While working in Academia, I have found a number of useful resources that have greatly aided my work flow and progress. Many of these resources I discovered online through other people's websites - I hope to similarly provide a useful resource repository for graduate students in the sciences below.
Software
I mainly use free and open source software, thus the majority of software here is open source and free to download from respective sites unless otherwise indicated. All software is multi-platform unless otherwise indicated.
Statistics, Mathematics, Programming
- R: http://www.r-project.org/ Popular statistics software, can do a large array of statistical analyses, large user contributions, command line interface, but GUIs also available
- RStudio: http://www.rstudio.com/ An incredibly useful IDE (Integrated Development Environment) for R, excellent for creating a smooth workflow
- NetLogo: http://ccl.northwestern.edu/netlogo/ Agent Based Modelling software
- Sage: http://www.sagemath.org/ Free alternative to Matlab and Mathematica, uses the Python scripting language, uses many of Python's scientific libraries, e.g. Maxima, SciPy, NumPy, Matplotlib
- Text Wrangler: http://www.barebones.com/products/textwrangler/ Mac alternative to notepad, good for scripting code
- OpenBUGS: http://www.openbugs.info/w/FrontPage An open source alternative to WinBUGS, a Windows software for Bayesian analyses using Gibbs sampling. Usable on a Mac with Wine Bottler (see Miscellaneous below)
Productivity and Organization
- LibreOffice: http://www.libreoffice.org/ Free alternative to MS Office.
- Skim: http://skim-app.sourceforge.net/ Mac PDF reader, allows multiple annotations including underlining, notes, highlighting, etc.
- Mozilla Thunderbird: http://www.mozilla.org/en-US/thunderbird/ Email client, can localize email from several accounts, e.g. gmail and school emails, accessible offline. No longer updated.
- LyX: http://www.lyx.org/ A GUI (Graphical User Interface) document processor that uses LaTeX to create clean, well formatted documents with ease. An excellent alternative to MS Word if you don't mind learning a little bit of programming. Also allows comments if your reviewer has LyX.
Citation and Reference Managers
- Zotero: http://www.zotero.org/ Citation reference and pdf manager, free alternative to EndNote, integratetable with MS Word, LibreOffice, and features many citation styles for behavior and ecological journals.
- Mendeley: http://www.mendeley.com/ Citation reference and pdf manager, free alternative to EndNote, integratetable with MS Word, LibreOffice, and features many citation styles for behavior and ecological journals.
Online File Sharing
- Dropbox: http://www.dropbox.com/ Online file sharing system, can sync between computers, extra space available for education
- Google Drive: https://drive.google.com/ Online file sharing system, can sync between computers, 15 GB free, also access to google docs
Image and Video Editing and Analysis
- Inkscape: http://inkscape.org/ Vector graphics editor, free alternative to Adobe Illustrator
- GIMP: http://www.gimp.org/ Picture editing software, free alternative to Adobe Photoshop
- ImageJ: http://rsb.info.nih.gov/ij/ Picture editing software, can also do analyses on color, etc.
- JWatcher: http://www.jwatcher.ucla.edu/ Video coding software, great for doing behavioral analyses
Miscellaneous
- Wine and Wine Bottler: http://winebottler.kronenberg.org/ Wine is a sort of Windows emulator (i.e. application that lets you run Windows programs in a Mac); alternatively, Wine Bottler allows you turn install a Windows program (.exe extension) as a Mac application on your computer. Useful for Windows specific programs, such as OpenBUGS.