«

Freiburg Galaxy Team at the Galaxy Community Conference 2021


»

The Freiburg Galaxy Team participated in the Galaxy Community Conference 2021 with:

To learn more about the Galaxy Community Conference 2021, please read our post: “Highlights from the Galaxy Community Conference 2021”

Talks

Analysis of Microscopy Data in Galaxy

Beatriz Serrano-Solano

With Yi Sun; Jeremy Goecks; Jean-Karim Hériché

Abstract, Slides

Modernizing the Galaxy Backend - Typing and the API

David López

With Galaxy Backend Working Group

Abstract, Slides

Posters / Demos

Automating Galaxy tool requirement updates with Planemo

Simon Bray

With Lorraine Coelho; Björn Grüning

Abstract

BoF

GTN-Español - Bioinformatics resources in human-translated Spanish

Co-organized by Beatriz Serrano-Solano

We’re trying to move beyond Google-translate into manually translated tutorials, slide-decks, and videos in Spanish for a workshop. Anyone who speaks Spanish and would be keen to get involved in developing or testing these resources would be very welcome! And double gold star if you know anything about translation or automated translation, as long-term we want to see how we can power this up bigger scale.

Galaxy for Microbiome - Kickoff

Co-organized by Bérénice Batut

Many efforts on microbiome analysis are done in Galaxy but we do not communicate so much together about them. To avoid redundancy and coordinate our efforts, we would like to start a “Galaxy for Microbiome” community.

We started to collect ideas about this community in a shared document. We would like now to properly kickoff this community. What is better to kickoff a community than a BoF at GCC?

Galaxy & Training / Teaching

Co-organized by Bérénice Batut; Björn Grüning

Discussions on using Galaxy for training / teaching and the Galaxy Training Network community:

  • training material (recent and future developments)
  • using Galaxy for undergraduate instruction
  • training / teaching delivery and events
  • community building (instructors, contributors, users, mentoring)

CoFest

GCC ends with two days gathering community members who are interested in contributing to Galaxy’s code base, available tool set, documentation, training materials, and anywhere else that expands the Galaxy ecosystem.

The Freiburg Galaxy team participated in several projects

  • Microbial & Microbiome tool integration and update
  • Community Directory
  • Creating learning paths within the Galaxy Training Network
  • Populating FAQ (Frequently Asked Questions) pages in the GTN
  • Workflows (IWC)
  • and many more informal projects

Training

The Freiburg Galaxy team supported the GCC2021 Training Week by providing videos (below), developping and updating material, helping participants by answering their questions on Slack, helping with captions for videos, etc!

Running Workflows from the Command Line using Planemo

Simon Bray

With Wolfgang Maier

Material

  • Tutorial

Assembly: Unicycler assembly of SARS-CoV-2 genome

Cristóbal Gallardo

Material

  • Slides
  • Tutorial

Reference-based RNA-Seq data analysis

Bérénice Batut

Material

  • Tutorial

Whole transcriptome analysis of Arabidopsis thaliana

Cristóbal Gallardo

Material

  • Slides
  • Tutorial

Analysis of plant scRNA-Seq Data with Scanpy

Mehmet Tekman

Material

  • Tutorial

Introduction to Machine Learning

Anup Kumar

Material

  • Slides

Classification in Machine Learning

Anup Kumar

Material

  • Tutorial
  • Slides

Regression in Machine Learning

Anup Kumar

Material

  • Tutorial
  • Slides

High Throughput Molecular Dynamics and Analysis

Simon Bray

Material

  • Tutorial

Creating a new Tutorial

Bérénice Batut

Material

  • Tutorial