BioBash Python

BioBash Python workshop is a 5 day workshop designed for life science researchers and bioinformaticians who are already working on data analysis and are eager to learn some basic and not-so-basic Python skills.

  • Build solid programming foundations in Python using carefully crafted hands-on tutorials with biological examples.
  • Learn about Python data types and control flow statements.
  • Build your own Python scripts that will run on any platform.
  • Develop your own functions and learn to work with files.
  • Document your code and learn about methods of reproducible research.
  • Learn about bugs and exceptions.
  • Interact with the Linux command line from within your Python script.
  • Plot your data using matplotlib.
  • Upgrade to BioPython to access online databases, parse biological file formats and use online and local BLAST.

Please note that all workshops are held in English.

Workshop Agenda

Our Python workshop consists of 9 learning modules that cover setting up Linux environment, getting to know Linux command line, introduction to Python, functions and dictionaries in Python, regular expressions in Python, introduction to the standard library, working with files and sequences in BioPython, retrieving data from online databases with BioPython and BLAST basics.

Day 1

9.00 – 10.00 Introduction
10.00 – 11.00 Linux: Basics; Command Line
11.00 – 11.15 Coffe Break
11.15 – 12.30 Linux: Command Line (continued)
12.30 – 13.30 Lunch
13.30 – 15.00 Python: Basic Data Types
15.00 – 15.15 Coffe Break
15.15 – 17.00 Python: Loops and Conditional Expressions

Day 2

9.00 – 11.00 Python: Defining Custom Functions
11.00 – 11.15 Coffe Break
11.15 – 12.30 Python: Dictionary
12.30 – 13.30 Lunch
13.30 – 15.00 Python: Regular Expressions
15.00 – 15.15 Coffe Break
15.15 – 17.00 Python: Regular Expressions (continued)

Day 3

9.00 – 11.00 Python: Introduction to Standard library
11.00 – 11.15 Coffe Break
11.15 – 12.30 Lecture: Coding Style
12.30 – 13.30 Lunch
13.30 – 15.00 Python: Exceptions and Bugs
15.00 – 15.15 Coffe Break
15.15 – 17.00 Python: Exceptions and Bugs

Day 4

9.00 – 11.00 Python: Interactive computing with iPython
11.00 – 11.15 Coffe Break
11.15 – 12.30 Lecture: Reproducible Research
12.30 – 13.30 Lunch
13.30 – 15.00 Python: Plotting
15.00 – 15.15 Coffe Break
15.15 – 17.00 Python: Plotting (continued)

Day 5

9.00 – 11.00 BioPython: Files and Sequences
11.00 – 11.15 Coffe break
11.15 – 12.30 BioPython: Public Databases
12.30 – 13.30 Lunch
13.30 – 15.00 BioPython: BLAST
15.00 – 15.15 Coffe Break
15.15 – 16.00 Closing

What Is Covered by the Workshop Fee?

The cost of the 5 day workshop includes a comprehensive & easy to follow handbook, a 32 GB USB flash drive with Linux working environment, and lunch and coffee breaks each day of the workshop. At week’s end, you will receive a professional certificate of completion.

Please note, the price does not cover accommodation or travel to the location of the workshop.

USB Flash Drive Boot

All participants will be provided with a Linux working environment installed on an external USB flash drive at no additional cost. This will ensure proper learning setup. The USB key can later also be used as a portable Linux data analysis environment on any laptop or PC.

Laptop & Equipment

Participants should bring a laptop with WiFi support able to boot from USB keys. In case we fail to boot your computer into Linux from the USB keys, you will need to agree to install a VirtualBox and run Linux from within your current operating system. Instructions and software will be provided at the workshop. Note that you need at least 15 GB of free disk space and at least 4 GB of memory (RAM) for this option, and that you can safely and completely remove the software after the workshop.

Available Python Workshops to Apply

No workshop dates currently available.