But maybe the Dundee server is down. Or maybe you think your local machine will do things faster. Or maybe you work on über secret sequences in some Faraday cage bunker with no permanent network connection. In each of these cases, you may want to run your own local JABAWS server and use that instead. In this case, read on.

Download the JABAWS war file (direct link here).

Install Apache Tomcat and the management interface:

sudo apt-get install tomcat6 tomcat6-admin

As root, edit the /etc/tomcat6/tomcat-users.xml file to enable admin access.

Between the <tomcat-users></tomcat-users> tags, add:

<role rolename="admin"/>
<user username="tomcat" password="s3cret" roles="admin"/>

where ‘s3cret’ is a secret password for the user ‘admin’.

Go to http://localhost:8080/manager/html/ and login as ‘admin’ and the password you set.

Under “WAR file to deploy”, click on the “Choose File” button, and select the jaba.war file you downloaded.

Now you need to set the permissions of the Muscle/Mafft/Clustal etc binaries that come packaged with JABAWS. Type the following commands:

cd /var/lib/tomcat6/webapps/jaba/binaries/src

sudo chmod +x setexecflag.sh

sudo ./setexecflag.sh

This should do it .. in Jalview, go to Preferences, and under the “Web Services” tab add a new service URL “http://localhost:8080/jaba” (no quotes, no trailing backslash).  Now when you load an alignment, your local JABAWS server should appear under the “Web Service->JABAWS Alignment menu”.

For the record .. I tried this under the version of Jetty packaged with Ubuntu 11.04, but I couldn’t get it to work so I gave up and just did it with Tomcat as per the JABAWS documentation.

Links:

This HOWTO is an Ubuntu specific regurgitation of the docs below.

http://www.compbio.dundee.ac.uk/jabaws/manual_qs_war.html

https://help.ubuntu.com/10.04/serverguide/C/tomcat.html

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)

For example, typing:

gg open science on friendfeed

into the YubNub search box searches Google for “open science on friendfeed“, via YubNub.

I thought I’d highlight a few life science- and bioinformatics-related YubNub commands I find myself using quite often in my day-to-day work. Some are commands I created, others someone else created. This is the beauty of YubNub … often someone has already made the ‘obvious’ command … it’s worth just trying to search with a command you expect to exist, since it often does.

Onward, with the list:

• pubmed — Searches PubMed
• hubmed — Searches HubMed (Alf Eatons featureful alternative interface to PubMed)
• gopubmed — Searches GoPubMed (an ontology enhanced PubMed search)
• doi — Redirects you based on a Digital Object Identifier (DOI), via http://dx.doi.org/
• pdb — Searches the Protein DataBank for 3D structures. Usually the search term should be a 4 letter pdb code.
• uniprot — Searches the Uniprot database (use an accession, id or keyword as the query).
• ihop — Searches iHOP, information Hyperlinked over Proteins, for views of the biomedical literature guided by gene networks. Nothing to do with pancakes (or prayer).

There is also a class of more general, non-biomedical commands which I often use:

• gg — The Google.
• gim — The Google Image Search.
• wp — Good ol’ Wikipedia.
• ucc – The universal currency converter at XE.com. Use it like ucc 399 aud usd, to convert $399 Australian dollars to US dollars. Then, if you have your cash in Australian dollars, weep about the recent drop in the exchange rate
• man — Like *nix man ‘manual pages’, but for YubNub commands. Eg, man ucc will give the manual page describing how to used the ucc command.
• ls — A bit like the *nix shell ls, this command lists existing YubNub commands that contain your query in their name, description or url. eg. searching ls protein gives you a short list of all the commands related to proteins.

I’ve installed the YubNub opensearch plugin so I can search directly from the search box (or location bar) in Firefox. Maybe one day Ubiquity will fulfill this purpose, since in many way it is the natural progression of the YubNub idea. But for the moment YubNub is the fastest, most streamlined way I’ve found to quickly fire off a search when I need to hunt down a reference, protein sequence or 3D structure. Nothing like instant gratification