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Microbial analysis using Galaxy

Community, Projects, Workflows, Tools, and Training

By Paul Zierep (Galaxy Freiburg)

OSA2Micro, Turin, July 2023

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Content

Galaxy

Introduction
Frontend
Running a tool
Interactive tools
Workflows
Architecture

The EU server
Training and the Galaxy Training Network
microGalaxy Community

Community
Survey

Galaxy for Genomics and Metatranscriptomics

Tools
Workflows

Microbiome analysis

Tools
Workflows

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Galaxy Introduction - Huge increase in Sequencing Data

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Galaxy Introduction

Strong increase of generating scientific data: Sequencing technology has become fast and costs are low
Galaxy allows bioinformatics analysis for everyone
No programming skills required
Enable wet-lab scientists to do their own data analysis
Open source framework for high-throughput sequencing data and other big data analysis

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Galaxy Introduction

Galaxy is a gateway for transparent & reproducible data analysis using FAIR principles
Easy accessing (no installation) & sharing of data, tools, analysis, workflows
Multiple interfaces

intuitive web portals for biologists
unified API for bioinformaticians

International: 138+ public instances, 12,000+ citations
UseGalaxy.eu, UseGalaxy.org.au, UseGalaxy.org ...
Funded as international infrastructure project (EuroScienceGateway, ELIXIR, EOSC)

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Galaxy Introduction

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Galaxy GUI

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Galaxy Tools

Galaxy tools are wrappers that export inputs and outputs of command-line tools to the Galaxy GUI
> 9.000 tools
> 3.000 tools on usegalaxy.eu
Large tool suits (Mothur > 100)
New tools can be added by anyone via an open infrastructure
Internally tools require a conda, docker and/or singularity container

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Galaxy behind the scenes - Wrapping a tool

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Wrapping a tool

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Update infrastructure

Planemo: a command-line toolkit for developing, deploying, and executing scientific data analyses, 2022

Training

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Running a tool

Select your

Input data from history
Parameter for analysis
Output data

Each tool comes with

Documentation
Example input and results
Reference
Versioning

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Running a tool - database interaction

Admin based data management via Data Managers
No limit for DBs
No user quota increase

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Running a tool - interactive tools

RStudio
Jupyter Notebooks and specific flavors

Interactive MGnify Notebook
ML
Material Science (PyIron)

Interactive Hdfview tool
Pavian
Phinch

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Running a tool - interactive tools (Phinch)

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Running a tool - interactive tools (Phinch)

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Running a tool - interactive tools (Phinch)

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History - handle the data

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History - handle the data

Move data between histories without quota (or actual space) increase
No limit of histories
Can be shared, downloaded, published

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Data Preview and visualization

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Data Preview and visualization

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Data Preview and visualization

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Workflow building

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Workflow building

How?

Extracted from history (step-by-step)
Built manually (graphical workflow editor)
Import a shared workflow

Why?

Automatize your analysis
Re-run same analysis on different inputs or reproduce results
Change parameter, tool version, DB, workflows logic (add, remove, modify)
Use/create sub workflows
Share them, publish them (peer-reviewed in IWC!) + WorkflowHub

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Workflow building - graphical workflow editor

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Workflow building - share, import, store, update

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The European Galaxy server

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Galaxy - Training - Gallantries

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Galaxy - Training

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Galaxy - Training

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Galaxy - Training

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Galaxy - Training

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Galaxy - learn more

How?

Join training (https://galaxyproject.org/events/) e.g. GTN Smörgåsbord 2024
Galaxy Training Network https://training.galaxyproject.org/
Matrix/Element chat: https://matrix.to/#/#galaxyproject_Lobby:gitter.im
Try it out (free usage of the servers with 250 GB space)

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microGalaxy Community - a community of practice for everything related to micro*

https://galaxyproject.org/projects/microbial/
https://microgalaxy.usegalaxy.eu/
Roadmap development
Collect tools, workflows and tutorials
Bring people together and support each other
https://lists.galaxyproject.org/lists/microgalaxy.lists.galaxyproject.org/
Next community call: during GCC

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microGalaxy Community - Working Groups

Tool working groups

Community oriented updated tool list

Increasing the findability, visibility, and impact�of Galaxy tools for specialized scientific Communities�(https://biohackathon-europe.org/ - Project)

Coordinate:

New wrapper development
Updates
Pitfalls (Huge tools suits)
Discuss ideas

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microGalaxy Community - a community of practice for everything related to micro*

Community oriented paper - working groups

Survey

What is the need, what are the problems �for the community ?

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Target the global south !

Aggregate information
Use cases

Learn from others

Roadmap

Next 2, 5, 10 years

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