Reflection time, how to measure it and how to improve it.

As I wait for a docker container to restart for the 1001st time, an artifact of poor design decisions made on an old project I have been lumbered with, I can't help but feel the need to try to define in more clear terms what I have been referring to as "reflection time". Reflection time is simply the time it takes for a developer to go from a location in [Read More]

Halloumi & Mushroom Pie

Ingredients 2 medium onions 2 medium packs of (different) mushrooms 1 head of garlic 2 red chillies 1 pack of halloumi Flour Oregano Salt Lea & Perrins (Worcestershire Sauce) Pre rolled puff pastry Olive oil Whisky (optional) Equipment Big pan (wok even) Pie tray Prep Slice the two onions into thin strands, the idea is to carmelise them, I tend to find thinner longer peices work nicer. Dice up the [Read More]

Everyday Carry

One of my small obsessions and favourite subjects to nerd out on is everyday carry items, or EDC for short. For people like me the idea is that the things you EDC are the things you use most in life, and if you invest in them they can make your life a lot easier and last a lifetime! Pocket Carry I like to be a minimalist when it comes to [Read More]

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]