This is a list of software I use and why, mostly as a record for myself, but perhaps useful for others.
- OS: Apple OS X. Unix underneath, ease of use above that.
- Email: Apple's Mail. Chosen by default (after Eudora failure years ago)
- Web: Safari or Firefox. Firefox has good tools for debugging web pages
- Word processing: MS Word 2004. Track changes and EndNote integration are useful for collaborations.
- Citations: EndNote X2. Fairly convenient.
- PDF management: Papers. Good for organizing and reading PDFs. Downsides: 1) only one pdf per article, so no supplemental materials, 2) does not work as citation software when writing, 3) Binary database (so can't be hacked or used in other ways).
- Project management: MonkeyGTD. Fast way to implement GTD. I use subversion to keep copies under version control and backed up.
- Version control: subversion. I use it for code and for all projects (including keeping track of paper revisions and the like). Makes it easy to synchronize across computers, track progress, provide effective backups.
- Code hosting: Google code (most things), R-forge (R). Google code is a lot cleaner and easier to use than sourceforge. R-forge is good for hosting R projects as it allows for easy installs and checks for errors.
- Command line editor: vi. Force of habit