Revision as of 20:29, 13 September 2013

This page contains information on open source projects in different scientific/technology disciplines.

Instructions

Please add information and testimonials wherever you see fit. If a discipline is missing, please add it.

Please format disciplines in the following way:

Name of Discipline
- Recommended
  - OSS that is commonly used within the discipline, that an undergraduate reasonably might know about.
  - There can be multiple projects!
  - Make sure to include a URL to project website, and if possible a brief description of the software.
- Other
  - This are projects that are less well known or highly specific, but still active and interesting.
  - There can be multiple projects!
- Testimonials
  - A testimonial should be a brief statement of how using/contributing to an OSS project in your discipline improved your work/career!
  - Feel free to include your name & bibliographical info/url, if you want, or leave it anonymous
- Resources
  - Links to places to find more info.

General resources for finding additional projects:

Astronomy
- Recommended
  - Java Mission-planning and Analysis for Remote Sensing (JMARS)
- Other
- Testimonials
- Resources:
  - Wikipedia Article

Biology
- Recommended
  - BioPython - a set of tools for biological computation written in Python
  - BioPerl
  - ImageJ
- Other
  - R - a programming language for statistical analysis
- Testimonials
- Resources

Biochemistry
- Recommended
  - BioPython - a set of tools for biological computation written in Python
  - BioPerl
  - OpenBabel - allows anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas
  - ImageJ
- Other
  - R - a programming language for statistical analysis
- Testimonials
- Resources

Chemistry
- Recommended
  - OpenBabel - allows anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas
- Other
- Testimonials
- Resources:
  - Wikipedia article

Economics
- Recommended
  - R - a programming language for statistical analysis
- Other
- Testimonials
- Resources:

Geosciences
- Recommended
  - GeoForge
- Other
- Testimonials
- Resources:
  - Wikipedia article

Mathematics
- Recommended
  - Sage Math - a popular software system combining many projects into a common Python-based interface
  - GAP - a system for computational discrete algebra
  - CoCoA - a system for computations in commutative algebra
- Other
- Testimonials
- Resources

Neuroscience
- Recommended
  - R - a programming language for statistical analysis
  - NeuroDebian
- Other
  - Backyard Brains
- Testimonials
- Resources:
  - List of tools
  - another list of tools

Physics
- Recommended
  - R - a programming language for statistical analysis
  - Octave
  - Sage Math
- Other
- Testimonials
- Resources:
  - Wikipedia Article

Political science
- Recommended
  - | Civic Commons - a website for sharing government tools
- Other
  - Coding Analysis Toolkit (CAT) - a suite of tools for analysis of text datasets
  - R - a programming language for statistical analysis
- Testimonials
- Resources
  - A number of | these government/civic projects might be applicable, though there are some proprietary projects mized in. The site itself is an open source project.

Psychology
- Recommended:
  - PsychoPy
  - R - a programming language for statistical analysis
  - Octave
- Other
- Testimonials
- Resources:
  - List of tools

Statistics
- Recommended
  - R - a programming language for statistical analysis
  - NumPy
  - SciPy
- Other
- Testimonials
- Resources:
  - Wikipedia article

Aeronautics and astronautics
- Recommended
  - SunPy, a solar physics library actively maintained by NASA GSFC.
- Other
  - MakerPlane, a project for building personal planes (article)
- Testimonials
- Resources:
  - Portland State (open source) Aerospace Society: http://psas.pdx.edu/
  - NASA Open Source list at code.nasa.gov

Atmospheric sciences
- Recommended
  - CMAQ - EPA's development project: a suite of programs for conducting air quality model simulations
  - GEMPAK - soon to be replaced with AWIPS II - a weather forecasting, display and analysis package, lead developer: National Weather Service
- Other
  - OpenMadrigal - a database for accessing/archiving geospace data (does geospace == atmospheric science?)
- Testimonials
- Resources
  - MIT's Haystack has some open projects
  - OpenRadar has radio-related oss projects
  - UCAR list

Biomedical Engineering
- Recommended
  - BioSig - an open source software library for biomedical signal processing of biosignals such as EEG, ECoG, ECG, EOG and EMG
  - OpenSim - tool for modeling and simulation of movement
- Other
- Testimonials
- Resources

Linguistics
- Recommended
  - Python Natural Language Toolkit
- Other
  - Joshua Machine Translation Toolkit
  - Kura, a multi-user open source linguistic database
  - Apertium open source machine translation
- Testimonials
- Resources:
  - LINGUIST email discussion list and software index
  - List of open source statistical NLP tools
  - Sourceforge.net list of language-related software

Materials science
- Recommended
  - ESPRESSO - a software package for performing and analyzing simulations of “coarse-grained” models as used in soft-matter research

Nuclear Engineering
- Recommended
- Other
- Testimonials
- Resources
  - Article on OSS responses to Fukushima

@@ Line 205: / Line 205: @@
 ** Testimonials
 ** 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]