Metagenomics workshop

Utrecht Medical Center

December 8-9, 2022

09:30 - 17:00 CEST

Instructors: Eva Lekkerker, Tijs Bliek, Misha Paauw, Jesse Kerkvliet, Sam Nooij, Fatemeh Karimi Nejadasl

Helpers: Claudia Zirion Martinez, Tijs Bliek

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General Information

This workshop is organised by the Amsterdam Science Park Study Group, a local community of computational biologists working at the University of Amsterdam and the Data Science Center from the University of Amsterdam. This workshop has benefited from the collaboration of instructors from the Carpentries Foundation operating at academic institutions across the Netherlands.
Eva Lekkerker (Digital Skills Coordinator, Data Science Center, UvA) and Tijs Bliek (SILS, Faculty of Science, UvA) will jointly act as the lead instructors. We are very grateful to Anita Schurch from the Utrecht University Medical Center for hosting this workshop.

Data Carpentry develops and teaches workshops on the fundamental data skills needed to conduct research. Its target audience is researchers who have little to no prior computational experience, and its lessons are domain specific, building on learners' existing knowledge to enable them to quickly apply skills learned to their own research. Participants will be encouraged to help one another and to apply what they have learned to their own research problems. For more information on what we teach and why, please see our paper Good Enough Practices for Scientific Computing.

Who: The course is aimed at graduate students and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: Heidelberglaan 100, 3584 CX Utrecht. Get directions with OpenStreetMap or Google Maps.

When: December 8-9, 2022. Add to your Google Calendar.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below).

Accessibility: We are committed to making this workshop accessible to everybody. For workshops at a physical location, the workshop organizers have checked that:

Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.

Contact: Please email m.m.paauw@uva.nl , j.j.kerkvliet@umcutrecht.nl , S.Nooij@lumc.nl , f.kariminejadasl@uva.nl or claudia.zirion@cinvestav.mx for more information.

Roles: To learn more about the roles at the workshop (who will be doing what), refer to our Workshop FAQ.


Code of Conduct

Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.


Collaborative Notes

We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.


Surveys

Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey


Schedule

Day 1 - Thursday, December 8
Room Vredenburg/Neude

Before starting Pre-workshop survey
09:30 - 10.00 Welcome and Introduction (Eva)👋
10.00 - 10.30 Project Organization and Management (Claudia)
10:30 - 12.00 Introduction to the command-line (Fatemeh)
12:00 - 13.00 Lunch break 🥪 🍎 🥛
13.00 - 14.30Introduction to the command-line (Fatemeh)
14:30 - 14.45 Coffee ☕ tea 🍵 break
14.45 - 17.00Metagenomics: Introduction, QC, trimming (Misha).
Evening END

Day 2 - Friday, December 9
Descartes building

Before startingShort recap of day 1
09:30 - 11.00Metagenomics: assembly, binning (Jesse).
11:00 - 12.00Metagenomics: taxonomic assignment (Jesse).
12:00 - 13.00 Lunch break 🥪 🍎 🥛
13:00 - 14.30Metagenomics: diversity analysis with R (Sam).
14:30 - 14.45 Coffee ☕ tea 🍵 break
14.45 - 16.30Metagenomics: taxonomic analysis with R (Sam)
16.30 - 17.00Day 2 recap and next steps 🚀 😺
Evening Post-workshop survey
END

Setup

To participate in a Data Carpentry workshop, you will need access to software as described below. In addition, you will need an up-to-date web browser.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

The setup instructions for the Data Carpentry Genomics workshops can be found at the workshop overview site

.