dear buggy April 2008

Dear Buggy

I’m a new graduate student studying the mating behaviour of Grylloblattids. Before going to the field I purchased a new laptop which just about tapped out my bank account until I get my first stipend this Fall. The computer is great, but it didn’t come with the software I need to do my research. I don’t want to use pirated software but I don’t know what to do, any advice?

Word-less in Wawa

Well Word-less that’s quite the dilemma you’re facing. A quite serviceable laptop can be had for between $600 and $800 but the software your typical graduate student needs can quadruple that price. Unfortunately, this is a cost that most students (and some supervisors) fail to take into account when purchasing a new computer. To give you an idea, a typical graduate student can expect to need software for word processing, storing, managing and analyzing data, other software is needed to prepare publication quality graphs, images and figures. Word processing and presentation software is needed to write manuscripts, and design your presentations and posters. In addition many students use software to manage references and produce bibliographies and others require software for specialized analyses (e.g. genetics or GIS). As you would expect there is no magic graduate student all-in-one combo software suite to do this (but wow isn’t there a business opportunity!). To buy the various commercial software that would allow you do your research could run upwards of $4500. Ouch. So, besides downloading a file-sharing program, strapping on an eye patch and becoming a full-fledged software pirate what’s a grad student to do?

You’re in luck. Your university or department might already provide you access to some of the programs you need. It’s likely that your university has purchased site licences for some of the more popular commercial packages. What’s a site licence? Universities purchase software at a bulk rate from manufacturers and then re-distribute it for a yearly fee. You obtain a copy of the software from your universities IT department and, as long as your site license is current, you have full access to the software. Two caveats though, one it’s likely your supervisor will have to purchase the software for you as site licences usually aren’t sold to students. Second, you may not be allowed to install site-licensed software on your personal computer. Therefore this option is best for software like statistics and graphing packages that everyone in a lab group might need but that you won’t use everyday. Depending on the size of your department some highly specialized software (such as GIS software) might be offered in a shared lab that you can get access too. But what do you do for that software you will use everyday? Or what about when you’re in the field and don’t have access to your lab computer? Better yet, what about those of us who aren’t students?

Those with some internet-savy may be familiar with the term ‘Open-source software’. What is open source software? In a nutshell, groups of volunteer developers produce software that is released free for non-commercial use. Users are expected to contribute to the development of this software by donation, providing feedback or helping out. Open-source refers to the underlying software code that the software is based on. Open code can be obtained and modified by anyone as long as the original source is acknowledged. In the past 10-15 years networks of developers have managed to produce a number of viable software options that are ‘free’. Some people might be familiar with the Firefox internet browser and the R statistics package, these are probably the two most widely used pieces of open-source software. To help you get started I’ve assembled a list of open source and other free software that I’ve found useful. A few caveats, because open-source software is developed by volunteers it may not poses all the features of commercial software. Second, help may not be easy to find, although most open-source software tend to have excellent user forums and/or list-serv’s where you can search for or find advice. So as with anything free its possible to get what you pay for. However, if you’re willing to experiment and get your toes wet (and save a little money at the same time). I’d suggest you look into trying some of the free options to commercial software. If you like something try and contribute, or at least spread the word.

Trailing statement

This is the inaugural edition of the Bulletin’s advice column. We need your questions for future columns! Forward your questions or topic suggestions to cjkmacquarrie@gmail.com or post them in the Facebook group.

About me

Most of this software is available for PC, Mac and Linux based computers unless otherwise mentioned.

If you’re looking for: You might try:
Productivity (word processing, spreadsheet, presentation) – OpenOffice (www.openoffice.org)- Google docs (https://docs.google.com) not open-source but free, online only, requires a free google account
Statistics +Graphing -R (www.r-project.org). Extremely powerful with broad user base. Excellent documentation and expandable. But not for the faint of heart, requires a good knowledge to basic statistics, some programming familiarity as well.
Internet/Email Firefox/Thunderbird (www.mozilla.com) Widely used and expandable with small plug-in applications.
Image processing/manipulation -GIMP (www.gimp.org) The Gnu image manipulation project. Alter, re-colour, crop digital images.-Picassa (http://picassa.google.com), not open source but provides rudimentary image correction tools and image management. PC only
Image analysis -ImageJ (http://rsb.info.nih.gov/ij/) requires Java. With this software and a flatbed scanner it’s possible to build a quite serviceable leaf-area meter.
Figure construction -Inkscape (www.inkscape.org). Vector-based software for drawing and assembling figures, posters and images.
Reference management -JabRef (http://jabref.sourceforge.net)- Connotea (http://www.connotea.org) online from the Nature group-Zotero (www.zotero.org) a firefox plug-in

This column originally appeared in the April 2008 edition of the Bulletin of the Entomological Society of Canada

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