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:
- 2nd Nov. → JM2/04 (Journalism and Media building)
- 9th Nov. → LSG/14b (Lockside building)
- 16th Nov. → JM2/04
- 23rd Nov. → R2/36 (location TBC)
- 30th Nov. → LSG/14b (location TBC)
- 7th Dec. → R2/36 (location TBC)
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:
- if you have any flavour of Linux or a Mac, you don’t have to do anything, they have Bash installed by default;
- if you have a Windows 10, you have to enable Bash or install Git Bash (choose one or the other, not both);
- if you have an older version of Windows, you have to install Git Bash.
- Windows users need to install a free text editor Notepad++;
- Mac users need to install a free text editor BBEdit (the full version of BBEdit is paid, but we will be using features only from the free basic version);
- Linux users need to install Gedit (Ubuntu Linux users have it already installed as their default text editor).
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
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.
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.