EMBL Rome: Introduction to Unix and Python Programming

Malvika Sharan   2018-10-29   Comments Off on EMBL Rome: Introduction to Unix and Python Programming

Date(s) - 2018-10-29 - 2018-11-01
09:30 CET - 17:00 CET

About the course


Computational skills are becoming increasingly important for effective biological research. Many of the systems that are used to perform computational analyses – such as the EMBL compute cluster – run on a Linux operating system and require interaction via the command line. Mac computers also run on a similar architecture, sharing most of the features of Linux environments. An understanding of these environments and the skills and tools required to make use of them, can improve the efficiency of your work and help to prevent errors in your data analysis.


Python has grown in the last ten years to become one of the most widely-used programming languages in biology. This increasing popularity reflects how easy Python is to learn compared with other languages, and how adaptable it is to a wide variety of different tasks. Simultaneously, the rise of data-driven approaches to science means that programming skills are becoming more and more important for biologists.

Course content

  • The basic concepts and building blocks of Unix and Python programming language
  • Automating repetitive tasks and calculations
  • Reading and handling data from a file

Learning goals

This course aims to teach Unix and basic programming skills to the life scientists who wish to carry out repeated tasks to deal with biological data. The goal of the course is to enable them to use Unix and Python scripting to automate their tasks and carry out analysis of their data reproducibly.

Course Outcome

After attending the sessions on Unix modules, you will be able to use the most basic UNIX (linux/Mac OS X) commands and and should be confident and competent in navigating around a linux filesystem, performing basic file operations and finding help on the commandline.

After attending the sessions on Python modules, you will have a good understanding of the core themes of programming, and be able to write your own Python programs, to automate repetitive analysis tasks.


We do not expect the participants to have any prior knowledge of scripting. This is a course for the researchers who wish to automate their tasks such as dealing with a large number of files to carry out identical or similar analysis using Unix and Python programming language.

Course Trainer

Malvika Sharan, more TBA

Possible Course Dates

This course can be offered for any consecutive 2 days between October 29 – November 2.

Important Notes

– The course will be offered for free.
– The installation guidelines will be shared with the participants via email.
– This course will be primarily offered to the participants from EMBL Rome, however it is possible for the participants from other EMBL location to attend it.
– The course may invite external students from Rome in case there is lower demand of this course EMBL Monterotondo.
– The participants will be responsible for organizing their accommodation, travel and any related cost.


Bookings are closed for this event.

About Malvika Sharan

I am a Community Outreach Coordinator for Bio-IT and Training Coordinator for ELIXIR Germany. Find me at EMBL-HD office 101 or at Bio-IT drop-in Sessions on Tuesdays 10:00-12:00 at the EMBL staff lounge. Contact Details: email - malvika.sharan@embl.de, Twitter - https://twitter.com/MalvikaSharan, GitHub - https://github.com/malvikasharan.