Category: Grad School

Tools for the savvy grad student

As a grad student, I was always looking out for tools to make my life simple (read: I’m quite lazy). Here are some of the tools I think every savvy grad student must know.

A good plotting library

Don’t even mention gnuplot. Not only is it old school (how many times have you looked at a graph in a paper and just known that it was produced using gnuplot?), but it is extremely limited in its feature set. My biggest gripe with gnuplot, however, is that it forced me to separate my data collection/analysis from the actual plotting of the data. I personally am a huge fan of matplotlib — it is an uber-plotting library written in Python. It can produce high-quality graphics in dozens of formats (including interactive plotting), it has an object-oriented API as well as a imperative API along the lines of Matlab (hence the name). You can create amazingly rich plots and best of all, you can combine your data collection and analysis (which I was doing in Python anyways) with your plotting.

If you are more a Ruby person, check out gruff.

Bibliography Management

There are two aspects of bibliography management. First is the context of a specific paper: you are working on a paper and you want to collect all the relevant bibliographic information for citing in the paper. BibTex is the tool that is most commonly used for this, in combination with LaTeX. However, BibTex is buggy, the syntax is inconsistent across implementations, it lacks simple features like variables and the ability to “import” other bibtex files etc. Enter CrossTeX — a drop-in replacement for BibTex. CrossTeX is written in Python. It has an object-oriented model for representing citations. So once you define an object for author “Foo Bar” aliased as foobar, you can simply use foobar wherever you would like to cite “Foo Bar”.  CrossTeX also makes it trivial to define new formatting styles for your citations. For instance, if you want to change the capitalization of the titles or abbreviate “Proceedings” to “Proc.” everywhere. Finally, CrossTeX was built by some nice folks at Cornell, so they know exactly what the pain points of BibTeX were.

The second aspect of bibliography management is simply keeping a track of all the papers you read and review. These will come in handy when you are writing a paper, a dissertation, preparing for a talk or an interview, or simply trying to recall prior work in a given field. I highly recommend using CiteULike — it is an online bibliography management portal. Some features I really like: CiteULike has a really nice bookmarklet that you adding new items to your bibliography using a single click from various sites such as ACM, USENIX, IEEE, PubMed, arXiv and so on; it has some really nice social features as well such as tagging, groups, watch lists etc.; you can download selected citations in multiple formats; you can search easily by keyword, tag, author, area, year etc.

A Text Editor

I don’t mean an IDE (like Eclipse) or a Word processor (like MS Word). I mean a text editor and only a text editor. AFAIC, that means Vim or Emacs (if that works for you). The bottom line is, learn a text editor and become really really good at it. You will be amazed at how much time will save you and how much can it impact your productivity. Some features that are essential: syntax highlighting, regular expression support, spell check, support for snippets etc.

On that note, learn to write in LaTeX. I’m horrified by the fact that so many people are still using Word like tools to write papers. I don’t have anything against Word, but it is the wrong tool for writing papers. Just reference management, formatting, including figures etc are so incredibly easier in LaTeX. And if you are struggling to find the code for the right symbol in LaTeX, you’ll love detexify (hat tip: Nate)!

Version Control

I can’t stress this more — you must get in the habit of versioning everything. Not just code, but your notes, write-ups and obviously papers. Having some version control has saved me from disasters many a times. And if you are collaborating on papers, I can’t imagine how people do it without some kind of version control system. Now there are a lot of choices out there. But if you are really savvy, you must use git :) Basically use any reasonable distributed VCS (Mercurial and Bazaar are also ok), but avoid Subversion and absolutely refuse to use CVS at all costs. CVS has lived a good life, but its time is now past and we must let it go.

Information Management

And by that, I mean staying on top of the news and research in your research area and/or academic community. I’ve found it very useful to add all the relevant blogs to a ‘research’ tag in my Google Reader (yes, the blogging bug has bit academia). Likewise, you can find a lot of current information on Twitter. I’m sure people have already started live-blogging and twittering from academic conferences as well!

Of course, for more conventional searches, DBLP and Google Scholar are invaluable. CiteSeer used to be the go-to website a few years ago, but I personally find Google Scholar much nicer to use and with just as much information, if not more.

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Tools I use: beamer

This is largely a rip-off of my original article. I figured I should repost it for posterity and it fits in line with my tools theme.

Being a grad student (for that matter, in almost any profession these days), I frequently need to give talks or present some material. I have finally settled on Latex Beamer as my preferred presentation tool, and this article describes why.

Introduction

Presentation is one of the most effective means of communication for a small audience with diverse backgrounds. Both in the industry and the acedemia, it is becoming increasingly important to create affective and compelling presentations. Not surprisingly then, the presentation tool you use becomes very important in the work place.

The de facto tool for presentation out there is Microsoft Powerpoint. For more reasons than one, I prefer not to use it. I have tried several alternatives, and finally decided to use Latex Beamer for my presentations. Here I try to describe why I made this choice. I must mention here that the beamer web page looks ostentiously simple and naive — don’t be fooled by it. Beamer is one of the most sophisticated and extensively documented (user manual has more than 300 pages of professionally written documentation) presentation tools I have come across. Take a look at one of the sample slides to get a feel of what beamer can do.

Things I dislike about other presentation tools

While I’m not talking about any one tool in particular, the general flavor is of tools belonging to the Powerpoint family (this includes OpenOffice.org’s Impress, KOffice‘s KPresenter etc)

  • I have to worry about layout
  • Font sizes are a function of amount of content
  • Changing parts of a “theme” is hard
  • Powerpoint slides won’t run nicely on Impress or KOffice. The latter two won’t run at all on Powerpoint. Why do I need something as bulky as powerpoint just to do the presentation? While making, I can understand that we might need significant software complexity, but can’t we have something more lightweight for presenting?

Things I like about beamer?

  • Its LaTeX: latex and friends have survived the test of time and for more than 2 decades people have been using tex derived technologies for typesetting their writings. With latex, beamer makes it easier than ever to put mathematical formualae and all kinds of symbols in your presentations, embed images, make tables and do everything else that you can do with latex. Since many of us already use latex, it means there is less tool to learn — I can make my presentations in a language that I’m already familiar with! And I don’t need any bulky tool to manipulate my presentation, just a text editor is enough, thank you.
  • Its PDF: We all know what PDF stands for — Portable Document Format. Thats it! Portable! Latex runs on all major operating systems and architectures out there. Once you get a PDF from Latex, you can display it using any regular PDF viewer. Imagine how easy it now becomes to move your presentation around. You don’t have to worry if your laptop breaks down and the other laptops in the room don’t have the right version of Powerpoint installed. Put your PDF in a USB key and stop worrying about it!
  • Takes care of layout
  • Themes are endlessly customizable: beamer comes with dozens of pre-packages themes, and its very easy to modify an existing theme. Same thing with fonts and colors (you can even do alpha transparency!)
  • Notes and handouts made the way you want them
  • Organize your presentation in a logical manner: beamer sort of follows the MVC philosophy. In each presentation, there is a content structure, which determines how your content flows through (just like a regular article with sections and subsections). Then there is a slide structure, which determines how this content fits onto your slides. The content structure controls the generation of navitation and table of contents. The slide structure controls the slides and the control flow between them.
  • Amazing documentation: The beamer user manual is over 200 pages long, and its all good solid documentation. It is amazing well written considering the fact that its mostly done by a single person. It starts off with a nice tutorial, followed by detailed references and examples.
  • Accompanying packages: Just check out the documentations for xcolor and pgf. The documentation is just as comprehensive as beamer itself, and these packages make it easy and fun to do fancy stuff with beamer. Like draw pretty pictures and do some basic animation. Again, all with the comfort of latex.

But nothing is perfect

  • No knowledge of projectors or screens — the user has to deal with that (or the operating system)
  • Animation is still hard.
  • In general, multimedia is hard: embedding audio and video clips may not work reliably on all platforms.

I highly recommend beamer to anyone who wants to try an alternative to Powerpoint, and if you write a lot of technical papers in latex, you’ll immediately love beamer. Check out my NSDI talk for a sample of what beamer can do for you.