Bioc Meetup, Adelaide

Dr Stevie Pederson (They/Them)
Black Ochre Data Labs
The Kids Research Institute Australia / ANU

June 25, 2025

A Brief Personal History

• First encountered limma & R v1.5.? in Nov 2002
• PhD 2008-2018 \(\implies\) developed an (unpublished) microarray package
  • No RStudio, No Rcpp, No tidyverse
  • MCMC engine written in C \(\implies\) using .Call()

• No-one in Adelaide knew how to make R talk to C (~2009)
  • Attended UseR (Coventry, 2011)
  • Started Adelaide R Users Group (~2012, Gary Glonek & Jono Tuke)

• Looked the distant Bioconductor Community with awe
  • No connection to the community in Adelaide \(\implies\) only WEHI in Australia
  • Tiny Adelaide bioinformatics community in 2008 (Greg Goodall, Simon Barry, Jozef Gecz)

• Attending UseR was my best attempt at finding help & support
  • Was lucky enough to be the moment JJ Allaire launched RStudio
• Stopped attending User Group after 12 months as I’d returned to guitar teaching

A Brief Personal History

• Was probably asked to apply by Gary because I’d started the User Group & I’d tutored stats for him
• Never had any bioinformatics mentorship or trained with someone with more experience than me
• To complete the picture of perfection: I was also homeless
• Within DVCR I answered to Kerry Jaeger who was extremely supportive through out entire existence
• Wasn’t out as Non-Binary yet \(\implies\) my most striking experience of male privilege
• No idea how to write a Bioc package. Didn’t know anyone else in Adelaide who did

• Was offered position in 2014 to start Bioinformatics Hub at University of Adelaide
  • 1 Yr contract (DVCR funded project)
  • No PhD (until 2018)
  • No experience in academia
  • Never seen a FastQ file or used an HPC

• Build bioinformatics capacity in Adelaide
  • White, mid-40s & male \(\implies\) everyone assumed I knew what I was talking about
  • Fumbled & stumbled early \(\implies\) eventually found our way (Hien + Jimmy joined 2015)

• Started helping with BiocAsia in 2016

• Developed both strandcheckR & ngsReports
  • 2018-2019: Chris Ward & Hien To

More Recently

• I believe many of Kerry’s projects within DVCR were no longer supported & she retired

• Bioinformatics Hub was closed in 2020
  • Change in DVCR (Anton Middelberg appointed in 2019)

• 2020 - 2022: Dame Roma Mitchell Cancer Research Labs
  • Worked on ChIP-Seq + multiomics of Breast Cancer
  • Developed extraChIPs

• 2022 - 2025: Black Ochre Data Labs
  • PROPHECY: Type 2 Diabetes + Vascular complications in Indigenous Australians
  • Working on transcriptomics layer (~1200 libraries)
  • Cohort-level analysis \(\implies\) Cohort-level multiomics

• Really pleased we now have multiple Bioc developers in Adelaide

The Community Advisory Board

• I joined the Bioconductor Community Advisory Board (CAB) in late 2023

• A CAB term is 3 years
• Don’t know when to shut-up so have found myself as Co-Chair with Janani & Lori as Secretary
• CAB nominations are now open
• Looking for better representation from Central/Southern America, Asia & within Industry

Bioconductor As An Organisation

1. Scientific Advisory Board: https://bioconductor.org/about/scientific-advisory-board/
2. Technical Advisory Board: https://bioconductor.org/about/technical-advisory-board/
   • Currently no Australian representation
3. Community Advisory Board: https://bioconductor.org/about/community-advisory-board/

• The Core Team is currently 6 people: https://bioconductor.org/about/core-team/
  • Maria Doyle (Limerick, Ireland) as the Bioconductor Community Manager

• Multiple active Bioconductor working groups: https://workinggroups.bioconductor.org/currently-active-working-groups-committees.html
  • Resource Translation, Social Media, Package Review, Workflows/Publications, RLadies etc
  • Great way to contribute \(\implies\) can also be beneficial for career

Workflows Working Group (sic) Update

• Discovered when Nora was putting one together for sSNAPPY
• Are also contemplating changing the name on Bioc: Playbooks? Tutorials?
  • Trying to avoid confusion with snakemake, nextflow etc

• Workflows are a special type of package \(\implies\) extended tutorials
  • Reflect key decision making steps
  • Integration across multiple packages
  • No package building time-limits

• Used to be an F1000R ‘pipeline’ giving an indexed DOI for a Bioc workflow
  • Submit \(\LaTeX\) document with workflow \(\implies\) published on both Bioconductor & F1000R
  • F1000R now require MS Word documents \(\implies\) pipeline is broken

• Being addressed by Charlotte Soneson, Mike Love, Susan Holmes, Laurent Gatto, Lori Shepherd, Vince Carey, Sean Davis, Davide Risso + me (with raging imposter syndrome)

Workflows Working Group (sic) Update

• JOSE/JOSS etc are well down the track to being indexed publications
  • Mike has figured out how to manually add these to PubMed

• Relationship now established with Journal of Open Source Education (Lorena Barba)
• Workflow initially reviewed in-house
  • Need a team of internal Bioconductor reviewers
  • Developing key assessment criteria & checklist for reviewers
  • Needs to satisfy JOSE standards

• Then fast-tracked within JOSE if wanted
  • Have established a team of Bioc Editors at JOSE
  • Mike, Laurent, Vince, Charlotte

The Bioconductor Community

• Bioc has always been strongly DEI \(\implies\) impacts on funding are unclear
  • 2/6 Core Team members prefer They/Them
  • Software Carpentries are already feeling the anti-DEI threat
• Many contributors are immigrants to the USA

• Bioconductor officially left Twitter in late 2023
  • Staying was considered a breach of the Bioc Code of Conduct
  • Community hasn’t really reformed on Mastodon or BlueSky

• The Bioconductor Slack has been effectively archived
  • Community now on Zulip
  • Is the social media era over?
• Support site is still quite active

• BiocAsia feels like it’s at a crossroads \(\implies\) not BiocAustralia

• Attendance at Bioc (USA) not viable for many
  • UK also becoming hostile to gender diverse community

• US researchers are having a very tough time \(\implies\) keeping their heads down

The Bioconductor Community

• What does this mean for us?

Discussion Questions:

• Is social media over and what does this mean for the Bioconductor Community
• Role, need and strategy for BiocAsia?
  • Ellis Patrick (USyd) already proposed a Zoom Seminar Series
• What stages of our career did we feel most alone & needing help?
  • Early tutorials? Package Development?
  • What do we think is most helpful across key career stages?
• Could smaller meetups be a good strategy for the Asia/Pacific or globally?
  • Is there even a need? Are we all doing OK?
• Do we need more training as a local/national community?