This is a list of some of the tools that I use on a regular basis that have come to be an essential part of my workflow.
I use LaTeX for typesetting, and TexStudio for typing. References are managed using Bibtex. I also use JabRef, which is a simple GUI frontend for Bibtex files. Ideas with references are organized using Docear.
Most papers are kept in private repositories on CQuIC@GitHub and Bitbucket. My coauthors and I use Git to allow us to work remotely on a paper and merge our changes. If a coauthor is not comfortable with Git, papers are kept on Dropbox.
I keep abreast of the literature using Inoreader (an RSS feed reader) with subscriptions to about a dozen arXiv and journal feeds. I have a few alerts set up on Google Scholar, which I also use for finding specific papers. See the post on Searching the Scientific Literature.
Most of my coding is done with Matlab or Vim in Python or Julia. I also use the following:
[comment] # (## Teaching)
[comment] # ( 1. SageMathCloud) [comment] # ( 2. The Jupyter notebook (formerly IPython notebook).)