Graduate Student Software Tools

September 20, 2012

I’m laid up with a sprained ankle the size of a tennis ball from messing up a foot switch on a rock climbing problem. So, trying to look on the bright side of things, this means I can write a blog entry I have put off for far too long.
I like digging into software. I’ve learned that if I think there should be a better way to do something, someone has already thought of that and done it. When I switched from using a Mac as my primary computer to using a PC, I had to adjust to the user-unfriendlyness of it.

The following pieces of software have helped me in my first year of graduate school. Oh and they’re all free.


What is it? Mendeley is a PDF organizer. Think of it as iTunes for your PDFs.

What’s its killer feature? You can export your sources to a BibTeX or Endnote file.

Why do I need it? I loved BibDesk for my Mac, and I needed a replacement for it on my PC. Mendeley keeps my many, many journal articles, reports, dissertations, etc organized and browseable. I love being able to tag and take notes on articles, and then being able to search those notes and tags. Mendeley can also watch a folder and apply a renaming mask using the citation information it automatically pulls from the article. This means that “1-s2.0-0040603195904662-main.pdf” becomes “Alawode – 2005 – Oxidative Degradation of Piperazine in Absorption of Carbon Dioxide.pdf”. There are even a few features that I don’t use, like being able to sync your library across devices.

What are the alternatives? You could look into Zotero and Jabref. I briefly tried Qiqqa before deciding I didn’t like it.

Bonus Tip: Forced to use Word but and don’t want to import your bibliography into it? Use the BibTeX4Word macro set.


What is it? PDF Split And Merge. You can take apart one or many PDFs and rearrange their pages in any order.

What’s its killer feature? Nothing glorious, just the simply ability to muck a PDF.

Why do I need it? Windows is sorely lacking a competitor to Apple’s Preview. I remember being able to easily rearrange PDFs on my Mac, and I was appalled to find that I had to dig up an application to do that on Windows. Sure, PDFSam gets the job done, but it’s not nearly as polished as Preview is. It has particular trouble displaying the pages as your rearrange them, so I often forgo that.

What are the alternatives? Shelling out for Adobe Reader Pro.


What is it? A text editor for coding.

What’s its killer feature? Color coding any language allowing you to at a glance separate out blocks of executable code from comments.

Why do I need it? Let’s face it. Notepad is a bit too lightweight, and MS Word would love to autocorrect all the code you run through it. Notepad++ lets me edit Fortran subroutines in peace. Simple features like line and column numbers let me track down coding mistakes (gotta start in column seven or the punch card reader will jam!), while the variety of appearances lets me customize my display for maximum happiness.

You can also install add-ins, which fills another Windows gap: diff. I can’t believe there is no easy way to diff line by line on Windows, but luckily Notepad++ lets me figure out what has changed between code revisions as coders cannot be bothered to add comments.

What are the alternatives? I honestly haven’t looked around as this has satisfied my coding needs.

LyX and MikTeX

What are they? These are a typesetting alternative to MS Word.

What are the killer features? LyX has the best equation editor around. MikTeX has an excellent package manager for installing all those journal specific styles.

Why do I need it? I can’t stand typing anything of quality in MS Word. If you are unfamiliar with LaTeX, you should educate yourself. I love the absolute control over the document that I have as well as the ability to change a couple of settings and suddenly my document looks totally different. Practically, it means being able to write without worrying about formatting. Most journals have a TeX template that you can just run with, and the whole product will be to their specifications. I have gotten multiple comments on how professional my writing looks simply thanks to using the fancyhdr package.

What are the alternatives? TeXLive, but I haven’t touched it.

So that’s all the software you may be unfamiliar with, but what about the software you think you know how to use? I thought I was good with Excel, until I read the Missing Manual. Now, I’ve embraced the power of pivot tables, normal tables, conditional formatting, and other skills. It’s changed how I layout my workbooks and made getting work done faster. I don’t want to list all the neat tricks, unless people want to hear them. So let me know if you want a post about what you’re missing in Excel.


2 Responses to “Graduate Student Software Tools”

  1. Matthew Hausknecht said

    Sorry to hear about the ankle, get better soon! There are some higher powered code editors out there such as VIM + Emacs but I’m not sure how well they run on Windows and they have a bit of a learning curve.

    • logisticalmiasma said

      I don’t do enough coding for me to sit down and learn them. All I’ve done in Emacs is talk to the doctor. ;)

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