British geneticist interested in splicing, RNA decay, and synthetic biology. This is my blog focusing on my adventures in computational biology. 

Compbio 000: Introduction

Welcome to my blog. This is the blog of a weblab biologist trying to learn some computational biology. I have learnt a lot in the past couple of years and I want to use this blog to share some of the tools, code and know hows I have picked up. Hopefully others will use this to take some shortcuts to boost their productivity; I want to help people to cut out some of the trial and error that I had to go through. 

I have done a lot of RNA-seq analysis and am coding/scripting in Python with plotting in R. Both are very common in compbio so others learning can pick up some relevant tips. But the most important thing I have learnt since enting compbio is the command line. Learning bash and how to use the many amazing tools for the command line has been a real eye-opener. And the more I learn, the more of the verbose and time consuming things I do in Python and R I can replace with simple and quick one-liners on the command line. So there will be some post about cool tools and things that I wished I had known about when I was start out on the command line and with programming. 

Initially, I will start posting in a series on compbio tips and guides. In the future I may expand the scope of the blog to include other things that interest me outside of compbio. 

Finally, onto the name of the blog: Bad Grammar, Good Syntax. So I am dyslexic, so I have always struggled with spelling and grammar. There will be more than one spelling mistake, missed typo and poor grammar as I post. Please forgive me. Feel free to point it out, I am quite used to that. But one thing that is both infuriating and beautiful that I learnt about programming was the importance of syntax. The human is an amazing machine. Despite spelling mistakes and grammatical "errors", humans can usually get the meaning of a sentence. Machine cannot do the same with code. A misplaced comma or semicolon will make the code meaningless. This is the syntax of the code and by the very nature of programming, you are forced to have good syntax, otherwise the code just will not work. Hence the name of this blog, no one is stopping me putting bad grammar online, by the machine will refuse to take anything but good syntax (that doesn't mean my code will be elegant, but at least it will be functional). 

Also, 50 points to anyone who can spot the intentional spelling/grammatical error in this first post. 

Compbio 001: A what is programming guide for a biologist