GitHub:
My personal GitHub account is here.

SOCKS proxy via SSH Tunnel:
A simple Python script that creates an SHH tunnel and uses “networksetup” on Mac OS X to create a SOCKS proxy using the tunnel.  Simply run the script in a terminal window with a command line option telling it which network interface you’d like to use the tunnel with (e.g. “Wi-Fi”, “Ethernet”, etc).  The script will continue running and to end the tunnel simply quit with Control+C.  The script also nicely resets your network settings if the SSH tunnel closes due to a lose of network connectivity, which is nice when moving a laptop from home to work.  I created this after after upgrading to Mac OS 10.7 and having an issue with SSHTunnel, which is otherwise a great program.

For Mac OS 10.8+, the security settings have changed and the program “networksetup”, which is run by the setproxy.py script, requires admin privileges. Thus, running the script by itself will bring up TWO annoying password dialog boxes. A simple fix(?) for this is to run the script as root (e.g., sudo setproxy.py –off). You still have to enter your password, but only once and not in a dialog box.

Bibdesk:

  • Fork of Zot2Bib.
    When Zotero downloads a reference and PDF, Zot2Bib transfer only the reference to BibDesk. In my fork, I have added functionality that also attaches the PDF to the BibTeX file.
  • Perl script to toggle between full journal titles and abbreviations and Applescripts to do this in Bibdesk in a manner similar to JabRef.
    – Perl script for journal title abbreviation.  The script contains links to journal abbreviations lists; these should be changed to your local lists.
    – Applescript for toggling between full title, ISO abbreviation (i.e. with periods after abbreviated words), and Medline abbreviation (no periods).  It needs to be modified for the appropriate location of the Perl script.
    – Applescript that can be attached to the “Add File or URL” script hook so that journal titles are automatically abbreviated before using them in the file name for linked PDFs.  It needs to be modified for the appropriate location of the Perl script.
    – Sample list of journal abbreviations. Note that you can add your preferred abbreviation and full title first then followed by alternate titles and abbreviations that you’d like to convert to the preferred version.  For example, see the entries for the Philosophical Transactions of the Royal Society of London in this file to see how this works.