Oss projects by domain: Difference between revisions

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** Projects
 
** Projects
 
*** OSS project that is used within this discipline. Make sure to leave a URL to the project website and if possible a brief description of the software.
 
*** OSS project that is used within this discipline. Make sure to leave a URL to the project website and if possible a brief description of the software.
**** Comments:
+
**** Comments & Testimonials:
 
***** This project is poorly documented.
 
***** This project is poorly documented.
 
***** This project has a really active, friendly maintainer.
 
***** This project has a really active, friendly maintainer.
 
***** "This is a testimonial about the project. It's great, I use it all the time in my research! I am totally okay with OpenHatch using my testimonial in outreach emails and similar materials." (Optional attribution - name, position, url of person leaving the testimonial.)
 
***** "This is a testimonial about the project. It's great, I use it all the time in my research! I am totally okay with OpenHatch using my testimonial in outreach emails and similar materials." (Optional attribution - name, position, url of person leaving the testimonial.)
*** Another project!
+
*** Another project
**** Comments:
+
**** Comments & Testimonials:
***** Comment!
+
***** Comment
***** Testimonial!
+
***** Testimonial
  +
*** A project previously mentioned in another discipline: please see 'name of other discipline'
 
** Resources
 
** Resources
 
*** Links to places to find more info about projects in this discipline.
 
*** Links to places to find more info about projects in this discipline.
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* Projects
 
* Projects
 
*** [http://cmascenter.org/cmaq/ CMAQ] - EPA's development project: a suite of programs for conducting air quality model simulations
 
*** [http://cmascenter.org/cmaq/ CMAQ] - EPA's development project: a suite of programs for conducting air quality model simulations
 
**** Comments & Testimonials:
 
*** [http://www.unidata.ucar.edu/software/gempak/ GEMPAK] - soon to be replaced with [http://www.unidata.ucar.edu/software/awips2/ AWIPS II] - a weather forecasting, display and analysis package, lead developer: National Weather Service
 
*** [http://www.unidata.ucar.edu/software/gempak/ GEMPAK] - soon to be replaced with [http://www.unidata.ucar.edu/software/awips2/ AWIPS II] - a weather forecasting, display and analysis package, lead developer: National Weather Service
 
**** Comments & Testimonials:
 
*** [http://www.openmadrigal.org/ OpenMadrigal] - a database for accessing/archiving geospace data (does geospace == atmospheric science?)
 
*** [http://www.openmadrigal.org/ OpenMadrigal] - a database for accessing/archiving geospace data (does geospace == atmospheric science?)
 
**** Comments & Testimonials:
 
**** Comments & Testimonials:
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* '''Astronomy'''
 
* '''Astronomy'''
** Recommended
+
** Projects
 
*** [http://jmars.asu.edu/ Java Mission-planning and Analysis for Remote Sensing (JMARS)]
 
*** [http://jmars.asu.edu/ Java Mission-planning and Analysis for Remote Sensing (JMARS)]
 
**** Comments & Testimonials:
** Other
 
** Testimonials
 
 
** Resources:
 
** Resources:
 
*** [http://en.wikipedia.org/wiki/Category:Free_astronomy_software Wikipedia Article]
 
*** [http://en.wikipedia.org/wiki/Category:Free_astronomy_software Wikipedia Article]
   
 
* '''Biochemistry'''
 
* '''Biochemistry'''
** Recommended
+
** Projects
 
*** [http://biopython.org/wiki/Main_Page BioPython] - a set of tools for biological computation written in Python
 
*** [http://biopython.org/wiki/Main_Page BioPython] - a set of tools for biological computation written in Python
 
**** Comments & Testimonials:
 
*** [http://www.bioperl.org/wiki/Main_Page BioPerl]
 
*** [http://www.bioperl.org/wiki/Main_Page BioPerl]
 
**** Comments & Testimonials:
 
*** [http://openbabel.org/wiki/Main_Page OpenBabel] - allows anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas
 
*** [http://openbabel.org/wiki/Main_Page OpenBabel] - allows anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas
 
**** Comments & Testimonials:
 
*** [http://rsbweb.nih.gov/ij/ ImageJ]
 
*** [http://rsbweb.nih.gov/ij/ ImageJ]
 
**** Comments & Testimonials:
** Other
 
 
*** [http://www.r-project.org/ R] - a programming language for statistical analysis
 
*** [http://www.r-project.org/ R] - a programming language for statistical analysis
** Testimonials
+
**** Comments & Testimonials:
 
** Resources
 
** Resources
   
 
* '''Biology'''
 
* '''Biology'''
** Recommended
+
** Projects
  +
*** BioPython (see Biochemistry)
*** [http://biopython.org/wiki/Main_Page BioPython] - a set of tools for biological computation written in Python
 
  +
*** BioPerl (see Biochemistry)
*** [http://www.bioperl.org/wiki/Main_Page BioPerl]
 
  +
*** ImageJ (see Biochemistry)
*** [http://rsbweb.nih.gov/ij/ ImageJ]
 
  +
*** R (see Biochemistry)
** Other
 
*** [http://www.r-project.org/ R] - a programming language for statistical analysis
 
** Testimonials
 
 
** Resources
 
** Resources
   
 
* '''Biomedical Engineering'''
 
* '''Biomedical Engineering'''
** Recommended
+
** Projects
 
*** [http://biosig.sourceforge.net/ BioSig] - an open source software library for biomedical signal processing of biosignals such as EEG, ECoG, ECG, EOG and EMG
 
*** [http://biosig.sourceforge.net/ BioSig] - an open source software library for biomedical signal processing of biosignals such as EEG, ECoG, ECG, EOG and EMG
 
**** Comments & Testimonials:
 
*** [http://opensim.stanford.edu/work/index.html OpenSim] - tool for modeling and simulation of movement
 
*** [http://opensim.stanford.edu/work/index.html OpenSim] - tool for modeling and simulation of movement
 
**** Comments & Testimonials:
** Other
 
** Testimonials
 
 
** Resources
 
** Resources
   
 
* '''Chemistry'''
 
* '''Chemistry'''
** Recommended
+
** Projects
  +
*** OpenBabel (see Biochemistry)
*** [http://openbabel.org/wiki/Main_Page OpenBabel] - allows anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas
 
** Other
 
** Testimonials
 
 
** Resources:
 
** Resources:
 
*** [http://en.wikipedia.org/wiki/Category:Free_chemistry_software Wikipedia article]
 
*** [http://en.wikipedia.org/wiki/Category:Free_chemistry_software Wikipedia article]
   
 
* '''Economics'''
 
* '''Economics'''
** Recommended
+
** Projects
  +
*** R (see Biochemistry)
*** [http://www.r-project.org/ R] - a programming language for statistical analysis
 
** Other
 
** Testimonials
 
 
** Resources:
 
** Resources:
   
 
* '''Geosciences'''
 
* '''Geosciences'''
** Recommended
+
** Projects
 
*** [https://code.google.com/p/geoforge/ GeoForge]
 
*** [https://code.google.com/p/geoforge/ GeoForge]
 
**** Comments & Testimonials:
** Other
 
** Testimonials
 
 
** Resources:
 
** Resources:
 
*** [http://en.wikipedia.org/wiki/List_of_free_geology_software Wikipedia article]
 
*** [http://en.wikipedia.org/wiki/List_of_free_geology_software Wikipedia article]
   
 
* '''Linguistics'''
 
* '''Linguistics'''
** Recommended
+
** Projects
 
*** [http://nltk.org/ Python Natural Language Toolkit]
 
*** [http://nltk.org/ Python Natural Language Toolkit]
 
**** Comments & Testimonials:
** Other
 
 
*** [https://github.com/joshua-decoder/joshua Joshua Machine Translation Toolkit]
 
*** [https://github.com/joshua-decoder/joshua Joshua Machine Translation Toolkit]
 
**** Comments & Testimonials:
 
*** [http://www.kura.ats.lmu.de/index.php Kura], a multi-user open source linguistic database
 
*** [http://www.kura.ats.lmu.de/index.php Kura], a multi-user open source linguistic database
  +
**** Comments & Testimonials:
 
*** [http://www.apertium.org/ Apertium] open source machine translation
 
*** [http://www.apertium.org/ Apertium] open source machine translation
** Testimonials
+
**** Comments & Testimonials:
 
** Resources:
 
** Resources:
 
*** [http://linguistlist.org/ LINGUIST] email discussion list and software index
 
*** [http://linguistlist.org/ LINGUIST] email discussion list and software index
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* '''Materials science'''
 
* '''Materials science'''
** Recommended
+
** Projects
 
*** [http://espressomd.org/wordpress/about/summary/ ESPRESSO] - a software package for performing and analyzing simulations of “coarse-grained” models as used in soft-matter research
 
*** [http://espressomd.org/wordpress/about/summary/ ESPRESSO] - a software package for performing and analyzing simulations of “coarse-grained” models as used in soft-matter research
  +
**** Comments & Testimonials:
** Other
 
** Testimonials
 
 
** Resources
 
** Resources
 
*** [http://www.tms.org/pubs/journals/jom/0805/powell-0805.html 2008 discussion of open source in materials science]
 
*** [http://www.tms.org/pubs/journals/jom/0805/powell-0805.html 2008 discussion of open source in materials science]
   
 
* '''Mathematics'''
 
* '''Mathematics'''
** Recommended
+
** Projects
 
*** [http://www.sagemath.org/ Sage Math] - a popular software system combining many projects into a common Python-based interface
 
*** [http://www.sagemath.org/ Sage Math] - a popular software system combining many projects into a common Python-based interface
  +
**** Comments & Testimonials:
 
*** [http://www.gap-system.org/ GAP] - a system for computational discrete algebra
 
*** [http://www.gap-system.org/ GAP] - a system for computational discrete algebra
  +
**** Comments & Testimonials:
 
*** [http://cocoa.dima.unige.it/ CoCoA] - a system for computations in commutative algebra
 
*** [http://cocoa.dima.unige.it/ CoCoA] - a system for computations in commutative algebra
  +
**** Comments & Testimonials:
** Other
 
** Testimonials
 
 
** Resources
 
** Resources
 
*** [http://en.wikipedia.org/wiki/Category:Free_mathematics_software Wikipedia article]
 
*** [http://en.wikipedia.org/wiki/Category:Free_mathematics_software Wikipedia article]
Line 141: Line 141:
   
 
* '''Neuroscience'''
 
* '''Neuroscience'''
** Recommended
+
** Projects
*** [http://www.r-project.org/ R] - a programming language for statistical analysis
 
 
*** [http://neuro.debian.net/ NeuroDebian]
 
*** [http://neuro.debian.net/ NeuroDebian]
  +
**** Comments & Testimonials:
 
*** [http://www.fil.ion.ucl.ac.uk/spm/software/ SPM] - software for doing statistical parametric mapping analysis
 
*** [http://www.fil.ion.ucl.ac.uk/spm/software/ SPM] - software for doing statistical parametric mapping analysis
  +
**** Comments & Testimonials:
 
*** [http://www.gnu.org/software/octave/ Octave]
 
*** [http://www.gnu.org/software/octave/ Octave]
  +
**** Comments & Testimonials:
*** [http://biosig.sourceforge.net/ BioSig] - an open source software library for biomedical signal processing of biosignals such as EEG, ECoG, ECG, EOG and EMG
 
** Other
 
 
*** [https://github.com/BackyardBrains/Backyard-Brains-Android-App#readme Backyard Brains]
 
*** [https://github.com/BackyardBrains/Backyard-Brains-Android-App#readme Backyard Brains]
  +
**** Comments & Testimonials:
 
*** [http://www.psychopy.org/ PsychoPy] - a set of tools for doing stimulus presentation and capturing behavioral data
 
*** [http://www.psychopy.org/ PsychoPy] - a set of tools for doing stimulus presentation and capturing behavioral data
** Testimonials
+
**** Comments & Testimonials:
  +
***** Very friendly, active maintainers but difficult setup process, especially for Windows.
  +
*** R (see Biochemistry)
  +
*** BioSig (see Biomedical Engineering)
 
** Resources:
 
** Resources:
 
*** [http://opensourcecognitivescience.wordpress.com/2009/07/29/tools-for-psychology-and-neuroscience/ List of tools]
 
*** [http://opensourcecognitivescience.wordpress.com/2009/07/29/tools-for-psychology-and-neuroscience/ List of tools]
Line 156: Line 160:
   
 
* '''Nuclear Engineering'''
 
* '''Nuclear Engineering'''
** Recommended
+
** Projects
 
*** [http://lammps.sandia.gov/ LAMMPS] - a molecular dynamics library that can be used to model parallel atomic/subatomic processes at large scale, lead by Sandia National Laboratories
 
*** [http://lammps.sandia.gov/ LAMMPS] - a molecular dynamics library that can be used to model parallel atomic/subatomic processes at large scale, lead by Sandia National Laboratories
  +
**** Comments & Testimonials:
** Other
 
 
*** [http://code.google.com/p/open-geiger-development-kit/ OpenGeiger] - an open source, open hardware Geiger Counter
 
*** [http://code.google.com/p/open-geiger-development-kit/ OpenGeiger] - an open source, open hardware Geiger Counter
** Testimonials
+
**** Comments & Testimonials:
 
** Resources
 
** Resources
 
*** [http://fukushimaforum.wordpress.com/workshops/sts-forum-on-the-2011-fukushima-east-japan-disaster/manuscripts/session-3-radiation-information-and-control/new-expert-eyes-over-fukushima-open-source-responses-to-the-nuclear-crisis-in-japan/ Article on OSS responses to Fukushima]
 
*** [http://fukushimaforum.wordpress.com/workshops/sts-forum-on-the-2011-fukushima-east-japan-disaster/manuscripts/session-3-radiation-information-and-control/new-expert-eyes-over-fukushima-open-source-responses-to-the-nuclear-crisis-in-japan/ Article on OSS responses to Fukushima]
   
 
* '''Physics'''
 
* '''Physics'''
** Recommended
+
** Projects
  +
*** R (see Biochemistry)
*** [http://www.r-project.org/ R] - a programming language for statistical analysis
 
  +
*** Octave (see Neuroscience)
*** [http://www.gnu.org/software/octave/ Octave]
 
*** [http://www.sagemath.org/ Sage Math]
+
*** Sage Math (see Physics)
** Other
 
** Testimonials
 
 
** Resources:
 
** Resources:
 
*** [http://en.wikipedia.org/wiki/Category:Free_physics_software Wikipedia Article]
 
*** [http://en.wikipedia.org/wiki/Category:Free_physics_software Wikipedia Article]
   
 
* '''Political science'''
 
* '''Political science'''
** Recommended
+
** Projects
*** [http://commons.codeforamerica.org/apps | Civic Commons] - a website for sharing government tools
 
** Other
 
 
*** [http://cat.ucsur.pitt.edu/ Coding Analysis Toolkit (CAT)] - a suite of tools for analysis of text datasets
 
*** [http://cat.ucsur.pitt.edu/ Coding Analysis Toolkit (CAT)] - a suite of tools for analysis of text datasets
  +
**** Comments & Testimonials:
*** [http://www.r-project.org/ R] - a programming language for statistical analysis
 
 
*** [http://commons.codeforamerica.org/apps | Civic Commons] - a website for sharing government tools
** Testimonials
 
  +
**** Comments & Testimonials:
  +
***** Seems to be abandoned by its maintainers.
  +
*** R (see Biochemistry)
 
** Resources
 
** Resources
*** A number of [http://commons.codeforamerica.org/apps | these government/civic projects] might be applicable, though there are some proprietary projects mized in. The site itself is an open source project.
+
*** A number of [http://commons.codeforamerica.org/apps | these government/civic projects] might be applicable, though there are some proprietary projects mixed in. The site itself is an open source project, though an abandoned one.
   
 
* '''Psychology'''
 
* '''Psychology'''
  +
** Projects
** Recommended:
 
  +
*** BioSig (see Biomedical Engineering)
*** [http://www.psychopy.org/ PsychoPy] - a set of tools for doing stimulus presentation and capturing behavioral data
 
  +
*** PsychoPy (see Neuroscience)
*** [http://www.r-project.org/ R] - a programming language for statistical analysis
 
  +
*** R (see Biochemistry)
** Other
 
*** [http://biosig.sourceforge.net/ BioSig] - an open source software library for biomedical signal processing of biosignals such as EEG, ECoG, ECG, EOG and EMG
 
** Testimonials
 
 
** Resources:
 
** Resources:
 
*** [http://opensourcecognitivescience.wordpress.com/2009/07/29/tools-for-psychology-and-neuroscience/ List of tools]
 
*** [http://opensourcecognitivescience.wordpress.com/2009/07/29/tools-for-psychology-and-neuroscience/ List of tools]
   
 
* '''Statistics'''
 
* '''Statistics'''
** Recommended
+
** Projects
*** [http://www.r-project.org/ R] - a programming language for statistical analysis
 
 
*** [http://www.numpy.org/ NumPy]
 
*** [http://www.numpy.org/ NumPy]
  +
**** Comments & Testimonials:
 
*** [http://www.scipy.org/ SciPy]
 
*** [http://www.scipy.org/ SciPy]
  +
**** Comments & Testimonials:
** Other
 
  +
*** R (see Biochemistry)
** Testimonials
 
 
** Resources:
 
** Resources:
 
*** [http://en.wikipedia.org/wiki/Category:Free_statistical_software Wikipedia article]
 
*** [http://en.wikipedia.org/wiki/Category:Free_statistical_software Wikipedia article]

Revision as of 20:52, 22 October 2013

We'd like to improve our outreach to non-CS majors in the sciences by finding open source projects in their disciplines. We plan to use this information both in our publicity and when we're looking for projects to help students contribute to. To that extent, we're asking both for short testimonials (for publicity) as well as insight on how accessible these projects are to newcomers.


Instructions

Please add information and testimonials wherever you see fit. If a discipline is missing, please add it. You can add the same project to multiple disciplines.

Please format disciplines in the following way:

  • Name of Discipline
    • Projects
      • OSS project that is used within this discipline. Make sure to leave a URL to the project website and if possible a brief description of the software.
        • Comments & Testimonials:
          • This project is poorly documented.
          • This project has a really active, friendly maintainer.
          • "This is a testimonial about the project. It's great, I use it all the time in my research! I am totally okay with OpenHatch using my testimonial in outreach emails and similar materials." (Optional attribution - name, position, url of person leaving the testimonial.)
      • Another project
        • Comments & Testimonials:
          • Comment
          • Testimonial
      • A project previously mentioned in another discipline: please see 'name of other discipline'
    • Resources
      • Links to places to find more info about projects in this discipline.

Domains/Departments

  • Aeronautics and astronautics
    • Projects
      • SunPy, a solar physics library actively maintained by NASA GSFC.
        • Comments & Testimonials:
      • MakerPlane, a project for building personal planes (article)
        • Comments & Testimonials:
    • Resources:
  • Atmospheric sciences
  • Projects
      • CMAQ - EPA's development project: a suite of programs for conducting air quality model simulations
        • Comments & Testimonials:
      • GEMPAK - soon to be replaced with AWIPS II - a weather forecasting, display and analysis package, lead developer: National Weather Service
        • Comments & Testimonials:
      • OpenMadrigal - a database for accessing/archiving geospace data (does geospace == atmospheric science?)
        • Comments & Testimonials:
    • Resources
  • Biochemistry
    • Projects
      • BioPython - a set of tools for biological computation written in Python
        • Comments & Testimonials:
      • BioPerl
        • Comments & Testimonials:
      • OpenBabel - allows anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas
        • Comments & Testimonials:
      • ImageJ
        • Comments & Testimonials:
      • R - a programming language for statistical analysis
        • Comments & Testimonials:
    • Resources
  • Biology
    • Projects
      • BioPython (see Biochemistry)
      • BioPerl (see Biochemistry)
      • ImageJ (see Biochemistry)
      • R (see Biochemistry)
    • Resources
  • Biomedical Engineering
    • Projects
      • BioSig - an open source software library for biomedical signal processing of biosignals such as EEG, ECoG, ECG, EOG and EMG
        • Comments & Testimonials:
      • OpenSim - tool for modeling and simulation of movement
        • Comments & Testimonials:
    • Resources
  • Economics
    • Projects
      • R (see Biochemistry)
    • Resources:
  • Neuroscience
    • Projects
      • NeuroDebian
        • Comments & Testimonials:
      • SPM - software for doing statistical parametric mapping analysis
        • Comments & Testimonials:
      • Octave
        • Comments & Testimonials:
      • Backyard Brains
        • Comments & Testimonials:
      • PsychoPy - a set of tools for doing stimulus presentation and capturing behavioral data
        • Comments & Testimonials:
          • Very friendly, active maintainers but difficult setup process, especially for Windows.
      • R (see Biochemistry)
      • BioSig (see Biomedical Engineering)
    • Resources:
  • Nuclear Engineering
    • Projects
      • LAMMPS - a molecular dynamics library that can be used to model parallel atomic/subatomic processes at large scale, lead by Sandia National Laboratories
        • Comments & Testimonials:
      • OpenGeiger - an open source, open hardware Geiger Counter
        • Comments & Testimonials:
    • Resources
  • Physics
    • Projects
      • R (see Biochemistry)
      • Octave (see Neuroscience)
      • Sage Math (see Physics)
    • Resources:
  • Political science
    • Projects
      • Coding Analysis Toolkit (CAT) - a suite of tools for analysis of text datasets
        • Comments & Testimonials:
      • | Civic Commons - a website for sharing government tools
        • Comments & Testimonials:
          • Seems to be abandoned by its maintainers.
      • R (see Biochemistry)
    • Resources
      • A number of | these government/civic projects might be applicable, though there are some proprietary projects mixed in. The site itself is an open source project, though an abandoned one.
  • Psychology
    • Projects
      • BioSig (see Biomedical Engineering)
      • PsychoPy (see Neuroscience)
      • R (see Biochemistry)
    • Resources: