If I were standing for office...

With the general election suddenly looming and seeing how none of the parties running really represent my set of ideals, I thought I would write down what I really want to see represented. Ideally I would have research conducted on all of these areas and follow their findings. Science comes before tradition. My ill informed policies so far would be: ´┐╝Democracy Abolish the House of Lords, build a new parliament [Read More]

[Project log #4] Finally a chance to build something!

After looking at the data I was given, I have been using my limited biology knowledge to come up with theories as to how the data was created, what it means, and how it would best be used. This process has taken about three weeks, and in that time I spent good chunk of it lamenting over the blast2go outputs that I had been given. I thought they were the [Read More]

Vim text objects, extend Vim's natural language!

One of the magical things about Vim is that it uses nouns and verbs to construct an editing language. For example d (delete) is a verb and w (word) is a noun. By combining a noun & verb we make an edit. Learning this language is key to getting the most out of your editing, I recommend this great talk by Chris Toomey if this concept is new to you. [Read More]

[Project Log #3] Pipeline for annotating DNA contigs

This is the set of steps I have followed in an attempt to annotate the data I have been given, and put it into a database. At the moment is is almost entirely a manual task, but if the scope for my project allows I would like to make this into a fully automated process that is compatible with the web front end that I produce. Raw contigs First set [Read More]

[Project Log #2] A better understanding of the task at hand

Today I was able to meet with two of the researchers who are studying the yeasts that I will be working with. It was great to finally meet them, although they said a lot of long scary words, but were very reassuring! Their research has been looking at three species of yeast, Candida Tropicalis, Candida Boidinii, and Candida Shehatae. Candida Tropicalis is very good at metabolising Arabinose & Xylose, however [Read More]

Github style diff in terminal with icdiff

Improved Colour Diff or icdiff gives you nice github style diffs in the terminal. It does work well, however getting it to work with git smoothly was a little fiddly so I thought I would share. Just add this to your ~/.gitconfig. [alias] showtool = "!f() { git difftool $1^ $1; }; f" added = difftool --cached [diff] tool = icdiff [difftool] prompt = false [difftool "icdiff"] cmd = /usr/bin/icdiff --line-numbers $LOCAL $REMOTE [pager] difftool [Read More]

Solving reddits missing features with simple PRAW scripts

I love reddit, and let's be honest I'm probably a bit of an addict. When you come to use the site a lot, you will end up noticing that it is missing a few key features. Thankfully with a little bit of Python and the amazing PRAW (Python Reddit API Wrapper) library, you can solve these problems really quickly. Search saved links Have you ever wanted to search for that [Read More]

Evaluate a URL to get it's domain and port

In NodeJS if you need to take a URL and extract the domain, protocol and port out, you may have noticed it is harder than it sounds. We came across this problem when creating itsback.at, and this is what we came up with. It currently only checks for http(s) and not other protocols like ftp links. It should return you the domain and port number, defaulting to port [Read More]

ES6 boilerplate, with Webpack, Mongoose, Pug, Stylus and a bunch of other goodies

During my industrial year at Clock Limited I was exposed to a lot of new javascript technologies, however working on an existing code base means you can't always use the latest and greatest tools that you want to. As a side project myself, Kenan, Ben and Matt decided to work on something a little bit different on friday afternoons to keep the noodles ticking over. We came up with itsback. [Read More]

[Project Log #1] Today I found out rm can only take 100,000 arguments at a time...

I've just began working on my final year project, and was advised to document my progress in a diary or blog, so here we go. My project is going to be based around genomic data that has been sequenced from three strains of yeast. The plan is to annotate the sequenced contigs of DNA, and then compare them against each other to see where the genes of the yeasts differ. [Read More]