Difference between revisions of "Software"
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* [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.mendeley.com/ Mendeley reference manager] (AVOID! Use Zotero instead!!!) - manage references & automatic bibliography generator for MSWord, LibreOffice and BibTeX | ||
| − | * [https://www.zotero.org/ Zotero] (free) article and biography manager for Word, LibreOffice, and Google Docs | + | * [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://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://miro.com/ Brainstorming virtual whiteboard] (free) | ||
| − | * [https://marktext.app/ | + | * [https://marktext.app/ Mark Text desktop Markdown editor] (free) |
== Online teaching / collaborations / broadcasting == | == Online teaching / collaborations / broadcasting == | ||
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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. | * [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. | * [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 Analysis == | == Imaging Analysis == | ||
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*[https://github.com/merwan/ml-class Andrew Ng's ML Programming Exercises] | *[https://github.com/merwan/ml-class Andrew Ng's ML Programming Exercises] | ||
| − | == Vector Graphics == | + | == (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://scidraw.io/ Scientific drawings] (free) premade graphics | * [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.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 == | == Statistics == | ||
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* [https://www.r-project.org/ R] (free) - general purpose with [http://r4ds.had.co.nz/ great online book]! | * [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 | ||
| − | * [https://jasp-stats.org/ JASP] (free) is especially useful for Bayesian stats! | + | * [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 == | == Experiments == | ||
* [https://peterscarfe.com/ptbtutorials.html?s=03 Psychtoolbox Demos] by Peter Scarfe lab | * [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
