When initially setting up your machine, you will want some kind of internet access.
NEXT, before you do anything else, make sure to select App Store under the top left apple menu and click on Updates. Install all updates. This may take awhile, but I only did it part of the way, did other stuff, and then came back and got wedged (as in the app store could not connect at all). I ended up having to reset the nvram (https://josephscott.org/archives/2013/12/mac-os-x-app-store-not-loading-try-resetting-nvram/) to fix things.
Download and install Xcode (https://developer.apple.com/osx/).
To write weekly research reports and papers, you will need latex. Download the MacTex (http://tug.org/mactex/) distribution and install it. It comes with TeXShop (http://pages.uoregon.edu/koch/texshop/), which is a serviceable latex editor. It also comes with LaTeXiT (http://www.chachatelier.fr/latexit/), which is really handy! You can create pdfs of latex equations and maintain libraries of latex equations. The pdf images created by LaTeXiT are much smaller than what the equation editor does in powerpoint. I copy these equations into powerpoint.
In our research group, I insist on students maintaining a bibtex database of the papers they have read, the pdfs of the papers, and notes about each paper. I was in the same lab at UCSD as Michael O. McCracken (http://michael-mccracken.net) started writing BibDesk (http://bibdesk.sourceforge.net). I asked for the minimal bibtex entry feature, which Mike provided. I am so grateful that Michael, Christiaan M. Hofman, and Adam R. Maxwell continue to maintain BibDesk. It is great! There are other bibtex management tools out there. As long as you have one, that is sufficient.
If you are a University of Arizona student, faculty, or staff, then go to http://softwarelicense.arizona.edu/faculty-and-staff to obtain some software licenses. The Microsoft Office Suite is a necessity. In our group we use powerpoint to share presentations and excel to show preliminary results.
For Python, I use Canopy (https://www.enthought.com/products/canopy/). You can get a free academic license. With one install it gives my iPython, NumPy, and a bunch of other useful goodies. It doesn’t provide Python 3+ though. For that check out Anaconda (https://store.continuum.io/cshop/anaconda/). See http://www.quora.com/How-does-Enthought-Canopy-compare-to-Anaconda for a comparison.
Here is a list of other useful applications:
- Skype and Google Hangouts for meeting with collaborators.
- Password database like Data Guardian.
- Textwrangler for text editing
- OmniGraffle, students should come talk to me about buying this.
- Graphviz, http://www.graphviz.org/Download_macos.php. Downloaded 10.38.0 pkg. Needs X11 http://xquartz.macosforge.org/landing/ 2.7.7, must install X11/XQuartz first.
- Chapel compiler, http://chapel.cray.com.
- mercurial, http://academy.cba.mit.edu/content/tutorials/02_Project_Management/mercurial_install_mac.html
- Sourcetree for git and mercurial.
- Evernote
I am still trying to decide between Homebrew, MacPorts, and Fink. Comments and suggestions are welcome.
