Difference between revisions of "Software"
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This page contains useful information about research software used in the lab.
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== General ==
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* [https://git-scm.com/ Git] (free) - version control software and [[Media:Canada-git-presentation_Dmytro.pdf | Dmytro's tutorial]]
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== General useful software ==
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* [http://www.ghisler.com/ Total Commander] (free) - file manager
 
* [http://www.ghisler.com/ Total Commander] (free) - file manager
 
* [https://winscp.net/eng/index.php WinSCP] (free) - file transfer tool
 
* [https://winscp.net/eng/index.php WinSCP] (free) - file transfer tool
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* [https://www.mendeley.com/ Mendeley reference manager] (AVOID! Use Zotero instead!!!) - manage references & automatic bibliography generator for MSWord, LibreOffice and BibTeX
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* [https://www.zotero.org/ Zotero] (free) article and biography manager for Word, LibreOffice, and Google Docs. [https://gdalle.github.io/phd-resources/tutorials/zotero/?s=03 Here is a tutorial to get started...]
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* [http://www.seamonkey-project.org/ SeaMonkey] (free) - internet application suite including web editor
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* [https://pandoc.org/ Pandoc] (free) - the ultimate document converter (supporting all kinds of formats, including LaTeX, Markdown, DocX, etc)
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* [https://miro.com/ Brainstorming virtual whiteboard] (free)
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* [https://marktext.app/ Mark Text desktop Markdown editor] (free)
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== Online teaching / collaborations / broadcasting ==
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* [https://obsproject.com/ Open Broadcaster Software] (free) for recording / editing / creating videos and live streaming
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* [https://meet.jit.si/ Jitsi] (free) secure fully featured video conferencing
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* [https://zoom.us/ Zoom] video communications platform
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* [https://lifehacker.com/the-best-alternatives-to-zoom-for-remote-meetings-1842431075 Article about Zoom alternatives...]
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* [https://whereby.com/ Whereby] - free basic version for video meetings
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== Text Editors ==
 
* [http://www.texniccenter.org/ TeXnicCenter] (free) - LateX editor
 
* [http://www.texniccenter.org/ TeXnicCenter] (free) - LateX editor
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* [https://www.mendeley.com/ Mendeley reference manager] (free) - manage references & automatic bibliography generator for MSWord, LibreOffice and BibTeX
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* [https://www.lyx.org/ LyX] (free) - graphical document processing interface using LaTeX
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* [http://www.seamonkey-project.org/ Seamonkey] (free) - internet application suite including web editor
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* [https://atom.io/ Atom] - Customizable text editor by GitHub. Allows for real-time collaboration (!) and has not-too-clumsy Git integration.
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* [http://spacemacs.org/ Spacemacs] - A distribution of Emacs, at the deep end of customizable text editors. Emacs has many "modes"; the most useful is probably [https://orgmode.org/ Org mode], which is a kind of outliner+agenda that can be used to rapidly create LaTeX/Beamer files, and for [https://hal.archives-ouvertes.fr/hal-00591455 literate programming] (think Jupyter), among [http://ehneilsen.net/notebook/orgExamples/org-examples.html other uses]. Compared to plain Emacs, Spacemacs starts with a better configuration that is more modular and easier to customize, and allows for the (optional) use of Vim keybindings.
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* [https://typora.io/ Typora] (free) - an awesome minimalist MarkDown editor
  
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== Vector graphics ==
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== Imaging Analysis ==
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* [http://www.fil.ion.ucl.ac.uk/spm/ SPM] (free) - general purpose (fMRI oriented)
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* [http://www.lcs.poli.usp.br/~baccala/pdc/CRCBrainConnectivity/AsympPDC/ PDC] (free) - partially directed coherence analysis
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* [http://www.fieldtriptoolbox.org/ FieldTrip] (free) - general purpose (EEG/MEG oriented)
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* [http://cheynelab.utoronto.ca/brainwave Brainwave] (free) and [http://cheynelab.utoronto.ca/httpdoc/Brainwave_v3.1_Documentation_6October_2015_final.pdf documentation] - MEG analysis toolbox
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* [http://brainvis.wustl.edu/wiki/index.php/Caret:Download CARET] (free) - anatomical reconstruction toolkit for structural and anatomical data ([http://prefrontal.org/blog/2009/04/using-caret-for-fmri-visualization/ simple tutorial])
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* [http://neurosynth.org/ Atlas for identifying brain regions / function] based on fMRI meta-analyses
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== Machine Learning ==
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* [http://www.cs.ubc.ca/~murphyk/Software/Kalman/kalman.html Kevin Murphy's Kalman filter toolbox] (free)
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*[http://www.csie.ntu.edu.tw/~cjlin/libsvm/oldfiles/index-1.0.html libSVM] - Support Vector Machine Library
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*[https://github.com/merwan/ml-class Andrew Ng's ML Programming Exercises]
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== (Vector) Graphics ==
 
* [http://www.coreldraw.com/ca/ CorelDraw] - ask Gunnar for installation CD
 
* [http://www.coreldraw.com/ca/ CorelDraw] - ask Gunnar for installation CD
 
* [https://inkscape.org/en/ Inkscape] (free)
 
* [https://inkscape.org/en/ Inkscape] (free)
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* [https://biorender.com/ BioRender] (free) graphics for life sciences
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* [http://betterposters.blogspot.com/ Better Posters] blog with lots of great tips!
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* [https://scidraw.io/ Scientific drawings] (free) premade graphics
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* [https://www.nature.com/articles/s41467-020-19160-7 Better use of color], paper with good suggestions on colors in figures
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* [https://www.photopea.com/ Photopea] - free online photo editor
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* [https://glimpse-editor.org/ Glimpse] - free image editor
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* [https://bioicons.com/ Bioicons] - another free database of scientific graphics
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* [https://bioart.niaid.nih.gov/ NIH bioart] (free)
  
 
== Statistics ==  
 
== Statistics ==  
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* [http://statcheck.io/ statcheck] - Use this to check papers for errors in statistical reporting!
 
* SPSS - general purpose
 
* SPSS - general purpose
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* [https://www.r-project.org/ R] (free) - general purpose
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* [https://www.r-project.org/ R] (free) - general purpose with [http://r4ds.had.co.nz/ great online book]!
 
* [http://psignifit.sourceforge.net/ psignifit] (free) - psychometric function fitting
 
* [http://psignifit.sourceforge.net/ psignifit] (free) - psychometric function fitting
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* [https://jasp-stats.org/ JASP] (free) is especially useful for Bayesian stats! And [https://www.youtube.com/watch?v=YIA3x6rp7cE&t=59s this is a great YouTube video] to understand Bayesian ANOVAs with JASP...
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* [https://www.jamovi.org/ jamovi] - another great open statistics program (with R integration)
  
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== Imaging analysis ==
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== Experiments ==
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* [http://www.fil.ion.ucl.ac.uk/spm/ SPM] (free) - general purpose (fMRI oriented)
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* [https://peterscarfe.com/ptbtutorials.html?s=03 Psychtoolbox Demos] by Peter Scarfe lab
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* [http://www.lcs.poli.usp.br/~baccala/pdc/CRCBrainConnectivity/AsympPDC/ PDC] (free) - partially directed coherence analysis
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* [http://www.fieldtriptoolbox.org/ FieldTrip] (free) - general purpose (EEG/MEG oriented)
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* [http://cheynelab.utoronto.ca/brainwave Brainwave] (free) and [http://cheynelab.utoronto.ca/httpdoc/Brainwave_v3.1_Documentation_6October_2015_final.pdf documentation] - MEG analysis toolbox
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* [http://brainvis.wustl.edu/wiki/index.php/Caret:Download CARET] (free) - anatomical reconstruction toolkit for structural and anatomical data
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Latest revision as of 13:30, 30 October 2024

General

Online teaching / collaborations / broadcasting

Text Editors

  • TeXnicCenter (free) - LateX editor
  • LyX (free) - graphical document processing interface using LaTeX
  • Atom - Customizable text editor by GitHub. Allows for real-time collaboration (!) and has not-too-clumsy Git integration.
  • Spacemacs - A distribution of Emacs, at the deep end of customizable text editors. Emacs has many "modes"; the most useful is probably Org mode, which is a kind of outliner+agenda that can be used to rapidly create LaTeX/Beamer files, and for literate programming (think Jupyter), among other uses. Compared to plain Emacs, Spacemacs starts with a better configuration that is more modular and easier to customize, and allows for the (optional) use of Vim keybindings.
  • Typora (free) - an awesome minimalist MarkDown editor

Imaging Analysis

Machine Learning

(Vector) Graphics

Statistics

  • statcheck - Use this to check papers for errors in statistical reporting!
  • SPSS - general purpose
  • R (free) - general purpose with great online book!
  • psignifit (free) - psychometric function fitting
  • JASP (free) is especially useful for Bayesian stats! And this is a great YouTube video to understand Bayesian ANOVAs with JASP...
  • jamovi - another great open statistics program (with R integration)

Experiments

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