- 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
- 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)
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
- 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.
- 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
- Kevin Murphy's Kalman filter toolbox (free)
- libSVM - Support Vector Machine Library
- Andrew Ng's ML Programming Exercises
- 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