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Training - Bioinformatics with Bash and Python
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10 months ago

Course: Bioinformatics with Bash and Python

Where: Free University of Berlin (Germany)

When: 14-18 October 2019

Instructor: Dr. Martin Jones (founder, Python for biologists)


A fundamental part of bioinformatics (in contrast to simply computational biology) is the idea of scaling and automation. We want to arrange our tools into pipelines which can be executed with minimal supervision. Reliable automation of this type is key to many of the things that we want from our analyses; chiefly the ability to reproduce our results, and to extend them to other datasets.

In this course we will examine two different systems for automating bioinformatic analyses. For situations where we are mostly running existing command line tools, bash scripting will allow us to build pipelines with minimal overhead. We'll start with simple command lines and see how the Linux environment - though not designed with biology in mind - is well suited to the type of automation we need.

For situations where we don't have an existing tool available, and hence need to implement our own logic, bash quickly becomes unwieldy - it's theoretically possible to write complex programs in bash, but the experience is painful! It's much better to use a more modern programming language, and for most biological tasks Python fits the bill.


Session 1 – connecting to the server and basic Linux commands

Session 2 – assembling Linux commands into pipelines

Session 3 – introduction to bash scripting and variables

Session 4 – flow control in bash, aliases and paths

Session 5 – introduction to Python, text and files

Session 6 – lists and loops in Python

Session 7 – conditions in Python

Session 8 – writing functions in Python

Session 9 – paired data and dicts in Python

Session 10

The afternoon of Friday 18th is reserved for finishing off the next-gen workflow exercise, working on your own datasets, or leaving early for travel.

For more information, please visit the course website:

Here is the full list of our courses and Workshops:


Carlo Pecoraro, Ph.D

Physalia-courses DIRECTOR

Twitter: @physacourses

mobile: +49 17645230846!forum/physalia-courses


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