Python for biologists
Science course
- Start: Apr 20, 2023 09:00 AM (Local Time Germany)
- End: Jun 1, 2023 11:00 AM
- Speaker: Dr. Maurice Maurer
- Training Scientists is run by Dr. Maurice Maurer who graduated in 2020 with a Ph.D. in computational physics. He specialized on High Performance Computing (HPC) already during his Masters degree. Additionally to teaching scientists in graduate schools like the Max Planck School of Photonics or the MPI IMPRS schools, he is doing Python consulting work for various companies.
- Location: Online
Summary
Biologists need programming skills in Python to analyze their data but have rarely had any programming education during their Bachelor’s and Master’s degrees. Hence, this course has two distinct goals and teaches:
1. to analyze, interpret and visualize scientific data to create publication ready plots
2. good programming practice, version control with GIT and virtual environments
Course structure
The course is held in English and currently consists of 6 modules. Every module contains:
- a 60-90 minute video lecture on moodle.training-scientists.de that the participants can watch when it suits them
- exercises for the participants to apply what they have learned
- a live Zoom tutorial to answer questions (90-120min)
Content
- Installation, Anaconda, Jupyter, GIT, Notebook extensions
- Syntax, PEP8, keyboard shortcuts, Notebook structure
- Numpy, Data analysis, Pandas, File IO: Ascii, HDF5, Excel
- Matplotlib, Visualization, Advanced Plotting, String Formatting
- Video creation, Symbolic Calculation with Sympy, Biopython
- HTSeq, Pysam, Data Analysis example
The times for the six online tutorials are as follows:
20.4. | 27.4. | 4.5. | 11.5. | 25.5. | 1.6. - these are all Thursdays - from 9am - 10.30/11am
Before the first tutorial you should have watched the first
lecture and set up your computer accordingly. Please plan 2-4 h for this.