Tools

Things that make my work easier

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.

Writing papers

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 [email protected] 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.

Reading papers

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.

Presentations

Lately, I write most presentations in Powerpoint. I use texpoint to typeset equations onto slides.
For drawn diagrams and graphics, I use Omnigraffle and Inkscape.

Code

Most of my coding is done with Matlab or Vim in Python or Julia. I also use the following:

  1. IPython and IJulia. For interactive running and debugging.
  2. The Jupyter notebook (formerly IPython notebook). For organizing, recording, and sharing code with animations and mathematics.
  3. Github and BitBucket. For collaborative code development.

Plotting

Matlab, Matplotlib and VisClaw.

[comment] # (## Teaching)

[comment] # ( 1. SageMathCloud) [comment] # ( 2. The Jupyter notebook (formerly IPython notebook).)

Notes and productivity

  1. OneNote from MicroSoft.
  2. NValt. For managing plain-text notes.
  3. Omnifocus. For managing all the non-research stuff I do.
  4. Gitit. Wiki software could be useful for internal collaboration within a group.

Websites

  1. Jekyll. For building this website and a few others on GitHub.
  2. Coda.
  3. Wordpress. For the CQuIC website I participated to build.