Welcome to BrykLab.

Coding club - the shell

Date, time and place

Coding club - the shell edition :-) will start on Thursday, 2nd November 2017 at 1-3pm. Due to various building works and general timetabling challenges, we will need to change rooms every week - the updated list of locations is below:

Requirements: Bash, Dropbox and a text editor

To participate in the course, you will need to bring a computer with the following programmes and datasets:

Bash

Text editor

Data

The data required to run almost all the examples from the shell lessons is available from Software Carpentry’s repository on Github. Download the whole set as a zip file; extract it and only keep the folder data-shell.

Dropbox

For the course materials, quizzes and answer submissions, we will use a shared Dropbox folder, so you will need to have Dropbox installed. You will receive the link to the shared folder during the first meeting. If you are going to attend the coding club but will not be present on the first meeting, let me know via email that you need the link to the Dropbox folder.

Recommended reading

Before the first meeting, please complete the free lessons from Code Academy’s Learn The Command Line tutorial (no installation necessary).

I also maintain a webpage of various computational biology resources that includes a short overview of the most basic shell commands. You will find there links to recent good papers arguing for computational biology skills, recommended textbooks and online sources plus various bits and pieces I use during the coding club and Software Carpentry lessons. Have a look: Computational Biology Resources FTW.

Software Carpentry workshops!

In 2017 and 2018 I am co-organising a series of 3-day-long workshops on essential computational skills for life scientists, along with Dr Maju J. O’Connell and Martin Callaghan from the University of Leeds. The workshops are sponsored by BBSRC and therefore are free for all BBSRC-funded researchers and staff and students from Universities of Leeds and Huddersfield. The detailed info about the upcoming workshop (there will be up to 10 workshops throughout a year) is available on the course webpage: Next Generation Biologists.

In terms of content, during the coding club we will cover topics roughly covered in day 1 of the workshop, so even if you attending coding club you are very much encouraged to apply.