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Mihai Lefter authoredMihai Lefter authored
- Coordinates
- Teachers
- Audience
- This session:
- Topics to be covered
- Introduction to Python (2.5h)
- More Python Goodness (2h)
- IPython Notebook (1h)
- Data manipulation (1h)
- Data visualisation (2h)
- Object-oriented programming (1h)
- Biopython (1h)
- Putting everything together
- Program
- Assignments
- Installation
- Previous sessions issues
plan.md 5.01 KiB
Coordinates
- When: 18/9 - 21/9
- Where: V7-41 booked between 9:00 - 13:00
Teachers
- Jeroen
- Jonathan
- Guy
- Mark
- Mihai
Audience
- Aimed at PhD students, Postdocs, researchers, analysts, ...
- Prerequisites:
- Linux
- Git
This session:
| Function | Department | Organization |
|---|---|---|
| PhD student | Clinical Genetics | EMC |
| computational biologist | Human Genetics | LUMC |
| PhD student | Hematopoiesis | Sanquin/EMC |
| PhD student | Limes Institute | University of Bonn |
| researcher | Hematologie | LUMC |
| researcher | Human Genetics | LUMC |
| audioloog | KNO | LUMC |
| Geneeskundig medewerker | Medical Microbiology | LUMC |
| research analyst | Human Genetics | LUMC |
| postdoctoral researcher | Molecular Epidemiology | LUMC |
| PhD student | Molecular Epidemiology | LUMC |
| researcher (PhD student?) | Molecular Cell Biology | LUMC |
| PhD student | Molecular Cell Biology | EMC |
| research technician | Genetic Identification | EMC |
| postdoctoral researcher | Genetic Identification | EMC |
| researcher | Clinical Genetics/Ophthalmology | EMC |
| postdoctoral researcher | Anatomy and Embryology | LUMC |
| researcher | Molecular Epidemiology | LUMC |
| PhD student | Human Genetics | LUMC |
| PhD student | Molecular Cell Biology | LUMC |
| researcher | Molecular Cell Biology | LUMC |
Topics to be covered
Introduction to Python (2.5h)
- History.
- Python 2 vs Python 3.
- Running python code.
- Indentation.
- Operations, variables, and Python's type system.
- Data types:
- Lists.
- Tuples.
- Sets.
- Strings.
- Dictionaries.
- Useful built-ins:
- range.
- zip.
- Flow control and iteration.
- Functions.
- Virtual environments.
More Python Goodness (2h)
- Working with scripts.
- The standard library.
- String methods.
- Comments and docstrings.
- Detour: PEP8 and other PEPs.
- Errors and exceptions.
- Working with modules.
- Reading and writing files.
IPython Notebook (1h)
Data manipulation (1h)
- NumPy
- Pandas
Data visualisation (2h)
- Matplotlib
- Bokeh
Object-oriented programming (1h)
Biopython (1h)
Putting everything together
- Packaging
- Real world project examples
Program
- Mornings: presentations.
- Afternoons: assignments.
| Day | Time | Lesson | Teacher |
|---|---|---|---|
| Monday, 18/9 | 9-10 | Welcome, Introduction to Python (1) | Mihai |
| 10-11 | Introduction to Python (2) | Jeroen | |
| 11-12 | Introduction to Python (3) | Mihai | |
| 12-13 | Practical help | ||
| Tuesday, 19/9 | 9-10 | Assignments review | |
| 10-11 | More Python Goodness (1) | Mihai | |
| 11-12 | More Python Goodness (2) | Mihai | |
| 12-13 | IPython Notebook | Mark | |
| Wednesday, 20/9 | 9-10 | Assignments review | |
| 10-11 | Data manipulation (NumPy, Pandas) | Mark | |
| 11-12 | Data visualisation (1) | Guy | |
| 12-13 | Data visualisation (2) | Guy | |
| Thursday, 21/9 | 9-10 | Assignments review | |
| 10-11 | Object-oriented programming | Jonathan | |
| 11-12 | Biopython | Guy | |
| 12-13 | Putting everything together | Jeroen |
Assignments
- Make special document?
- Special repository with the material?
- Students submit merge requests for check-up and feedback?
Installation
There is a tutorial at the moment here.