Amsterdam Science Park Study Group

LET'S MAKE RESEARCH FASTER, BETTER AND MORE OPEN!

EVENTS

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).

Please find a complete list of our past events on the dedicated events page.

WHAT WE DO

The Amsterdam Science Park Study Group is dedicated to building a community of computational scientists in biology and other disciplines.

This Amsterdam Science Park Study Group promotes skill sharing and collaboration by:

All are welcome regardless of their scientific research area, affiliation or training level.

Lessons

Workshops

Two-day Data and Software Carpentry workshops to practice and learn coding. We also do shorter themed sessions.

Pair Programming

Tool development

Creation of ad hoc applications and pipelines for research

Community Building​

Meet your peers and start working together. Ask and answer questions.