScienceProgramming * DebianSciencePublishing * DebianScienceTips |
== Related links in this wiki == <<PageList(regex:case:^DebianScience.*$)>> |
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(many still missing) == Unfilled needs == * [http://lists.debian.org/debian-science/2005/08/msg00002.html good free software to work with tomographic datasets] == 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 * 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:Self:NorduGrid]) * ["Boinc"] (see also {alioth:pkg-boinc}) * MPI / PVM * Statistics * [http://www.r-project.org R] * Maple/Octave * A community side of things * This wiki page * Debian at large * Others * This |
---- ## This page is referenced from http://www.debian.org/News/2011/20110205a CategoryPermalink |
Goals
- Provide researchers and scientists a better experience using Debian.
- Classify, package and distribute free software useful to science and research.
- Support any quality efforts around free scientific software.
- Manage the efforts dealing with various implementations (MPI, BLAS, LAPACK...).
Maintaining the Debian Science Blend
How to use it?
- You can use Debian Science just as you are using Debian because it is a completely internal project and is nothing other than Debian itself. We felt a need to found a team that works as a strike force for scientific software inside Debian.
#metapackages provide an easy way of installing a range of software appropriate to your particular field.
Related Blends
metapackages
The aim of the Debian Science metapackages is to provide a useful set of packages for someone working in a specific field of science.
sentinel |
Wiki |
debtag [1] |
ITP/RFP [2] |
Bugs [3,4] |
Economics |
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Engineering-dev |
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?DebianScience/MathematicsDev |
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Meteorology-dev |
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?DebianScience/NanoscalePhysicsDev |
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?DebianScience/DataAcquisitionDev |
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Image Analysis |
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Numerical Computation |
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[1] Debtags are a means of classifying packages.
[2] RFP/ITP - Request for package / Intent to package - these are pseudo bugs that track which packages have been requested and whether someone is working on them.
[3] The list of bugs is a work in progress. It is not yet regenerated automatically, so may be out of date.
[4] The debian-science QA page at http://qa.debian.org/developer.php?login=debian-science-maintainers@lists.alioth.debian.org&ordering=3 provides additional information.
How to join
Debian Science has a mailing list debian-science. This mailing list should be used for general questions. If you wonder why the mailing-list reply-to is set to the author instead of the list itself, read this.
The packaging team has also two mailing lists available on Alioth: debian-science-maintainers for general packaging discussions & debian-science-commits for commit notifications.
Contributing to Debian Science
General advice for helping Debian is available at http://www.debian.org/intro/help in addition to the DebianScience specific suggestions below.
* If you are willing to help: DebianScience/ContributingToDebianScience & Debian Science Policy
Don't let the fact that you aren't a Debian Developer put you off - there are still lots of useful things you can do to improve the scientific software in Debian. A list of #efforts being undertaken is below.
How Non-Debian Developers can help
- Propose new scientific packages to sponsor.
Test the software and provide informative bug reports. See http://www.chiark.greenend.org.uk/~sgtatham/bugs.html for one view on how to report bugs effectively
- Sometimes bugs are difficult to reproduce - you can help by reproducing them and providing test cases.
- Send patches that fix bugs to the bug tracking system.
- Translations
Add debtags to classify packages. See http://debtags.debian.org/
How Debian Developers can help
- NMU bug fixes.
- Sponsor package uploads.
- Package useful software.
Encourage upstream authors to release their software with a free license. DebianScienceSampleLetter may be useful for this.
Resources
DebianEdu - a Debian project to make the best distribution for educational purposes.
DebianMed - The Debian Med project presents packages that are associated with medicine, pre-clinical research, and life science. Its developments are mostly focused on three areas for the moment: medical practice, imaging and bioinformatics.
DebianGis - Geographic Information Systems (GIS)
DebianAstro - Astronomy related packages
Inside Debian: DebianScience/DebianLinks
Outside resources related to science or scientific projects: DebianScience/OtherLinks
Efforts that could be undertaken
DebianScience/Blend - There have been efforts to create a Debian Pure Blend for Debian/Science; at the moment no installer is available.
?DebianScience/Debsci - Add autopkgtest to enhance debian-science package QA.
DebianScience/Sage - Packaging the computer algebra system Sage
DebianScience/References - Provide bibliographic references to the software and data we ship.
Related links in this wiki
- DebianScience
- DebianScience/Astronomy
- DebianScience/Biology
- DebianScience/Bits
- DebianScience/Blend
- DebianScience/CDD
- DebianScience/Chemistry
- DebianScience/Citations
- DebianScience/Classification
- DebianScience/ComputerAlgebraSystems
- DebianScience/ConferenceTools
- DebianScience/ContributingToDebianScience
- DebianScience/DataAcquisition
- DebianScience/DataFormats
- DebianScience/Debci
- DebianScience/DebianLinks
- DebianScience/Electronics
- DebianScience/Engineering
- DebianScience/Geant4
- DebianScience/Geography
- DebianScience/Grid
- DebianScience/Hardware
- DebianScience/LinearAlgebraLibraries
- DebianScience/LiveCD
- DebianScience/Logic
- DebianScience/Mathematics
- DebianScience/Meetings
- DebianScience/Meteorology
- DebianScience/MxCuBE
- DebianScience/NanoscalePhysics
- DebianScience/News/Draft
- DebianScience/OtherLinks
- DebianScience/Physics
- DebianScience/ProblemsToWorkOn
- DebianScience/ProblemsToWorkOn/DebTags
- DebianScience/Programming
- DebianScience/R
- DebianScience/ROOT
- DebianScience/ROOT (root-system-build.sh)
- DebianScience/ROOT (root-system-changes.sh)
- DebianScience/References
- DebianScience/Robotics
- DebianScience/Robotics/ROS
- DebianScience/Robotics/ROS (jade-debian-desktop-full-missing-packages.rosinstall)
- DebianScience/Robotics/ROS (jade-debian-desktop-full-missing-packages_20160216.rosinstall)
- DebianScience/Robotics/ROS/DebianPackages
- DebianScience/Robotics/ROS/DebianRoboticsPackages
- DebianScience/Robotics/ROS/Development
- DebianScience/Robotics/ROS/Motivation
- DebianScience/Robotics/ROS/OnBuster
- DebianScience/Robotics/ROS/OnBuster (kinetic_debian_moveit.rosinstall)
- DebianScience/Robotics/ROS/Packages
- DebianScience/Robotics/ROS/Packages (ros-order.sh)
- DebianScience/Robotics/ROS/Todo
- DebianScience/Robotics/ROS2
- DebianScience/Robotics/ROS2/Packages
- DebianScience/Robotics/ROS2/Packages (ros2-order.sh)
- DebianScience/Sage
- DebianScience/Sponsoring
- DebianScience/Statistics
- DebianScience/Typesetting
- DebianScience/UnofficialRepository
- DebianScience/UpstreamAuthorsContactingQA
- DebianScience/Usertags
- DebianScience/Viewing
- DebianScience/Wallpapers
- DebianScience/cctbx
- DebianScience/cctbx (cctbx-depends.png)
- DebianScience/cctbx (libtbx_config_to_dot.py)
- DebianScienceFftw
- DebianScienceFortran
- DebianScienceGRASS
- DebianScienceGSL
- DebianScienceGnuplot
- DebianScienceGshhsMaps
- DebianScienceMaxima
- DebianScienceMetPython3
- DebianScienceOctave
- DebianSciencePkgConfig
- DebianSciencePolicy
- DebianSciencePsychology
- DebianScienceSampleLetter
- DebianScienceTips
- DebianScienceVisitPackaging