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%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
<span style="font-size: 200%">Programming in Python</span> <span style="font-size: 200%">Programming in Python</span>
=== ===
<br> <br>
<img src="../images/python_logo.svg" alt="Python Logo"> <img src="python_logo.svg" alt="Python Logo">
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
About the course About the course
=== ===
* Aimed at PhD students, Postdocs, researchers, analysts, ... * Aimed at PhD students, Postdocs, researchers, analysts, ...
* Focus on: * Focus on:
- Basic understanding of Python. - Basic understanding of Python.
- Programming as a tool to do your research. - Programming as a tool to do your research.
- Slightly biased on bioinformatics. - Slightly biased on bioinformatics.
**Note:** This is its third session. **Note:** This is its third session.
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
Hands on! Hands on!
=== ===
**Programming is fun!** **Programming is fun!**
* You only learn programming by doing it. * You only learn programming by doing it.
* Lecture format: * Lecture format:
- Blended teaching + exercising. - Blended teaching + exercising.
* Have your laptop open during the lessons. * Have your laptop open during the lessons.
* Repeat the code from the slides, play around with it. * Repeat the code from the slides, play around with it.
* Do the session exercises. * Do the session exercises.
* There will be a few assignments to submit. * There will be a few assignments to submit.
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
Teachers Teachers
=== ===
* Jeroen Laros<br> * Jeroen Laros<br>
[j.f.j.laros@lumc.nl](mailto:j.f.j.laros@lumc.nl) [j.f.j.laros@lumc.nl](mailto:j.f.j.laros@lumc.nl)
* Mihai Lefter<br> * Mihai Lefter<br>
[m.lefter@lumc.nl](mailto:m.lefter@lumc.nl) [m.lefter@lumc.nl](mailto:m.lefter@lumc.nl)
* Jonathan Vis<br> * Jonathan Vis<br>
[j.k.vis@lumc.nl](mailto:j.k.vis@lumc.nl) [j.k.vis@lumc.nl](mailto:j.k.vis@lumc.nl)
* Mark Santcroos<br> * Mark Santcroos<br>
[m.a.santcroos@lumc.nl](mailto:m.a.santcroos@lumc.nl) [m.a.santcroos@lumc.nl](mailto:m.a.santcroos@lumc.nl)
* Guy Allard<br> * Guy Allard<br>
[w.g.Allard@lumc.nl](mailto:w.g.allard@lumc.nl) [w.g.Allard@lumc.nl](mailto:w.g.allard@lumc.nl)
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
Program Program
=== ===
| Day | Time | Lesson | Teacher | | Day | Time | Lesson | Teacher |
|-------------------|-------|------------------------------------ |----------| |-------------------|-------|------------------------------------ |----------|
| **Monday, 18/9** | 9 - 9:30 | Welcome, Setup | Mihai | | **Monday, 18/9** | 9 - 9:30 | Welcome, Setup | Mihai |
| | 9:30 - 10:30 | Introduction to Python (1) | Mihai | | | 9:30 - 10:30 | Introduction to Python (1) | Mihai |
| | 10:30 - 11:30 | Introduction to Python (2) | Jeroen | | | 10:30 - 11:30 | Introduction to Python (2) | Jeroen |
| | 11:30 - 12:30 | Introduction to Python (3) | Mihai | | | 11:30 - 12:30 | Introduction to Python (3) | Mihai |
| | 12:30 - 13:00 | Practical help | | | | 12:30 - 13:00 | Practical help | |
| **Tuesday, 19/9** | 9-10 | Assignments review | | | **Tuesday, 19/9** | 9-10 | Assignments review | |
| | 10-11 | More Python Goodness (1) | Mihai | | | 10-11 | More Python Goodness (1) | Mihai |
| | 11-12 | More Python Goodness (2) | Mihai | | | 11-12 | More Python Goodness (2) | Mihai |
| | 12-13 | IPython Notebook | Mark | | | 12-13 | IPython Notebook | Mark |
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
| Day | Time | Lesson | Teacher | | Day | Time | Lesson | Teacher |
|---------------------|-------|------------------------------------ |----------| |---------------------|-------|------------------------------------ |----------|
| **Wednesday, 20/9** | 9-10 | Assignments review | | | **Wednesday, 20/9** | 9-10 | Assignments review | |
| | 10-11 | Data manipulation (NumPy, Pandas) | Mark | | | 10-11 | Data manipulation (NumPy, Pandas) | Mark |
| | 11-12 | Data visualisation (1) | Guy | | | 11-12 | Data visualisation (1) | Guy |
| | 12-13 | Data visualisation (2) | Guy | | | 12-13 | Data visualisation (2) | Guy |
| **Thursday, 21/9** | 9-10 | Assignments review | | | **Thursday, 21/9** | 9-10 | Assignments review | |
| | 10-11 | Object-oriented programming | Jonathan | | | 10-11 | Object-oriented programming | Jonathan |
| | 11-12 | Biopython | Guy | | | 11-12 | Biopython | Guy |
| | 12-13 | Putting everything together | Jeroen | | | 12-13 | Putting everything together | Jeroen |
All slides are linked as one-page documents from the course website: [https://git.lumc.nl/courses/programming-course](https://git.lumc.nl/courses/programming-course) All slides are linked as one-page documents from the course website: [https://git.lumc.nl/courses/programming-course](https://git.lumc.nl/courses/programming-course)
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
Software requirements Software requirements
=== ===
* Anaconda: * Anaconda:
* Python 2.7 * Python 2.7
* Comes with all that's required: * Comes with all that's required:
- NumPy, matplotlib, Biopython - NumPy, matplotlib, Biopython
* [Installation instructions](https://docs.anaconda.com/anaconda/install/). * [Installation instructions](https://docs.anaconda.com/anaconda/install/).
* Git * Git
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
Assignments Assignments
=== ===
* We make use of GitHub Classroom: * We make use of GitHub Classroom:
- GitHub account required. - GitHub account required.
- Link with assignment repository. - Link with assignment repository.
- Own forked repository to work on - automated by GitHub. - Own forked repository to work on - automated by GitHub.
- Direct file upload to repository is possible. - Direct file upload to repository is possible.
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
Getting help Getting help
=== ===
* Ask a teacher. * Ask a teacher.
* If it's private, mail one of the teachers. * If it's private, mail one of the teachers.
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
from IPython.display import HTML from IPython.display import HTML
def css_styling(): def css_styling():
styles = open('../styles/custom.css', 'r').read() styles = open('../styles/custom.css', 'r').read()
return HTML('<style>' + styles + '</style>') return HTML('<style>' + styles + '</style>')
css_styling() css_styling()
``` ```
%% Output %% Output
<IPython.core.display.HTML object> <IPython.core.display.HTML object>
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
License: [Creative Commons Attribution 3.0 License (CC-by)](http://creativecommons.org/licenses/by/3.0) License: [Creative Commons Attribution 3.0 License (CC-by)](http://creativecommons.org/licenses/by/3.0)
......
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