The Nowgen Centre, University of Manchester
Nov 10-14, 2014
9:00 am - 5:00 pm
Instructors: Aleksandra Pawlik, Aleksandra Nenadic
Helpers: Andy Brass, Mike Cornell
General Information
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.
Where: 29 Grafton Street, Manchester, M13 9WU. Get directions with OpenStreetMap or Google Maps.
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 admin-uk@software-carpentry.org for more information.
Etherpad is an on-line collaboration environment which will be used for sharing information and notes during the workshop.
Schedule
Day 1, Monday 10th November
| 9:00 | iPad induction |
| 10:30 | Coffee break |
| 11:00 | Introduction and learning objectives |
| 12:00 | Lunch break |
| 13:00 | Working effectively with command line - part 1 |
| 15:00 | Coffee break |
| 15:30 | Working effectively with command line - part 2 |
| 16:45 | Wrap-up |
Day 2, Tuesday 11th November
| 09:00 | Version control with Git - part 1 |
| 10:30 | Coffee break |
| 11:00 | Version control with Git - part 2 |
| 12:00 | Lunch break |
| 13:00 | Collaborative work using Git and GitHub |
| 14:00 | Introduction to IPython Notebook |
| 14:15 | Building programs with Python - part 1 |
| 15:00 | Coffee break |
| 15:30 | Building programs with Python - part 2 |
| 16:45 | Wrap-up |
Day 3, Wednesday 12th November
| 09:00 | Building programs with Python - part 3 |
| 10:30 | Coffee break |
| 11:00 | Running Python programs from command line |
| 12:00 | Lunch break |
| 13:00 | Testing your Python code |
| 15:00 | Coffee break |
| 15:30 | Working with XML files in Python |
| 16:15 | Feedback |
| 16:30 | Summary and wrap up |
Day 4, Thursday 13th November
| 09:00 | User requirements gathering and testing - part 1 |
| 10:30 | Coffee break |
| 11:00 | User requirements gathering and testing - part 2 |
| 12:00 | Lunch break |
| 13:00 | ELIXIR requirements gathering |
| 14:00 | Case study – design and implementation of a gene file parser - part 1 |
| 15:00 | Coffee break |
| 15:30 | Case study - design and implementation of a gene file parser - part 2 |
| 16:45 | Wrap-up |
Day 5, Friday 14th November
| 09:00 | Case study (continued) - complete the writing and documentation of a parser appropriate for a clinical bioinformatics lab in the NHS |
| 10:30 | Coffee break |
| 11:00 | Case study - part 4 |
| 12:00 | Lunch break |
| 13:00 | Case study - part 5 |
| 15:00 | Coffee break |
| 15:30 | Case study - part 6 |
| 16:00 | Wrap-up |
Syllabus
The Unix Shell
- Files and directories:
pwd,cd,ls,mkdir, ... - History and tab completion
- Pipes and redirection
- Looping over files
- Creating and running shell scripts
- Finding things:
grep,find, ... - Reference...
Lessons
Programming in Python
- Using libraries
- Working with arrays
- Reading and plotting data
- Creating and using functions
- Loops and conditionals:
for,if,else, ... - Defensive programming
- Using Python from the command line
- Reference...
Lessons
- "Computable" app for IPython Notebook for IPads
- Lesson 1: Introduction
- Lesson 2: Functions
- Lesson 3: Loops
- Lesson 4: Branching and conditionals
- Lesson 5: Running your code from commandline
- Lesson 6: Errors and exceptions
- Lesson 7: Testing your code and quality assurance
- Lesson 8: Working with XML files
Version Control with Git
- Creating a repository
- Recording changes to files:
add,commit, ... - Viewing changes:
status,diff, ... - Ignoring files
- Working on the web:
clone,pull,push, ... - Resolving conflicts
- Open licenses
- Where to host work, and why
Lessons
Setup
The participants will be working on the Software Carpentry Virtual Machines setup up on the computers at the university lab.
Overview
Virtual Machine
If you wish to try out the Virtual Machine on your own laptop/desktop, please follow these steps:
- Install VirtualBox.
- Download our VM image. Warning: this file is 1.7 GByte, so please download it before coming to your workshop.
-
Load the VM into VirtualBox by selecting "Import Appliance"
and loading the
.ovafile.