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Bridging Bioconductor and Galaxy: Enhancing Omics Data Training through Integration of Platforms

Maria Doyle,

Bioconductor Community Manager

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European Galaxy Days

October 4th, 2023

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What is Bioconductor

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Overview of Bioconductor

Bioconductor, is a global open source, open development software in R for genomics

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Comprehensive Collection of Tools

  • 22 years old project, over 2,000 open-source R packages�
  • Covers many aspects of omics (genomics, transcriptomics, proteomics) data analysis�
  • Preprocessing, normalization, visualization, statistical analysis, and functional annotation

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High-Quality Software and Interoperability

  • Rigorous review process for packages�
  • Daily package checks�
  • Standardized data structures and interfaces enable seamless integration of different tools and methods

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Bioconductor Global Community

  • Researchers, developers, and users collaborate�
  • Encourages knowledge sharing and continuous improvement�
  • Open science and reproducible research practices

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>10,000 followers

>2,000 members

>50,000 users

https://support.bioconductor.org

>1 million distinct downloads in 2022

>5,000 subscribers

>1,200 developers contributing packages

Join Slack https://slack.bioconductor.org/

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�Bioconductor’s connections with Galaxy

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Organization and Governance discussions

Bioconductor has

Connecting with Galaxy through

  • CAB member: Enis Afghan from Galaxy

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  • Quarterly Bioconductor & Galaxy meetings on governance and other topics

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Bioconductor Code of Conduct

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Ombudsperson:

Michelle Savage from Galaxy

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Bioconductor + Galaxy connecting through training

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-> Live Demo of workshop.bioconductor.org

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Used by Bioconductor since Smorgasbord 2023

  • 41 registered workshops (materials/containers)
  • 452 registered users
  • 1400+ workshop instances launched

Requested use at

  • EuroBioC2023
  • Monash Bioinformatics 2023*
  • ISCB 2023*
  • BioC 2023
  • ISMB 2023*
  • X-Meeting BSB 2023*
  • ARTNet 2023*
  • Smorgasbord 2023

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Workshop Galaxy: Stats

( * = single workshop)

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Infrastructure of workshop.bioconductor.org

Alex Mahmoud

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Bioconductor Workshop Galaxy https://workshop.bioconductor.org

Running Galaxy on Jetstream 2 on Kubernetes for launching RStudio workshops

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Deploy via comments in GH issues

https://github.com/Bioconductor/workshop-contributions/blob/main/.github/ISSUE_TEMPLATE/workshop-request.md

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Shiny App for submissions

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Scalable open-source stack (Cloudman from Galaxy)

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Future plans/ideas

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Future plans/ideas

  • Backup for current compute system (Jetstream)
  • “Try it out” button on Bioconductor packages that launches package in Galaxy
  • More training!

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