Difference between revisions of "Software"
(→Machine Learning) |
(→(Vector) Graphics) |
||
| (35 intermediate revisions by 3 users not shown) | |||
| Line 1: | Line 1: | ||
| − | + | == General == | |
| − | + | * [https://git-scm.com/ Git] (free) - version control software and [[Media:Canada-git-presentation_Dmytro.pdf | Dmytro's tutorial]] | |
| − | == General | + | |
* [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 | ||
| − | * [ | + | * [https://www.mendeley.com/ Mendeley reference manager] (AVOID! Use Zotero instead!!!) - manage references & automatic bibliography generator for MSWord, LibreOffice and BibTeX |
| − | * [https://www. | + | * [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...] |
* [http://www.seamonkey-project.org/ SeaMonkey] (free) - internet application suite including web editor | * [http://www.seamonkey-project.org/ SeaMonkey] (free) - internet application suite including web editor | ||
| + | * [https://pandoc.org/ Pandoc] (free) - the ultimate document converter (supporting all kinds of formats, including LaTeX, Markdown, DocX, etc) | ||
| + | * [https://miro.com/ Brainstorming virtual whiteboard] (free) | ||
| + | * [https://marktext.app/ Mark Text desktop Markdown editor] (free) | ||
| − | == | + | == Online teaching / collaborations / broadcasting == |
| − | * [ | + | * [https://obsproject.com/ Open Broadcaster Software] (free) for recording / editing / creating videos and live streaming |
| − | * [https:// | + | * [https://meet.jit.si/ Jitsi] (free) secure fully featured video conferencing |
| + | * [https://zoom.us/ Zoom] video communications platform | ||
| + | * [https://lifehacker.com/the-best-alternatives-to-zoom-for-remote-meetings-1842431075 Article about Zoom alternatives...] | ||
| + | * [https://whereby.com/ Whereby] - free basic version for video meetings | ||
| − | == | + | == Text Editors == |
| − | * | + | * [http://www.texniccenter.org/ TeXnicCenter] (free) - LateX editor |
| − | * [https://www. | + | * [https://www.lyx.org/ LyX] (free) - graphical document processing interface using LaTeX |
| − | * [http:// | + | * [https://atom.io/ Atom] - Customizable text editor by GitHub. Allows for real-time collaboration (!) and has not-too-clumsy Git integration. |
| + | * [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. | ||
| + | * [https://typora.io/ Typora] (free) - an awesome minimalist MarkDown editor | ||
| − | == Imaging | + | == Imaging Analysis == |
* [http://www.fil.ion.ucl.ac.uk/spm/ SPM] (free) - general purpose (fMRI oriented) | * [http://www.fil.ion.ucl.ac.uk/spm/ SPM] (free) - general purpose (fMRI oriented) | ||
* [http://www.lcs.poli.usp.br/~baccala/pdc/CRCBrainConnectivity/AsympPDC/ PDC] (free) - partially directed coherence analysis | * [http://www.lcs.poli.usp.br/~baccala/pdc/CRCBrainConnectivity/AsympPDC/ PDC] (free) - partially directed coherence analysis | ||
| Line 23: | Line 30: | ||
* [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 | * [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 | ||
* [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]) | * [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]) | ||
| + | * [http://neurosynth.org/ Atlas for identifying brain regions / function] based on fMRI meta-analyses | ||
== Machine Learning == | == Machine Learning == | ||
* [http://www.cs.ubc.ca/~murphyk/Software/Kalman/kalman.html Kevin Murphy's Kalman filter toolbox] (free) | * [http://www.cs.ubc.ca/~murphyk/Software/Kalman/kalman.html Kevin Murphy's Kalman filter toolbox] (free) | ||
*[http://www.csie.ntu.edu.tw/~cjlin/libsvm/oldfiles/index-1.0.html libSVM] - Support Vector Machine Library | *[http://www.csie.ntu.edu.tw/~cjlin/libsvm/oldfiles/index-1.0.html libSVM] - Support Vector Machine Library | ||
| − | *[Andrew Ng's | + | *[https://github.com/merwan/ml-class Andrew Ng's ML Programming Exercises] |
| + | |||
| + | == (Vector) Graphics == | ||
| + | * [http://www.coreldraw.com/ca/ CorelDraw] - ask Gunnar for installation CD | ||
| + | * [https://inkscape.org/en/ Inkscape] (free) | ||
| + | * [https://biorender.com/ BioRender] (free) graphics for life sciences | ||
| + | * [http://betterposters.blogspot.com/ Better Posters] blog with lots of great tips! | ||
| + | * [https://scidraw.io/ Scientific drawings] (free) premade graphics | ||
| + | * [https://www.nature.com/articles/s41467-020-19160-7 Better use of color], paper with good suggestions on colors in figures | ||
| + | * [https://www.photopea.com/ Photopea] - free online photo editor | ||
| + | * [https://glimpse-editor.org/ Glimpse] - free image editor | ||
| + | * [https://bioicons.com/ Bioicons] - another free database of scientific graphics | ||
| + | * [https://bioart.niaid.nih.gov/ NIH bioart] (free) | ||
| + | |||
| + | == Statistics == | ||
| + | * [http://statcheck.io/ statcheck] - Use this to check papers for errors in statistical reporting! | ||
| + | * SPSS - general purpose | ||
| + | * [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 | ||
| + | * [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... | ||
| + | * [https://www.jamovi.org/ jamovi] - another great open statistics program (with R integration) | ||
| + | |||
| + | == Experiments == | ||
| + | * [https://peterscarfe.com/ptbtutorials.html?s=03 Psychtoolbox Demos] by Peter Scarfe lab | ||
Latest revision as of 13:30, 30 October 2024
Contents
General
- Git (free) - version control software and Dmytro's tutorial
- Total Commander (free) - file manager
- WinSCP (free) - file transfer tool
- Mendeley reference manager (AVOID! Use Zotero instead!!!) - manage references & automatic bibliography generator for MSWord, LibreOffice and BibTeX
- Zotero (free) article and biography manager for Word, LibreOffice, and Google Docs. Here is a tutorial to get started...
- SeaMonkey (free) - internet application suite including web editor
- Pandoc (free) - the ultimate document converter (supporting all kinds of formats, including LaTeX, Markdown, DocX, etc)
- Brainstorming virtual whiteboard (free)
- Mark Text desktop Markdown editor (free)
Online teaching / collaborations / broadcasting
- Open Broadcaster Software (free) for recording / editing / creating videos and live streaming
- Jitsi (free) secure fully featured video conferencing
- Zoom video communications platform
- Article about Zoom alternatives...
- Whereby - free basic version for video meetings
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
- SPM (free) - general purpose (fMRI oriented)
- PDC (free) - partially directed coherence analysis
- FieldTrip (free) - general purpose (EEG/MEG oriented)
- Brainwave (free) and documentation - MEG analysis toolbox
- CARET (free) - anatomical reconstruction toolkit for structural and anatomical data (simple tutorial)
- Atlas for identifying brain regions / function based on fMRI meta-analyses
Machine Learning
- Kevin Murphy's Kalman filter toolbox (free)
- libSVM - Support Vector Machine Library
- Andrew Ng's ML Programming Exercises
(Vector) Graphics
- CorelDraw - ask Gunnar for installation CD
- Inkscape (free)
- BioRender (free) graphics for life sciences
- Better Posters blog with lots of great tips!
- Scientific drawings (free) premade graphics
- Better use of color, paper with good suggestions on colors in figures
- Photopea - free online photo editor
- Glimpse - free image editor
- Bioicons - another free database of scientific graphics
- NIH bioart (free)
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
- Psychtoolbox Demos by Peter Scarfe lab
