News: Workshop: Introduction to Linux and workflows for biologists
gravatar for carlopecoraro2
3.6 years ago by
carlopecoraro21.8k wrote:

Dear all,

We are happy to announce that we will be holding the second edition of the “Introduction to Linux and workflows for biologists” in Berlin (Germany) from the 31th July to the 4th August 2017.


Dr Martin Jones (Founder, Python for Biologists)


Most high-throughput bioinformatics work these days takes place on the Linux command line. The programs which do the majority of the computational heavy lifting — genome assemblers, read mappers, and annotation tools — are designed to work best when used with a command-line interface. Because the command line can be an intimidating environment, many biologists learn the bare minimum needed to get their analysis tools working. This means that they miss out on the power of Linux to customize their environment and automate many parts of the bioinformatics workflow. This course will introduce the Linux command line environment from scratch and teach students how to make the most of its tools to achieve a high level of productivity when working with biological data.

Intended audience

This workshop is aimed at researchers and technical workers with a background in biology who want to learn to use the Linux operating system and the command line environment. No previous experience of Linux is required.


Botanischer Garten und Botanisches Museum (BGBM) Berlin-Dahlem, Freie Universität Berlin, Königin-Luise-Straße 6-8, 14195 Berlin.

Course Programme

Monday 31th – Classes from 09:30 to 17:30

Session 1 – The design of Linux

Session 2 – System management

Tuesday 1sh – Classes from 09:30 to 17:30

Session 3 - Manipulating tabular data

Session 4 – Constructing pipelines

Wednesday 2nd – Classes from 09:30 to 17:30

Session 5 – EMBOSS

Session 6 – Using a Linux server

Thursday 3rd – Classes from 09:30 to 17:30

Session 7 – Combining methods

Session 8 – Combining methods

Friday 4th – Classes from 09:30 to 17:30

Session 9 – Customization

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.

Application deadline is June 30th 2017.

Available packages:

1) “only-course” (580 euros VAT included) includes refreshments, lunch and course material;

2) “all-inclusive” (795 euros VAT included) includes refreshments, course material, accommodation and meals (breakfast, lunch, dinner).

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