Soft tools for scientific computing

Turns out the scientific computing community is not always keeping up with the corporate software development trends. Shocker.

the-shocker

So, here I am to tell you about some cool tools you should definitely use, because I have had this conversation multiple times at different instances with the rich and famous in Computational Science, and some even found it interesting.

1. Sharelatex / Overleaf

https://www.sharelatex.com/

https://www.overleaf.com/

Write latex documents online in a collaborative fashion. Forget using github or, god forbid, dropbox to share papers in progress. I personally have more experience with ShareLatex, I wrote my master thesis and several papers (with one collaborator at a time because I don’t use the paid version) and it has always worked nicely.

The only thing is that it allows you to be pretty dumb and sloppy, so when you have to upload your paper on arxiv you might have to fight a bit. Anyone has used overleaf? Leave your comments below!

2. Github / Bitbucket

There are lots of guides out there to learn how to use github/bitbucket, but in a nutshell it’s a place where you can host your coding projects and keep track of changes. So you can stop copying files and having several versions of your code, sending code by email, and all that nasty stuff. Recently found the desktop graphical version: https://desktop.github.com/ It works really well in my opinion and it’s less daunting if you are not so familiar with terminal ~stuff~.

Introduction: https://guides.github.com/activities/hello-world/

3. Macdown (Mac only)

http://macdown.uranusjr.com/

This has been my best found of 2016. It’s basically a WYSIWYG* markdown editor, you can easily embed LaTeX plus all the nice stuff from markdown, code, images, highlighting. A lot easier than keeping a latex or a python notebook, in my opinion, in particular if you have the misfortune of not using python.

(*) What you see is what you get hurhurhur jargonsies!

4. Visualisation software

Recently started using VisIt (https://wci.llnl.gov/simulation/computer-codes/visit/). It eats up a lot of file formats and it seems pretty nice for CFD simulations. Until then I have been writing my own scripts using matplotlib, but that’s really dumb.

5. Referencing

I only know Mendeley. It works sorta well but I don’t consistently use it. Anyone has tips?

Yea, sorry, I didn’t really say anything that new. :3

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