Amsterdam Science Park Study Group

In this workshop, you will learn how to carry out a common metagenomics workflow – identifying Operational Taxonomic Unities (OTUs) among samples taken from two metagenomes within a location. We will be starting with a set of sequenced reads (.fastq files), performing some quality control steps, assembly those reads into contigs, and ending by identifying and visualizing the OTUs among these samples.

The microbial diversity will be further analysed using R enabling you to generate publication-grade figures and fully explore the outcomes of a metagenomics experiment.

As you progress through this lesson, keep in mind that, even if you aren’t going to be doing this same workflow in your research, you will be learning some very important lessons about using command-line bioinformatics tools as well as downstream analysis in R. What you learn here will enable you to use a variety of bioinformatics tools with confidence and greatly enhance your research efficiency and productivity.

People involved: Marc Galland (UvA, organiser), Jesse Kerkvliet (Utrecht UMC, instructor), Misha Paauw (UvA, SILS, instructor), .

Workshop website: https://scienceparkstudygroup.github.io/2022-12-08-shotgun-metagenomics-workshop/

How to register: to be announced.

Last October, Yu-Hsien Li, a postdoctoral researcher working at SILS, Plant Physiology Department, attended a training workshop focused on structural bioinformatics and organised by the European Molecular Biology Lab (EMBL). Yu-Hsien Li training was funded by the Amsterdam Science Park Study Grant in order to participate to the course in exchange for a small workshop based on what he learned. This workshop will consist of a free lunch followed by two parts on structural protein bioinformatics.

Workshop programme

12.30 – 13.00: free lunch

13:00-13:45 (part I, Yu-Hsien Li)

1. Introduction of EMBL Structural bioinformatics course and their free course resource
2. Protein database application (InterPro and UniProt)
3. Alphafold application

13:45-13:55: Break

13:55-14:40 (invited guest researcher: Bulah Wu)

1. Introduction of Molecular docking
2. Autodock Vina application
3. Visualization of docking result

14:40-15:00 Questions & Answers

Useful link: EMBL training course attented by Yu-Hsien.

Contact: Stacy Shinneman (organiser, s.shinneman@uva.nl) and Yu-Hsien Li (y.h.lin@uva.nl).