bIOINFORMATICS with Bash and Python


14-18 October 2019



Freie Universität Berlin; Otto-von-Simson-Straße 26, 14195 Berlin

Course overview

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.


Intended audience

This course is aimed at complete beginners - no previous Linux or Python experience is required. It will be helpful if you have a basic knowledge of molecular biology so that you will be able to follow the examples - i.e. you should know what DNA and protein sequences look like, what an intron is, etc. The course is most likely to be useful if you have some idea of the type of analyses that you will need to automate. If you have any questions about whether this course is likely to be suitable/useful, drop an email to the course tutor and we will figure it out.

Session content

Monday -Classes from 9:30 to 17:30


Session 1 – Connecting to the server and basic Linux commands

Session 2 – Assembling Linux commands into pipelines




Dr. Martin Jones


Martin started his programming career by learning Perl during the course of his PhD in evolutionary biology, and started teaching other people to program soon after.

Available Packages

Package 1:


Course and refreshments


Package 2:

Course material, refreshments, lunch and accommodation



480 €








  795 €


Please click HERE to get all the information about our packages.




Registration deadline: 26th September 2019



Cancellation Policy:


> 30  days before the start date = 30% cancellation fee

< 30 days before the start date= No Refund.


Physalia-courses cannot be held responsible for any travel fees, accommodation or other expenses incurred to you as a result of the cancellation.