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Line 13: 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. Line 27 ⟶ 28: * '''Aeronautics and astronautics''' ~~Recommended~~Projects * [http://www.sunpy.org/ SunPy], a solar physics library actively maintained by NASA GSFC. ** Comments & Testimonials: Other * [http://makerplane.org/ MakerPlane], a project for building personal planes ([http://opensource.com/life/13/1/open-source-aviation-makerplane article]) Comments & Testimonials: Resources: *** Portland State (open source) Aerospace Society: http://psas.pdx.edu/ Line 37 ⟶ 38: * '''Atmospheric sciences''' * Projects Recommended * [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 ** Comments & Testimonials: Other * [http://www.openmadrigal.org/ OpenMadrigal] - a database for accessing/archiving geospace data (does geospace == atmospheric science?) Comments & Testimonials: Resources * [http://www.haystack.mit.edu/atm/open/index.html MIT's Haystack] has some open projects * [http://www.openradar.org/cgi-bin/openradar.cgi/Projects OpenRadar] has radio-related oss projects *** [http://www.ucar.edu/tools/applications_desc.jsp UCAR list] * '''Astronomy''' ~~Recommended~~Projects * [http://jmars.asu.edu/ Java Mission-planning and Analysis for Remote Sensing (JMARS)] ** Comments & Testimonials: Other Testimonials Resources: *** [http://en.wikipedia.org/wiki/Category:Free_astronomy_software Wikipedia Article] * '''Biochemistry''' ~~Recommended~~Projects * [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] ** 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 ** Comments & Testimonials: * [http://rsbweb.nih.gov/ij/ ImageJ] ** Comments & Testimonials: Other * [http://www.r-project.org/ R] - a programming language for statistical analysis Comments & Testimonials: Resources * '''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 * '''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 ** Comments & Testimonials: * [http://opensim.stanford.edu/work/index.html OpenSim] - tool for modeling and simulation of movement ** Comments & Testimonials: Other Testimonials Resources * '''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: *** [http://en.wikipedia.org/wiki/Category:Free_chemistry_software Wikipedia article] * '''Economics''' ~~Recommended~~Projects * R (see Biochemistry) * [http://www.r-project.org/ R] - a programming language for statistical analysis Other Testimonials Resources: * '''Geosciences''' ~~Recommended~~Projects * [https://code.google.com/p/geoforge/ GeoForge] ** Comments & Testimonials: Other Testimonials Resources: *** [http://en.wikipedia.org/wiki/List_of_free_geology_software Wikipedia article] * '''Linguistics''' ~~Recommended~~Projects * [http://nltk.org/ Python Natural Language Toolkit] ** Comments & Testimonials: Other * [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 ** Comments & Testimonials: * [http://www.apertium.org/ Apertium] open source machine translation ** Comments & Testimonials: * [http://www.fon.hum.uva.nl/praat/ Praat] open source tool used to annotate speech / phonetics ** Comments & Testimonials: * [http://textblob.readthedocs.org/en/dev/ TextBlob] Natural Language Processing tool ** Comments & Testimonials: * [http://clic.cimec.unitn.it/composes/toolkit/ DISSECT] Distributional Semantics toolkit ** Comments & Testimonials: Resources: *** [http://linguistlist.org/ LINGUIST] email discussion list and software index Line 121 ⟶ 129: * '''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 ** Comments & Testimonials: Other Testimonials Resources *** [http://www.tms.org/pubs/journals/jom/0805/powell-0805.html 2008 discussion of open source in materials science] * '''Mathematics''' ~~Recommended~~Projects * [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 ** Comments & Testimonials: * [http://cocoa.dima.unige.it/ CoCoA] - a system for computations in commutative algebra ** Comments & Testimonials: Other Testimonials Resources *** [http://en.wikipedia.org/wiki/Category:Free_mathematics_software Wikipedia article] Line 141 ⟶ 149: * '''Neuroscience''' ~~Recommended~~Projects * [http://neuro.debian.net/ NeuroDebian] - a turnkey Linux distribution with major open source neuroimaging packages included * [http://www.r-project.org/ R] - a programming language for statistical analysis Comments & Testimonials: * [http://neuro.debian.net/ NeuroDebian] * [http://neurosynth.org/ Neurosynth] - an online platform to perform meta-analyses on neuroimaging studies Comments & Testimonials: * [http://afni.nimh.nih.gov/afni/ AFNI] - software for performing neuroimaging analyses maintained by the NIH ** Comments & Testimonials: * [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://~~biosig~~stnava.~~sourceforge~~github.~~net~~io/ANTs/ ~~BioSig~~ANTs] - ~~an open source~~ software ~~library~~to ~~for~~put ~~biomedical~~individual ~~signal~~fMRI ~~processing~~scans ofin ~~biosignals~~a ~~such~~common asspace ~~EEG,~~that ~~ECoG,~~can ~~ECG,~~be ~~EOG~~compared ~~and~~across ~~EMG~~subjects Comments & Testimonials: Other * [http://nipy.sourceforge.net/nipype/ Nipype] - a common Python interface to a variety of neuroimaging packages Comments & Testimonials: * [http://nipy.sourceforge.net/nibabel/ Nibabel] - a Python package to load in neuroimaging data files ** Comments & Testimonials: * [http://fcp-indi.github.io/ C-PAC] - a Python package to configure resting state fMRI analyses ** Comments & Testimonials: * [http://www.gnu.org/software/octave/ Octave] - an open source version of Matlab; many Matlabpbased neuroimaging packages could work with Octave with some extra development ** Comments & Testimonials: * [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 ** Comments & Testimonials: * Very friendly, active maintainers but difficult setup process, especially for Windows. * [https://pythonhosted.org/pyxnat/ PyXNAT] - allows Python to interface with a popular neuroimaging data management tool ** Comments & Testimonials: * [https://github.com/openworm/PyOpenWorm PyOpenWorm] - Python interface to fetch C. elegans data. ** Comments & Testimonials: * R (see Biochemistry) * BioSig (see Biomedical Engineering) Resources: *** [http://opensourcecognitivescience.wordpress.com/2009/07/29/tools-for-psychology-and-neuroscience/ List of tools] Line 156 ⟶ 184: * '''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 ** Comments & Testimonials: Other * [http://code.google.com/p/open-geiger-development-kit/ OpenGeiger] - an open source, open hardware Geiger Counter Comments & 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] * '''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] (see Physics) Other Testimonials Resources: * [http://en.wikipedia.org/wiki/Category:Free_physics_software Wikipedia Article] * '''Political science''' ~~Recommended~~Projects * [http://cat.ucsur.pitt.edu/ Coding Analysis Toolkit (CAT)] - a suite of tools for analysis of text datasets ** Comments & Testimonials: * [http://commons.codeforamerica.org/apps \| Civic Commons] - a website for sharing government tools ** Comments & Testimonials: Other *** Seems to be abandoned by its maintainers. * [http://cat.ucsur.pitt.edu/ Coding Analysis Toolkit (CAT)] - a suite of tools for analysis of text datasets * R (see Biochemistry) * [http://www.r-project.org/ R] - a programming language for statistical analysis Testimonials Resources *** A number of [http://commons.codeforamerica.org/apps \| these government/civic projects] might be applicable, though there are some proprietary projects ~~mized~~mixed in. The site itself is an open source project, though an abandoned one. * '''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: * [http://opensourcecognitivescience.wordpress.com/2009/07/29/tools-for-psychology-and-neuroscience/ List of tools] * '''Statistics''' ~~Recommended~~Projects * [http://www.r-project.org/ R] - a programming language for statistical analysis * [http://www.numpy.org/ NumPy] Comments & Testimonials: * [http://www.scipy.org/ SciPy] ** Comments & Testimonials: Other * R (see Biochemistry) Testimonials Resources: * [http://en.wikipedia.org/wiki/Category:Free_statistical_software Wikipedia article]