CrashPlan and github for versioning and backup
I cannot stress how important this is over and above all the other software you use in your research. The other software you use means nothing as long as a mistake by you, or a hardware failure, can destroy years of work.
CrashPlan is setup to backup my home directory, so I never worry about loosing things. Because the university internet connection is so fast I don't have to worry about upload bandwidth.
I have a
phd repository in which I commit ALL my notes, papers in progress, source code, etc. I'll commit and push this to a private github repo every day. This means I have a full, versioned, backup of all my work.
Having these backup plans in place has saved my ass TWICE. I've had the SSD on my old laptop die twice and lost only a minimal amount of work because of CrashPlan and git.
Mendeley for reference management
~/Downloads/bibtex for new .pdfs so that every paper I download is added to my reference library.
Automatically outputs my references as
.bib BibTeX files to
Renames and writes all my references as
~/Documents/Papers which I sync to Dropbox.
GoodReader on iPad for reading papers
GoodReader syncs with my Dropbox
Papers folder so that my iPad documents are always in sync with Mendeley.
When I annotate papers with highlights and notes I follow a colour scheme: Yellow for interesting aspects of the paper, Green for references I should follow up on, Blue for good ideas that may warrant further research.
Vim and LaTeX for writing papers
If you're compiling LaTeX documents by hand then have a look at rubber which lets you compile, bibtex, and pdf in a single command
rubber -d paper.tex.
Vim is setup so that if I press
mm then it compiles the currently open document into a
mv is compiles AND opens the resulting document in Evince.
I've created a LaTeX package
phd then includes all the packages I usually use so that a fresh LaTeX article is only four lines of boilerplate.
Google Tasks and Evernote for random note taking
For bigger notes I'll just create a new LaTeX document and commit it to my git repo.
For really small reminders when I think of something relevant to my research I'll create a Google task. When I come to review this little snippets I'll enter them as more permanents notes in Evernote.