Essential mac apps for the behavioural ecologist

I have been using a Mac for around four years now, and the switch made it necessary for me to track down new software to replace my toolkit. I had grown accustomed to using a certain set of software in Windows, and the lack of Mac versions for most of them meant that I had to find equivalents. So I hereby present a list of essential Mac software that I have grown to be completely reliant on. The list is a collection of tools that I consider essential for someone in the sciences. And also, since I still haven’t upgraded to Leopard (10.5), I haven’t been able to check out the new cool ones (such as Macnification). I have left out the more obvious ones such as Word, Endnote, Excel and Powerpoint.
1. Quicksilver
Quicksilver is an application that is hard to describe but I’ll give it a shot. It is at its most basic level an application launcher, but due to its infinitely extensible nature, you can use it for a whole variety of tasks such as file handling etc. I’ll point to a few good tutorials, but what makes it essential is that it completely changes your computing experience. Instead of endless clicking and drilling down the Finder windows, you can get the file you want by simply typing the first few letters of the name. Also, since Quicksilver learns the files that you use more frequently, they tend to pop up in the list very quickly. It take a while to get the hang of it, but once you get used to it, you’ll wonder how you did without it. Some plugins that may be of special use are the dictionary plugin, the unit conversion plugin and the calculator plugin. These plugins lets you do these tasks right there in Quicksilver without the bother of having to launch separate applications. So if you’re in the middle of a paper and you want to do a quick calculation, you can do so without launching the default calculator. Very smooth.
2. Scrivener
Scrivener is an application that makes the writing easy. It’s basically designed to get a draft out, and then worry about the formatting later. You can arrange a single Scrivener file (which is basically a text file) into several sections that deal with different parts of the document. In this way you can just focus on writing and get the words out. It also has a brilliant FullScreen mode, where it blanks out the rest of your desktop and lets you focus on the text. I’m writing this in Scrivener, and the last three papers I wrote were in Scrivener. Scrivener also lets you paste in Endnote temporary citation, that are then converted into actual Endnote citations when you export to Word or some other word processor for formatting. Scrivener has a feature called ‘Typewriter scrolling’, which makes sure that the line you’re typing stays midway across the screen. Other word processors scroll so that you end up always looking at the bottom of the screen. You can set a word count target and this lets you know how much more you have to write, which is especially useful for stuff like Abstracts and Grant proposals, which have strict word counts. In Scrivener, you can also import pdf or image files into a ‘Research’ section, which makes it ideal for referring to other papers or even graphs while you’re writing the paper.
3. Papers
Papers is a new program that drastically changes the way people normally deal with pdf files. Even the most organized of scientists have problems organizing their library and Papers solves this problem most elegantly. It’s a sort of iTunes for pdfs. You can import your pdf collection directly into papers, and then spend a bit of time getting it in order. There’s a bit of initial time investment with your old pdf files, but Papers makes it easy by using the Match feature. You select a pdf file in Papers, click on Match , and you can search for metadata (such as author, journal etc etc) through a variety of repositories such as JSTOR, Google Scholar and Web of Science. New papers are easier since you can download them directly to Papers, and since new articles have better metadata (such as DOI), it’s easy to deal with. Integrating Papers into your paper writing workflow (with respect to Endnote) is a bit tricky, but even without this, Papers is a godsend for the harried reference herder.
4. GraphPad Prism and JMP
GraphPad Prism is my first choice for exploratory data analysis. You paste the data from excel, it spits out a graph, and you have some idea of what the data looks like. Things like normality testing and simple tests such as t-tests and ANOVAs are a breeze; the software speaks English instead of spitting out interminable tables (E.g. Is the variable normally distributed? Yes). The graphs it produces are very much configurable, and very easy to use. There are a few types of analysis that Prism doesn’t do such as multiple regression, and for these and other more detailed analysis I then use JMP. JMP is hard to get the hang of at first, but if you persist, it becomes easier all the time. I now use JMP for any analysis that Prism doesn’t do, and the graphs that JMP produce are pretty decent as well.
5. Graph Sketcher
I still haven’t found a good dedicated graphing program, and I’ve tried a few. Deltagraph is downright annoying and the free ones that I found were quite mystifying. If I can’t tell immediately how to use the program, then it probably will prove to be more annoying as time goes on. But I did find this really cool software that draws blank graphs. I reckon Graphsketcher is very useful when you need to draw graphs of models, i.e. when you need to illustrate a hypothesis. It might be a bit of overkill to use a program meant only to draw blank graphs, but I have come to believe that it’s much better to have a small simple program that does one thing very well, than to use a big program that does many things but not so well.
6. Inkscape and Lineform
Occasionally you need to draw the setup of an experiment or to illustrate part of your paper with a line diagram. I have been dabbling with the opensource Inkscape (which needs X11 installed) and while it looks very competent and reliable, I still found it quite a bit annoying. Recently I downloaded the Demo version of Lineform and tried recreating a figure that I had just finished labouring over in Inkscape, and I found that it took a fraction of the time to do so. Lineform has recently won an Apple Design Award, which means that now everybody knows it’s good. I think I will get this program, and I foresee that it will become an integral part of my toolkit, and with luck replacing Powerpoint for poster making.
7. ImageJ
Images are all the rage and chances are you will use images as part of your data in some form or the other. I take photographs of spiders and webs and measure the photograph in the comfort of the lab rather than do a whole heap of measurements in the field. ImageJ is free, comes with a million plugins and macros that make image measurements a breeze. I’ve only recently started realizing the full extent of this application’s capabilities, so I can’t say very much but I am beginning to become a big fan. You can even import avi files and there are plugins that aim to do object tracking.
8. Skim
Skim is an alternative to Preview and Acrobat reader for reading pdf files. You can annotate and read fullscreen, but I guess it’s a matter of personal preference. If you’re happy with preview, I guess there’s really no need to switch to Skim. But it’s worth a look. Skim loads much faster than Acrobat reader, and has more options than Preview.
9. Carbon Copy Cloner
CCC is a highly configurable data backup software that make the job of backups a breeze. I use Carbon Copy Cloner, mainly because you can choose which folders to backup, and because it does incremental backups which means that if backs up only the files that have changed and new files. It’s a matter of seconds if you back up regularly.
10. Newsfire (Free)
Now that journals are starting to get the hang of this here interwebs, many of them are now offering their table of contents as a feed. So if you get your hands on good feed reader such as Newsfire, you can subscribe to the journals and saves you the trouble of checking whether the next issue is out, since Newsfire automatically checks the site for you. It also prevents you from having to get the table of content information in your email…but I guess that’s also a matter of personal preference. I think TOC feeds are ideal to keep abreast of the latest issues.


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