Teaching Bioconductor in Japanese, and Why Translations Are Moving Back to GitHub
The most useful outcome of Bioconductor's first Japanese-language workshops isn't the attendance figures. It's the decision that followed them. The community is retiring its Crowdin setup and moving translations into GitHub repositories, where AI drafts get reviewed by people. That's a bigger shift than it sounds, and it says something about how open-source teaching materials need to be maintained.
Two workshops, one hybrid format
In August and September 2025, the Japanese Bioconductor community ran two two-day workshops, co-hosted with the Japanese Society for Bioinformatics (JSBi). As far as the organisers know, these were the first Bioconductor workshops ever taught in Japanese. Both were hybrid, with an in-person classroom and a Zoom connection for remote participants. Kozo Nishida taught both sessions.
The timing mattered less than the setup. Bioconductor has been a member organisation of The Carpentries since August 2022, and its lesson modules range from an introduction to R and Bioconductor through to an advanced bulk RNA-seq course. The Japanese workshops were the first time the working group's translations of those lessons were used in front of a live class. Funding came from the Chan Zuckerberg Initiative Essential Open Source Software for Science grant, Delivering High Quality Bioconductor Training for a Worldwide Community.
Osaka: the foundations, in Japanese
The first workshop ran on 5–6 August 2025 at the Taniguchi Memorial Hall, Research Institute for Microbial Diseases, Osaka University. Naohisa Goto helped as local host.
- Day 1 used the Japanese translation of Introduction to data analysis with R and Bioconductor. It covered organising data for analysis, then manipulation and visualisation with tidyverse packages. Everyone typed along during live coding, which is the only way this material really sticks.
- Day 2 used the Japanese translation of The Bioconductor project. Topics included installing packages, getting help, S4 classes, biological sequences,
GenomicRanges, annotation resources andSummarizedExperiment.
The workshop website and slides are available in Japanese.
Kyoto: bulk RNA-seq from start to finish
The second workshop was the advanced course, held on 11–12 September 2025 at the Inamori Memorial Hall of Kyoto Prefectural University. Atsushi Fukushima served as helper and local host. The class used the Japanese translation of RNA-seq analysis with Bioconductor and live-coded the full bulk RNA-seq workflow, except the read quantification step that produces the count matrix.
- Day 1 covered RNA-seq basics, RStudio projects and the experimental data, importing quantified data into R and annotating it, and exploratory analysis and quality control. In other words, everything that comes before differential expression.
- Day 2 moved into differential expression, a closer look at design matrices, and gene set enrichment analysis for interpreting results.
The workshop website and slides are also online.
Who showed up
| Workshop | In person | Online |
|---|---|---|
| Osaka, August 2025 | about 3 | about 45 |
| Kyoto, September 2025 | about 6 | about 45 |
Attendance shifted across two long days, so treat these as rough numbers. The split is the real story. Most people joined online, which says a lot about how spread out Japan's bioinformatics community is. The hybrid format clearly lowered the barrier to attending, and that's a model worth copying for regional teaching.
A report on both workshops, written in Japanese with Goto and Fukushima, appeared in JSBi Newsletter No. 48 in January 2026. This English-language write-up came considerably later, and the delay is tied to the translation problem below.
Why the translation pipeline is changing
Nishida originally proposed using Crowdin to manage Bioconductor translations, modelled on The Turing Way. That project translates its handbook on Crowdin with strong results, and Crowdin's support for open-source projects has been generous.
The catch is the source format. The Turing Way uses plain Markdown. Carpentries lessons are written in R Markdown, with executable code chunks and custom fenced blocks for callouts, challenges and solutions. To push those lessons through Crowdin, the team had to convert R Markdown to Markdown in separate translation repositories, sync translated strings back, and reassemble buildable lessons. The Crowdin and GitHub integration that this requires is complex and fragile, and keeping it running has been hard.
Meanwhile, the tools have moved on. AI translation quality has improved substantially. With Agent Skills, an AI agent can produce a first draft that follows project rules: a shared glossary, consistent terminology, and clear instructions to leave code, package names and function names untouched. Qualified community reviewers then check the output. Under those conditions, keeping translated lessons beside their sources in GitHub and reviewing them through pull requests is simpler than maintaining a Crowdin integration.
So the project plans to retire bioconductor.crowdin.com. This isn't a complaint about Crowdin. The tool suited a different kind of source document, and a plainer workflow now fits Bioconductor's lessons better.
What comes next
New GitHub-only translation repositories are in progress, along with an Agent Skill for rule-following AI translation, documentation, and outreach to recruit more languages and more contributors. The work is supported by the Bioconductor Developer Champions Program. A formal announcement is still some way off, and it will appear on the Bioconductor blog when it's ready.
Where the materials live and how to use them
Everything used in the workshops sits in the bioconductor-translations GitHub organisation, and anyone can reuse it for their own teaching. The Japanese lessons are bioc-intro-ja, bioc-project-ja and bioc-rnaseq-ja. The workshop sites and slides are in 2025-08-05-osaka, 2025-08-05-osaka-slides, 2025-09-11-kyoto and 2025-09-11-kyoto-slides.
The organisation also hosts a French translation, bioc-intro-fr, which was used in the Bioconductor course in Benin. That's a second data point showing the translated lessons travel beyond their original context.
Get involved
- Teach with the materials. The Japanese lessons, workshop sites and slides are openly licensed.
- If you want to translate Bioconductor teaching materials into your own language, watch the bioconductor-translations organisation for the announcement.
- Join the community through the support site and the community chat.
Acknowledgements
Thanks to Naohisa Goto and Atsushi Fukushima for helping at and hosting the workshops, to JSBi for co-hosting, and to every participant. The work was supported by the Chan Zuckerberg Initiative EOSS program and the Bioconductor Developer Champions Program.
