Python programming course
On this Wiki you'll find information such as a program and course material for the programming course organised by the department of Human Genetics of the Leiden University Medical Center.
The course is targeted at PhD students, Postdocs, or anyone willing to learn how to program in Python. Students are assumed to have some experience with programming, but not necessarily in Python, and the UNIX shell. There will be a focus on bioinformatics and programming to suppor scientific research in general.
The program consists of four mornings with lessons and some assignments to be done in your own time (i.e., during the afternoons).
The next installment will be in the week of July 14-18, 2014. Registration is required and handled by MGC. Register at their website.
Thanks!
The organizers
Teachers
Program
| Day | Time | Lesson | Keywords | Teacher |
|---|---|---|---|---|
| Monday | 09-10 | Welcome, Introduction to Python (1) | arithmetic, variables, types | Martijn |
| 10-11 | Introduction to Python (2) | container types, control flow, iteration | Jeroen | |
| 11-12 | Introduction to Python (3) | functions, objects, files | Michiel | |
| Tuesday | 09-10 | More Python goodness (1) | strings, comments, errors | Michiel |
| 10-11 | More Python goodness (2) | modules, standard library, input/output | Wai Yi | |
| 11-12 | Working with NumPy arrays | indexing, slicing, reductions, broadcasting | Martijn | |
| Wednesday | 09-10 | IPython Notebook | reproducible research, cell types | Michiel |
| 10-11 | Plotting with matplotlib | plotting, figure layout | Jeroen | |
| 11-12 | Painting Pandas | data frames, reading data, plot types | Wai Yi | |
| Friday | 09-10 | Object-oriented programming | classes, special methods, inheritance | Jeroen |
| 10-11 | A sip of Biopython (1) | packages, sequences | Wai Yi | |
| 11-12 | A sip of Biopython (2) | input/output, online resources, blast | Martijn |
Instruction for uploading assignment solutions for review
Our etherpad is at tinyurl.com/leidencourse
Location: room J1-83, LUMC building 1.
Prerequisites
The following are required before taking the course:
- Programming experience in at least one language
- Affinity with the UNIX shell (our scripting course is more than enough, or you could go though tutorials 1-3 here)
We recommend taking our course on version control with git first, but this is not required.
We can provide you with a laptop that has all the required software installed. You can also use your own laptop, but make sure it has the necessary software installed (see below). The lessons are interactive, meaning that you really need a laptop.
Software installation
Contact
You can contact Martijn Vermaat or any of the other teachers for more information.
Attachments (1)
- INSTRUCTIONS.pdf (99.4 KB) - added by martijn 3 years ago.
Download all attachments as: .zip
