BioBash Essentials

BioBash Essentials workshop is designed to provide you with foundational tools that will be required routinely, regardless of your specific research question. The 5-day program brings to life the worlds of Linux and NGS data, and builds solid Python programming skills.

  • Become proficient working in the Linux command line.
  • Discover regular expressions that will provide you with clever ways of searching & manipulating text.
  • Work through an NGS study case to gain platform-independent understanding of raw data processing, assembly and mapping reads.
  • Uncover the full potential of building and querying local BLAST databases.
  • Build solid programming foundations in Python using carefully crafted hands-on tutorials with biological examples.
  • Learn about the Python data types and control flow statements.
  • Build your own Python scripts and run them from the command line.
  • Develop your own functions and learn to work with files.
  • Upgrade to BioPython to access online databases and parse biological file formats.

Please note that all workshops are held in English.

Workshop Agenda

Our Essentials workshop consists of 12 learning modules that cover setting up Linux environment, getting to know Linux command line, introduction to regular expressions, introduction to NGS data analysis, working with local BLAST, Python (introduction, functions and dictionaries, regular expressions and introduction to the standard library) as well as some BioPython (working with files and sequences, retrieving data from online databases and using BioPython to do BLAST searches).

Day 1

09.00 – 09.30 Introduction
09.30 – 11.00 Module 1 – Linux Environment
11.00 – 11.15 Coffee Break
11.15 – 12.30 Module 2 – Linux Command Line
12.30 – 13.30 Lunch
13.30 – 14.30 Module 2 continued
14.30 – 15.15 Module 3 – Regular Expressions
15.15 – 15.30 Coffee Break
15.30 – 17.00 Module 3 continued

Day 2

09.00 – 10.00 NGS Introduction – Lecture
10.00 – 11.00 Module 4 – NGS Data Analysis
11.00 – 11.15 Coffee Break
11.15 – 12.30 Module 4 continued
12.30 – 13.30 Lunch
13.30 – 15.15 Module 4 continued
15.15 – 15.30 Coffee Break
15.30 – 17.00 Module 5 – Local BLAST

Day 3

09.00 – 09.30 Python Introduction
09.30 – 11.00 Module 6 – Python (Introduction)
11.00 – 11.15 Coffee Break
11.15 – 12.30 Module 6 continued
12.30 – 13.30 Lunch
13.30 – 15.15 Module 6 continued
15.15 – 15.30 Coffee Break
15.30 – 17.00 Module 7 – Python (Functions and Dictionaries)

Day 4

09.00 – 11.00 Module 7 continued
11.00 – 11.15 Coffee Break
11.15 – 12.30 Module 8 – Python (Regular Expressions)
12.30 – 13.30 Lunch
13.30 – 15.15 Module 9 – Python (Standard Library)
15.15 – 15.30 Coffee Break
15.30 – 17.00 Module 9 continued

Day 5

09.00 – 11.00 Module 10 – BioPython (Working with files and sequences)
11.00 – 11.15 Coffee Break
11.15 – 12.30 Module 11 – BioPython (Retrieving data from online databases)
12.30 – 13.30 Lunch
13.30 – 15.15 Module 12 – BioPython (BLAST)
15.30 – 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 Essentials Workshops to Apply

No workshop dates currently available.