A very common task for anyone involved in genetics is the manipulation of DNA or RNA sequences. I need to find the reverse compliment of sequences all the time, and I’ve been getting increasingly frustrated with the lack of a simple, robust tool to do that – most require strictly formatted sequences, use Java applets which take ages to load, and are generally faffy.
I thought I’d do something about this, so I made my own:
http://www.tallphil.co.uk/bioinformatics/sequences/
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My college, Trinity Hall, was recently in need of a new system to allow students and staff to comment on Hall food. As I couldn’t find anything that specifically met our need, I put together a standalone package. You can see a live demo (without Raven authentication) here.
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Rather than sitting on my hard disk getting dusty, I thought I should start publishing the bioinformatics scripts that I’ve written over the past few years of my PhD.
The first to go up is a Perl script called “Genome RE Sites” – it searches a genome of your choice for a restriction endonuclease recognition site and outputs the co-ordinates of all cut sites.
[ Update ] : You can find an online version of this tool here.
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I was working on a project earlier where I was using the wp_nav_menu function in WordPress to create a menu. By default, WordPress creates menus which are wrapped in layers (<div>), an unordered list (<ul>), list items (<li>) and then a link (<a>). However, on this project I wanted to use jQuery UI to generate a navigation, and that required just links (<a> <a> <a>).
So, to strip out all of those extra HTML tags, I used the following javascipt (as I was already relying on jQuery and javascript anyway).
var newmenu = '';
jQuery("#nav ul li").each(function() {
newmenu += jQuery(this).html();
});
jQuery("#nav").html(newmenu);
This works by firstly looping through all of the list items in my navigation layer, and copying their contents (the menu link) into a variable. Then, I replace all of the HTML contained within my navigation layer with that string. Easy!
I just came across the Chosen JavaScript plugin, thanks to a link on the excellent CSS-Tricks RSS feed. It’s a jQuery / Prototype plugin which turns regular HTML <select> dropdown boxes into functional uber-awesome units of happiness.
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I’ve been using the excellent Flickr Press plugin to display flickr sets on a website that I’ve been working on lately, and I made a few changes to make life easier. In case anyone else may find them useful, I’ve uploaded the modified plugin here for general use. I’ve notified the original author, so hopefully if he likes the changes they may be pushed in a future update. For now you can download it here.
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I’ve been using the excellent flickr badge on a website lately, and decided that it would be nice to put the script in as a widget, with easy to update options to customise it. So, I wrote a quick plugin which does just that…
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My new favourite website: nikebetterworld.com.
By Ian Coyle, found through css-tricks.
I was doing some RNA-FISH today and was using some random fluff to find the focal plane when I came across this fella – kind of looks like a heart, no? Except it’s about 10µM across (roughly 10,000 times smaller than a human heart)
I don’t change my work desktop wallpaper very often, and when I do I’m usually very picky. I spent a while digging around deviantART yesterday and came across a new one by ~pr09studio called It’s my turn.
Think this one’s a keeper…