Nov 10-14, 2014
9:00 am - 5:00 pm
Instructors: Aleksandra Pawlik, Aleksandra Nenadic
Helpers: Andy Brass, Mike Cornell
Software Carpentry's mission is to help scientists and engineers become more productive by teaching them basic lab skills for computing like program design, version control, data management, and task automation. This workshop (lasting 3 days: 10-12th November) is a part of the 5-day MSc Clinical Bioinformatics programme (10-14th November). During the hands-on training sessions we will cover core skills such as effectively working with command line, structured software development and version control. The participants will be encouraged to help one another and to apply what they have learned to their own research problems.
Who: The course is aimed at the postgraduate students of the MSc Clinical Bioinformatics course at the University of Manchester.
Requirements: Participants will work on the Software Carpentry Virtual Machines provided by the University. They are also required to abide by Software Carpentry's Code of Conduct.
Contact: Please mail firstname.lastname@example.org for more information.
Etherpad is an on-line collaboration environment which will be used for sharing information and notes during the workshop.
|11:00||Introduction and learning objectives|
|13:00||Working effectively with command line - part 1|
|15:30||Working effectively with command line - part 2|
|09:00||Version control with Git - part 1|
|11:00||Version control with Git - part 2|
|13:00||Collaborative work using Git and GitHub|
|14:00||Introduction to IPython Notebook|
|14:15||Building programs with Python - part 1|
|15:30||Building programs with Python - part 2|
|09:00||Building programs with Python - part 3|
|11:00||Running Python programs from command line|
|13:00||Testing your Python code|
|15:30||Working with XML files in Python|
|16:30||Summary and wrap up|
|09:00||User requirements gathering and testing - part 1|
|11:00||User requirements gathering and testing - part 2|
|13:00||ELIXIR requirements gathering|
|14:00||Case study – design and implementation of a gene file parser - part 1|
|15:30||Case study - design and implementation of a gene file parser - part 2|
|09:00||Case study (continued) - complete the writing and documentation of a parser appropriate for a clinical bioinformatics lab in the NHS|
|11:00||Case study - part 4|
|13:00||Case study - part 5|
|15:30||Case study - part 6|
The participants will be working on the Software Carpentry Virtual Machines setup up on the computers at the university lab.
If you wish to try out the Virtual Machine on your own laptop/desktop, please follow these steps: