Latest revision as of 13:30, 30 October 2024

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