Ideas are cheap, implementation is expensive; act accordingly.
Those who have been watching may have noticed I quietly started developing an Android application in the last month or so. It’s still super-buggy and far from feature complete, but I thought it was time to announce it here (“release early, release often”). It’s not ready for real users yet, but developers may like to take a little look.
Continue reading ‘Occyd : tagging for locations’
A quick post to share some bookmarklets I made.
I’ve found QR-code “2D barcodes” really handy when playing with my Android phone.
Sometimes, I have a web page open on my desktop PC, and I want to quickly load it in the Android Chrome browser to see what it looks like. Rather than re-typing it with my thumbs, the Barcode Scanner application allows me to scan a QR-code from the screen of my computer, and if the decoded text contains a URL, open it in the Android browser.
These two bookmarklets turn the URL of the current page that is open in your browser into a scannable QR-code:
Google Charts API based bookmarklet: Drag this link –>Current URL to QR-code to your bookmarks toolbar.
The code is: javascript:location.href='http://chart.apis.google.com/chart?cht=qr&chs=350x350&chl='+escape(location.href);
Alternatively, I made a Kaywa QR-code generator version. Drag this link –>Current URL to QR-code to your bookmarks toolbar.
The code is: javascript:location.href='http://qrcode.kaywa.com/img.php?s=8&d='+escape(location.href);
They both do the same thing, so you probably only want one. Only tested on Firefox.
(Update: seemed WordPress ate the javascript in the bookmarklet links … should be okay now)
Sometimes it’s nice to quickly check how many sequences are in a FASTA format sequence file.
It barely warrants it’s own blog post, but here we go anyhow: my one-liner shell script for counting the number of sequences in a FASTA “flat-file database”, based on the presence of the “>” header symbol.
Dead easy huh ? I put this in ~/bin/countseqs, make it executable (chmod +x ~/bin/countseqs) and use it in lots of situations, as a quick sanity check.
(oh, btw, this is not public domain and u can’t use it for commercial gain without paying me a license fee. academic users can fax me something for a free license. k thx bye).
Couldn’t help myself … everyone else is doing it 
Many University libraries use some server software called Ezproxy to do authentication and arbitrate access to full-text online journal subscriptions. Essentially, Ezproxy uses some URL mangling, rewriting all hyperlinks, to pass traffic via the proxy (rather than using a conventional browser proxy setting). For example, http://www.sciencemag.org/cgi/content/full/313/5785/314 is changed to http://www.sciencemag.org.ezproxy.lib.unimelb.edu.au/cgi/content/full/313/5785/314 . If the user is not logged in to the proxy (ie has no fresh & valid cookie), a login screen is given before being forwarded to the journal site.
This plugin helps mangle URLs to add the proxy domain to outgoing links from various journal sites as well as NCBI PubMed (eg, like .ezproxy.lib.unimelb.edu.au), meaning that the user doesn’t actively have to go to their library site to follow “ezproxy-fied” links. It makes getting full-text articles via the institutional library proxy a more seamless experience (assuming that your library subscribes to the journal).
The plugin contains a list of journal and publisher sites at which it is active, plus some “special case” code for making sure only fulltext links outgoing from NCBI PubMed are handled. You can add your own journal sites as needed.
The user needs to edit the variable proxyname to make the script use their institutions EZproxy … I can’t really help you with that part, since I only know that my workplace (The University of Melbourne) uses .ezproxy.lib.unimelb.edu.au .. beyond that, you are on your own !
I’ve uploaded the Library Ezproxy Forwarder script to Userscripts.org
I recently needed to make a simple, two dimensional figure of a beta-barrel membrane protein. I went hunting for programs that might take a sequence and/or structure and produce a pretty looking diagram to save me constructing everything by hand. Here are two I found and tried.
Continue reading ‘Software review: producing two dimensional diagrams of membrane proteins’
