Here are some Mac tools (only tested on Leopard) that may be useful to other climate scientists. They are all created by me (Karen Shell), usually based on sample scripts by others.

Publication Tracking

I have just started using Applescript and Bibdesk. I would like to download bib info (including the abstract, ideally) for the journals that I follow into a BibDesk file regularly. Then, I can go through the BibDesk entries, delete the ones I don't want to read, and rank high priority papers that should go in the top of my paper queue. There are probably more elegant ways of doing this. Please let me know if you have suggestions.

• Reading emailed AGU Tables-of-Contents into BibDesk from Mail: I use BibDesk to manage my references. I'm subscribed to many of the AGU TOC emails. This applescript adds the papers in the email to a BibDesk file. (Bibdesk must already be installed on your computer, and you must use Mail for email.)
  • Download this script to the appropriate script directory on your machine.
  • (Optionally) open a BibDesk file. I recommend importing the new entries into a new file just in case.
  • Select a AGU TOC email and run the script. I use MailActOn (note: not free) to use the keyboard to run the script. You could also create a Mail rule to run the script when the email is first downloaded, though I prefer a little more manual control.
  • If you figure out how to get rid of the 2 extra empty entries, let me know.
  • Unfortunately, the abstract is not included currently. I use NetNewsWire (see below) to add abstracts to papers after I've downloaded them.
• Read AGU abstracts from NetNewsWire into BibDesk entries: As noted above, the emailed TOCs don't include the abstracts. However, the news feeds for the journals don't include all of the information either. My current solution is to read in the entries from the emailed TOC and then run a script in NetNewsWire to add the abstracts to the appropriate BibDesk entries.
  • Download the script.
  • Open NetNewsWire and select the subscribed RSS feed. (If you do not already have the AGU journal RSS feeds, go to the AGU Journal RSS feed page and select the journals you'd like to follow.) I put all of my AGU journal feeds into one folder, so I just select that folder in NetNewsWire and run the script once. It doesn't work with titles that have special symbols in them. Those, you have to copy and paste the abstracts manually if you want them.
• Coming soon: Read emailed American Meteological Society TOCs into BibDesk from Mail. The TOC just changed, so my script no longer works. AMS journal RSS feeds don't (presently) include abstracts, so the TOCs are the only source of paper info I use.
• Other journals I may add in the not-so-near future: Nature, Science, Nature Geophysics, Climate Dynamics, etc. I suspect there's a nice way to import Science and Nature Tables of Contents, but they haven't turned up in my searches yet.

• opencview.app: NetCDF is a data format commonly used in atmospheric science. ncview is a handy browser to look at data quickly without having to run Matlab, ncl, etc. You run it by typing "ncview filename.nc" in a terminal window. Sometimes, I like to use the Mac finder windows to move around and view different files. This simple application allows me to double click on a netcdf file and open it with ncview. It's an Automator application that just runs a shell script. (Note that ncview must already be installed.) There's probably a more elegant way to do this, but this app works for me.
  • To install, download this zipped file to wherever you want on your Mac. Double click it to unzip openncview.app.
  • To use openncview, select a NetCDF file and right-click on it (press control and click simultaneously), select "Open With" then "Other ..." and pick "openncview". If you click on the "Always Open With" option, in the future you should be able to open other *.nc files with openncview just by double-clicking on the file in finder. The script does create a terminal window, which you can close after you're done with ncview.
  • If you need to modify it (for example, to change the path of ncview, assumed to be /usr/local/bin/ncview), you'll need to open the app from within Automator.

Last modified: Wed Oct 12 13:04:11 PDT 2011