Role responsibilities

The mandate of this role is somewhat broad. Bioconductor, and academic computing generally face a myriad of distinct and interrelated challenges as hardware, computing paradigms, and education environments change rapidly. Improving developer resources for tackling new and existing challenges, modernizing Bioconductor developer onboarding materials (particularly for early career researchers), and improving recognition mechanisms for community members who volunteer time and effort to the Bioconductor project are all general themes within the role scope.

Some Specific Efforts

A few of the specific efforts I’ll be working on in this role include:

How to get in touch

For developer discussions and ideas, the Bioconductor Zulip is the best place to connect.

A Shared Mission: Tooling for Managed Repositories

R-universe was designed as a next-generation package distribution and build system for R. It provides:

• Continuous building and checking of R packages across platforms
  
• Binary packages for Windows, macOS, Linux, and WebAssembly
  
• Transparent and reproducible build environments managed via GitHub actions
  
• Dashboards and metadata APIs for monitoring ecosystem health and activity
  
• CRAN-like package repositories with discoverable metrics and documentation

From the outset, a key objective has been to support curated and reviewed communities — such as rOpenSci and Bioconductor — by offering modern infrastructure without requiring them to redesign their governance model or review processes.

For Bioconductor, this means incrementally introducing piece-wise functionality, with consideration for established release cycles and quality control mechanisms:

1. Setting up independent build and dashboard tooling, replicating processes from the current Bioconductor build systems on R-universe infrastructure
2. Mirroring Windows and macOS binaries produced on R-universe to Bioconductor
3. Exploring further integration of results and metadata produced by R-universe for Bioconductor health/activity monitoring and aiding the curation processes
4. Potential future steps toward deeper automation and harmonization

By taking small gradual steps towards adopting R-universe components, everyone gets the opportunity to experiment with new tooling and evaluate where adjustments may be needed in order to minimize disruption to existing practices.

An important milestone in this venture is that Bioconductor now uses R-universe to build the Windows and macOS binaries, which significantly reduces costs and the maintenance load on the Bioconductor team. Beyond binary distribution, we are currently exploring deeper integration of R-universe’s continuous check results into Bioconductor’s quality control and release processes.

Two Universes: Release and Development

Bioconductor maintains two distinct repositories:

• A release branch for stable packages
  
• A devel branch for ongoing development and the next release cycle

To mirror this structure, we currently operate two dedicated R-universe instances:

• Development branch: https://bioc.r-universe.dev
  
• Release branch: https://bioc-release.r-universe.dev

These universes integrate directly with Bioconductor’s existing Git infrastructure and provide continuous builds for packages in both branches.

Through the R-universe dashboard, package maintainers and users can:

• Inspect cross-platform check results
  
• Review extended BiocCheck diagnostics
  
• Monitor build logs and dependency graphs
  
• Explore rich package metadata and metrics
  
• Publish binary packages for Windows, macOS, and Linux

This provides a familiar yet modern interface for Bioconductor contributors, aligned with what users increasingly expect from contemporary R package infrastructure.

Information about each package is available on https://bioc.r-universe.dev/{pkgname}. For example, https://bioc.r-universe.dev/DESeq2 provides details on the DESeq2 package as shown below:

If this is your first time visiting R-universe, we recommend clicking the “Website Tour” button which will walk you through the most important information in 1 or 2 minutes.

Technical Documentation for Bioconductor Maintainers

The R-universe project maintains comprehensive technical documentation at https://docs.r-universe.dev. For Bioconductor specifically, we created a dedicated section summarizing the most relevant topics for developers to get started with R-universe: https://docs.r-universe.dev/bioconductor/

As the collaboration evolves and new components get introduced, the documentation will continue to be expanded. The goal is to provide Bioconductor maintainers with a clear reference point for understanding how R-universe fits into their development workflow, while maintaining compatibility with the established practices that have made Bioconductor a successful project within the R community.

Looking Ahead

Adopting new infrastructure inevitably involves adjustments. For Bioconductor developers, integrating with a new build and distribution system will likely require some changes to workflows, and time to become familiar with new or different package checks, build diagnostics, and binary distribution.

However, by gradually moving toward common infrastructure, the Bioconductor project will benefit from improvements that are being continuously developed and maintained for the broader R ecosystem. A system based on modern continuous integration (CI) will provide developers with improved tooling, and will give the core team more time to focus on community coordination and quality control, rather than on maintaining costly infrastructure. At the same time, the shared platform provided by R-universe can help to increase the visibility and accessibility of Bioconductor software to the greater R community.

We look forward to continuing this alliance and to working with the Bioconductor community to ensure that the next generation of infrastructure supports the project for many years to come.

Outreachy

Outreachy is a paid, remote internship program whose main goal is to support people from groups underrepresented in tech. They help newcomers to free software and open source make their first contributions.

Interns work remotely for 3 months with experienced mentors from open source communities, gaining hands-on experience, building real-world skills, and contributing to meaningful projects. They receive guidance, feedback, and the support of a diverse and welcoming community.

Our Journeys

Upcoming Opportunities

One of the core values of open source is Community, because it ensures projects remain active, relevant, and adaptable over time, preventing stagnation. The Bioconductor community is participating in the current Outreachy internship round (December 2025 to March 2026).

If you’re inspired by our journey and would like to contribute to the BugSigDB project, either through Outreachy or simply to share knowledge, feel free to join us on the Bioconductor Zulip channel.

Applications for the next internship round (May 2026 – August 2026) will open in early February 2026, so keep an eye out for announcements here.

What we taught and what was learned

During the week-long Bioconductor course at the University of Abomey-Calavi, participants were introduced to the foundations of R and RStudio, good coding practices, tidyverse workflows, data handling, and reproducible research, before progressing into hands-on Bioconductor analyses for bulk RNA-seq using DESeq2 and SummarizedExperiment. Participant feedback reflected exactly these learning goals. Many highlighted how practical and hands-on the sessions were, sharing that “the course was very practical with a lot of explanations” and that practicing directly on their laptops made the material easy to apply. The step-by-step guidance on dplyr, tidyverse, ggplot2, and RNA-seq workflows resonated strongly, with one participant noting “the step-by-step explanation about dplyr and tidyverse was highly useful,” while another said they especially appreciated “good step-by-step guidance on RNA-seq data analysis.” Participants repeatedly praised the teaching approach and the supportive environment, noting that “the trainers always came to help us when we had difficulties without judgment,” and “even when we didn’t understand at first, they always took the time to explain clearly.” Others valued the inclusive, interactive format: “the course was inclusive, with a participatory approach,” and “we all practiced directly with the trainers, who were highly attentive to our concerns.” Many also appreciated the organisation and materials, calling the course “well organized,” with “great interaction,” “well-accessible documents and scripts,” and resources they could return to later.

Agenda and instructor list are on the workshop page.

Language accessibility and bilingual support

This was the first Bioconductor Africa course where French translations of introductory materials were provided. Participants strongly appreciated having French-speaking instructors available throughout the week. Over half of the attendees (52%) found this support very helpful, with another 32% rating it helpful, emphasising that bilingual facilitation made it easier to follow explanations, ask questions, and stay engaged. While most participants felt comfortable with English as the primary teaching language (56% reported that English was sufficient), a significant portion noted that French support enhanced their understanding of the material. The French-translated Intro to R materials were also well received: one-third of participants used them during the workshop, and another third planned to consult them later.

Link to French translated materials here

Highlights

GBioS and URMAPha graciously offered us a tour of their laboratory facilities, providing the instructors and participants with an opportunity to learn more about the impactful research they lead, ranging from safeguarding seed diversity to identifying pharmaceutically active compounds.

Below is a photo of the instructors, hosts, and participants taken after the lab tours.

To close the workshop, the team also hosted a beautiful certificate ceremony, creating a memorable and celebratory end to an impactful week.

Carpentries Instructor Training and Capacity Building

Through support from the CZI EOSS6 grant, two researchers from local institutions in Benin, Kevin Sintondji (URMAPha) and Dédéou Tchokponhoue (GBioS), are participating in Carpentries instructor training to become certified instructors. This initiative is helping build local capacity to deliver high-quality training and support reproducible research practices within their teams and the wider community. As they shared: “The Carpentries training has been extremely valuable for strengthening our skills in data management and reproducible analysis. It helped us adopt more structured workflows, improve collaboration within our teams, and apply these methods directly in our AMR and environmental microbiology projects. This capacity building is already having a concrete impact on the quality of our research.”

In addition to the Carpentries training supported by the CZI EOSS6 grant, two of the other instructors at the Benin workshop, Marie Hidjo (Benin) and Amal Boukteb (Tunisia), were previously certified through the Bioconductor Carpentries program funded by the CZI EOSS4 grant (see summary blog post). This workshop was also an opportunity for these instructors to teach locally and share their expertise within the African bioinformatics community.

Impact of Bioconductor Training across East and West Africa

From surveys conducted across Kenya, Ethiopia, and Benin, 100% of participants reported that they would recommend the Bioconductor training course to colleagues, indicating a strong and meaningful impact. The impact was also evident in skills development: every participant reported a significant improvement in their R abilities. In Benin, 60% of the participants rated their learning gains as “very significant” (scale 5) and 40% as “significant” (scale 4), a clear indication that the training effectively strengthened practical, hands-on bioinformatics skills.

Looking ahead: what participants want

Across Kenya, Ethiopia, and Benin, participants expressed a strong interest in more advanced and diverse bioinformatics training that builds on the foundations of R and RNA-seq. The most recurring areas of interest were:

• Advanced transcriptomics: advanced RNA-seq, transcript-level workflows, and single-cell RNA-seq.

• Genomics & population genetics: variant calling, SNP/CNV analysis, and GWAS/genomic selection.

• NGS & sequence analysis: raw sequence handling, QC, genome assembly, and phylogenetics.

• Metagenomics & microbiome analysis using Bioconductor tools.

• Multi-omics integration: combining genomics, transcriptomics, proteomics, and metabolomics.

• Computational skills: Linux basics, command-line workflows, and version control (Git/GitHub).

• Reproducible research & visualisation: R Markdown/Quarto and more advanced data visualisation.

We’re exploring ways to make Bioconductor training more accessible, including webinars and other online formats. One example is our new online seminar series, which recently featured a talk on “Deep-learning-based Gene Perturbation Effect Prediction Does Not Yet Outperform Simple Linear Baselines” and attracted participants who attended our workshops in Africa this year.

Collaborators & Acknowledgements

This workshop was co-hosted by GBioS and URMAPha. We are deeply grateful for their leadership and commitment to strengthening bioinformatics capacity in Benin. Notably, there was a special link between the Kenya and Benin workshops: the Kenya training went so well that one of its participants, Abdou Mouizz Salaou, helped bring Bioconductor training to Benin, further expanding the impact of Bioconductor capacity-building efforts across the region.

The event was co-organised with the International Institute of Tropical Agriculture (IITA) and the University of Limerick, with funding support from the Chan Zuckerberg Initiative (CZI) EOSS6 grant.

Our organising team: Abdou Mouizz Salaou (GBioS, University of Abomey-Calavi), Aristide Carlos Houdegbe (GBioS, University of Abomey-Calavi), Prof. Enoch G. Achigan-Dako (GBioS, University of Abomey-Calavi), Prof. Victorien Dougnon (URMAPha, University of Abomey-Calavi), Trushar Shah (International Institute of Tropical Agriculture), Laurah Ondari (International Institute of Tropical Agriculture), Maria Doyle (University of Limerick / Bioconductor).

Get involved

• Workshop page
• About Bioconductor training
• Join the Bioconductor Africa mailing list or #bioc_africa channel in Bioconductor Chat

What we taught

A five-day, hands-on programme covering:

• R for data management, manipulation, visualisation, and reproducible analysis
  
• Bioconductor core data structures (e.g. SummarizedExperiment)
  
• Exploratory data analysis and quality control
  
• Differential expression with DESeq2
  
• Gene set enrichment analysis

Agenda and instructor list are on the workshop page.

We welcomed 26 participants from universities, national research institutes, and biotech groups across Ethiopia, reflecting a strong mix of MSc/PhD students, lecturers, and researchers working in agriculture, public health, genomics, and AI-driven biomedical research. The cohort was selected from more than 170 applicants - a clear sign of the growing demand for hands-on bioinformatics training.

Learning & Community

The workshop opened with a warm welcome from BETin leadership, including Dr Zewdu Edea and Dr Hailu Dadi with strong support from Prof Kassahun Tesfaye, and Dr Helen Nigussie from Addis Ababa University. Sessions were interactive and collaborative as participants worked through exercises together.

Participant voices

Impact snapshot:
From the post-course survey (n=24):

• 100% would recommend the workshop
  
• 92% rated the course “Excellent” or “Very good”
• Average self-reported improvement in R skills: 4.3/5
• 23 out of 24 respondents expressed interest in helping grow the Bioconductor Africa community

“It’s very hands-on and engaging… The instructors were very experienced, knowledgeable, and approachable. It was a great learning experience!”

“There were enough supporters for the trainees; those who were rounding and supporting when we got stuck were a wonderful approach. The training shoots the target from my side.”

“I would appreciate it if the time for the training were increased.”

These sentiments echoed the hosts’ reflections:

“Participants were thrilled to have been given the chance and vowed to utilise the new skills they gained in their research and future careers.” — Dr Zewdu Edea (BETin), LinkedIn

“The workshop highlights the importance of international collaboration and knowledge exchange in advancing research and training, particularly in the African context.” — Niguse Kelile Lema (BETin), LinkedIn

Encouragingly, many respondents expressed interest in helping grow the Bioconductor Africa community through teaching, webinars, or community sessions - a strong signal for sustainable, local leadership.

Lessons learned

A key part of building a sustainable training programme is listening to feedback. A few themes stood out:

• More time for deeper dives:
  Participants were keen for extra time to practise and explore. While extending the main workshop isn’t always possible, we’re exploring optional drop-in coding sessions or “hacky hours” after future events so participants can spend more time working through exercises with instructor support.

• Clearer signposting of pre-workshop reading: Although we shared pre-reading and background material, some participants noted they would have benefited from more emphasis on the publication describing the experimental dataset. We’ll highlight these resources more clearly in future courses.

• Mapping Future Topics: Feedback included a range of topics people would like to see next - including GWAS, single-cell analysis, and multi-omics integration. This helps us map out future workshops and tailor training to local research priorities.

Highlights

A short certificate ceremony on the final day was a lovely way to wrap up the week. BETin presented each participant with a certificate recognising their effort and commitment throughout the course. Participants were delighted to receive them, as reflected in the smiles during the ceremony.

Another note from the week is that two of the local instructors, Yohannes and Niguse, were completing their Carpentries Instructor Certification, and this workshop served as their final teaching checkout.

Collaborators & Acknowledgements

This workshop was hosted and funded by the Bio and Emerging Technology Institute (BETin). We are deeply grateful for their leadership and commitment to strengthening bioinformatics capacity in Ethiopia.

The event was co-organised with the International Institute of Tropical Agriculture (IITA) and the University of Limerick, with additional support from Bioconductor (CZI EOSS) and UL Global/Erasmus+.

Our instructor team: Dr Yohannes Gedamu Gebre (BETin), Niguse Kelile Lema (BETin), Dr Helen Nigussie (AAU), Trushar Shah (IITA), Dr Maria Doyle (UL).

We thank the Ministry of Innovation and Technology and Innobiz-K Ethiopia Incubation Center for generously providing their facilities for the training.

What’s next?

Our next workshop took place in West Africa, in Benin, from 17–21 November 2025. If your institute is interested in co‑hosting or contributing to future workshops, we’d love to hear from you.

Get involved

• Workshop page
• Materials
• About Bioconductor training
• Join the Bioconductor Africa mailing list or #bioc_africa channel in Bioconductor Chat

Preconference

Prior to the conference, EuroBioC2025 hosted two Bioconductor Carpentry workshops on Bulk RNA-seq and Single-cell RNA-seq analysis. Each workshop attracted about 20 participants and ran on September 15 and 16. The Bulk RNA-seq analysis module was taught by Estefania Mancini, Vasileios Panagoitis Lenis, and Jacques Serizay, while the Single-cell RNA-seq analysis workshop was taught by Robert Ivánek, Mireia Ramos, and Kevin Rue-Albrecht. The sessions combined live coding with short theoretical explanations of the covered materials. The feedback from participants was incredibly positive, with many appreciating how practical and engaging the sessions were. One participant shared that “the hands-on experience brought by the instructors is the kind of thing that would have been difficult to get while going through the materials on our own,” while another highlighted “the written materials that include theory and explanation of the obtained results” as particularly useful. Participants in the Single-cell RNA-seq workshop appreciated “the comprehensive overview the lectures provided on scRNA-seq analysis,” noting that “they outlined the different steps clearly, using comparable timelines and emphasizing key details,” which “offers a standard framework for performing such analyses.” Those in the Bulk RNA-seq module praised “the materials [that] were really well prepared,” the “super nice instructors” who “tried to accommodate all of your needs,” and “gave many useful tips,” adding that the content would be valuable for future reference. Overall, the majority of respondents rated the workshops as “Very good” or “Excellent,” describing them as well-organized, easy to follow, and “an incredible learning experience” that boosted both their confidence and technical skills in using Bioconductor.

Programme overview

EuroBioC2025 featured a dynamic three-day program that balanced scientific excellence, community exchange, and practical training. The schedule brought together keynotes from leading researchers, short and flash talks showcasing new Bioconductor packages and methods, and hands-on workshops that deepened participants’ technical skills.

The opening keynote by Vince Carey reflected on 25 years of Bioconductor as a coherent ecosystem for genomic data science, setting the tone for a conference that celebrated both innovation and collaboration. Keynotes by Helena Crowell, Susan Holmes, James Sharpe, Noelia Ferruz, and Jacques Serizay explored cutting-edge topics spanning whole-transcriptome imaging, statistical modeling, spatial omics, and AI-driven protein design.

The short talks highlighted exciting package developments across the Bioconductor landscape, from metabolomics and spatial transcriptomics to reproducible workflows. The poster sessions showcased over 60 contributions, offering a vibrant space for discussion, collaboration, and mentorship.

On the final day, Birds-of-a-Feather (BoF) sessions encouraged open community dialogue on key issues, reinforcing Bioconductor’s collaborative ethos.

Keynotes

The keynote sessions at EuroBioC2025 brought together leading voices in bioinformatics, highlighting advances across genomics, spatial biology, and community-driven software development. Each talk provided attendees with both inspiration and practical insights into the evolving landscape of computational biology:

• Vince Carey (Mass General Brigham - Harvard Medical School) opened the conference with “A coherent ecosystem for genomic data science: 25 years of Bioconductor,” reflecting on Bioconductor’s growth and its pivotal role in reproducible research.
• Helena Crowell (Centre Nacional d’Anàlisi Genòmica - CNAG) presented “Colorectal cancer through the lens of whole transcriptome imaging,” showcasing how spatial transcriptomics can reveal novel insights into cancer biology.
• Susan Holmes (Stanford University) delivered “Latent variables as the best medicine for heterogeneity,” exploring statistical approaches for understanding biological variation.
• James Sharpe (EMBL Barcelona) introduced “C3PO: Cell 3D Positioning by Optical encoding and its application to spatial transcriptomics,” detailing innovative imaging and computational methods for 3D cellular mapping.
• Noelia Ferruz (Centre de Regulació Genòmica - CRG) presented “Controllable protein design with language models,” demonstrating how AI and generative models are transforming protein engineering.
• Jacques Serizay (Institut Pasteur) closed the keynotes with “Enhancing genomic research with community-driven flexible software,” emphasizing collaboration and openness in advancing genomic analysis.

Short Talks

EuroBioC2025 featured a vibrant lineup of short talks highlighting new computational tools and methods across multi-omics, spatial, and single-cell biology. Presentations ranged from multi-omics integration frameworks and probabilistic models for transcription factor activity to improvements in widely used packages such as edgeR and new interoperability initiatives with ELIXIR. Speakers also introduced emerging software for mass spectrometry, microbiome, and spatial data analysis, showcasing the community’s ongoing innovation in data-driven biology.

Workshops

The workshop sessions were a major highlight, offering attendees interactive learning experiences with the latest Bioconductor tools set up in a workshop cloud platform to avoid participants having to spend time installing software. From Orchestrating Spatial (Transcript-)Omics Analysis and Microbiome Analysis with Bioconductor, to authoring and deploying workshops on the new Bioconductor platform, these sessions emphasized reproducible workflows and cross-language integration for biological data analysis.

Poster Sessions

The poster sessions at EuroBioC2025 showcased a diverse range of projects reflecting the richness of the Bioconductor ecosystem. Topics included multi-omics integration, benchmarking analytical methods, AI-driven microbiome and cancer research, and interactive visualization tools. Attendees particularly appreciated the concise poster pitches that provided quick overviews of ongoing research and facilitated meaningful discussions during the sessions.

Birds of a Feather (BoF) Sessions

This year’s BoF sessions provided space for informal, collaborative discussions on key community topics. Participants shared perspectives on integrating Bioconductor with the Nextflow workflow manager, improving interoperability across tools, enhancing developer onboarding, and shaping the future of Bioconductor training and governance. These conversations captured the conference’s spirit of open collaboration and community-driven growth.

Infrastructure and tools

EuroBioC2025 Zulip

In June 2025, Bioconductor’s community chat moved from Slack to Zulip. The motivation behind the transition was to ensure long-term access to discussions on a platform that better reflects the project’s open-source values. Therefore, EuroBioC2025 used a dedicated Zulip workspace as the main digital hub for conference coordination and discussions. Zulip provided an organized, threaded platform where participants and organizers could collaborate seamlessly before, during, and after the conference.

The main channel was:

• #eurobioc-conference-everyone – for announcements, updates, and general conference discussions.

Inside #eurobioc-conference-everyone, the following topics were available to keep everything organised: 

• eurobioc2025:travel – for coordinating taxi shares, asking about transit options, and exchanging travel tips.
  
• eurobioc2025:announcements – for conference updates, schedule changes, and important notices.
  
• eurobioc2025:helpdesk – for participants to ask questions and receive assistance from organizers or fellow attendees.
  
• eurobioc2025:general-chat – for casual conversations and connecting with other participants.
  
• eurobioc2025:photos – for sharing snapshots and favorite moments from EuroBioC2025.
  

Scholarships

Thanks to the generous support of the sponsors, EuroBioC2025 awarded 27 scholarships to participants, enabling them to attend the conference in person. These scholarships helped ensure broader participation and continued Bioconductor’s commitment to equity, diversity, and inclusion within the community.

Sticker contest winners

The EuroBioC2025 sticker was eagerly anticipated by the community, and this year’s design did not disappoint. This year’s sticker, designed by Chaima Hkimi, beautifully captured the essence of Barcelona, featuring the Sagrada Família and the vibrant colours of Park Güell. In a creative touch, Chaima replaced the “i” in BioC with the Bioconductor logo — a clever nod to the project and its global community.

Learn more about Chaima and her winning design in our Mastodon announcement.

Sticker Hexwall

A fun new addition to EuroBioc2025 was the sticker hexwall; a colorful visual display of Bioconductor package stickers showcased at the photo-call area. The design, created by Kevin Rue-Albrecht, captured the variety and creativity within the Bioconductor community.

Social interactions and networking

Conference dinner

The EuroBioC 2025 conference dinner was held at the Old Hospital de Sant Pau, a UNESCO World Heritage site. The cocktail-style event provided a relaxed setting to network, exchange ideas, and celebrate the vibrant Bioconductor community.

Walking Tour

As part of the conference’s social activities, attendees enjoyed a guided walking tour through Ciutat Vella, Barcelona’s historic old city. The tour wound through the vibrant neighborhoods of La Ribera and El Gòtic, offering glimpses of medieval streets, lively plazas, and ending at Plaça Reial, next to the famous La Rambla boulevard. Participants explored landmarks such as the former old market hall El Born, el Fossar de les Moreres, the Cathedral Santa Maria del Mar, and the old Roman city walls, while learning about the city’s evolution from its maritime roots to its modern cultural identity.

The tour was organized by Mireia Ramos Rodríguez and volunteers from the Bioconductor community who reside in Barcelona, making it a warm, locally guided experience for all participants.

Conference materials

Recordings from EuroBioC2025 are available on the Bioconductor YouTube channel. Presenters were encouraged to upload their slides and posters to the Bioconductor Zenodo community, which allows their work to be assigned a DOI and makes it easier for others to access and cite. A short guide was shared to help contributors prepare and upload their materials effectively.

Upcoming conferences

• Bioconductor Asia conference 2025 (BioCAsia2025) in Adelaide on Nov 27 - 28, 2025

• European Bioconductor conference 2026 (EuroBioC2026) in Turku on June 3 - 5, 2026

• Bioconductor conference 2026 (BioC2026) in Fred Hutch Cancer Center, Seattle, WA, on August 10 - 12, 2026

Acknowledgements

Sponsors

EuroBioC2025 was deeply grateful to all our sponsors for their generous support. Our Silver sponsors were Seqera, the Chan Zuckerberg Initiative, and the Department of Medicine and Life Sciences (UPF) and ISGlobal through their respective institutional grants Maria de Maeztu and Severo Ochoa. Bronze sponsors included the R Consortium, BigOmics Analytics, MedBio Informatics, and Physalia Courses.

Their contributions made it possible to deliver a high-quality in-person event and to promote equity, diversity, and inclusion by reducing registration costs and supporting scholarships for students and researchers from lower-income regions or with limited access to funding.

Hosts

Barcelona Biomedical Research Park (PRBB), Department of Medicine and Life Sciences - Universitat Pompeu Fabra (MELIS-UPF), Barcelona Institute of Global Health (ISGlobal)

Organising committee

Local Hosts and Organizers

• Robert Castelo, Universitat Pompeu Fabra, Spain
• Juan Ramon Gonzalez, Barcelona Institute of Global Health, Spain
• Mireia Ramos, Universitat Pompeu Fabra, Spain
• Helena Crowell, Centro Nacional de Análisis Genómico, Spain
• Lluís Revilla Sancho, Roche, Spain.

Community Organizers

• Annekathrin Nedwed, Friedrich Miescher Institute for Biomedical Research, Switzerland
• Charlotte Soneson, Friedrich Miescher Institute for Biomedical Research, Switzerland
• Dario Righelli, University of Naples “Federico II”, Italy
• Davide Risso, University of Padua, Italy
• Eliana Ibrahimi, University of Tirana, Albania
• Federico Marini, University Medical Center Mainz, Germany
• James Dalgleish, University of Oxford, UK
• Kevin Rue-Albrecht, University of Oxford, UK
• Laurent Gatto, Université catholique de Louvain, Belgium
• Lena Morrill Gavarro, University of Oxford, UK
• Leo Lahti, University of Turku, Finland
• Lieven Clement, Ghent University, Belgium
• Maria Doyle, University of Limerick, Ireland
• Michael Stadler, Friedrich Miescher Institute for Biomedical Research, Switzerland
• Najla Abassi, Institut Pasteur de Tunis, Tunisia
• Robert Ivánek, University of Basel, Switzerland
• Simone Bell, EMBL Heidelberg, Germany
• Tuomas Borman, University of Turku, Finland
• Wolfgang Huber, EMBL Heidelberg, Germany

GPU Support

The BBS GPU Software reports are available at

• devel BBS GPU report
• release BBS GPU report

Looking at the reports, you’ll notice three new build nodes:

• biocgpu in Jetstream2
• amarone at the University of Padova
• kakapo1 at the Dana-Farber Cancer Institute

The Nvidia CUDA compiler driver and the Nvidia System Management Interface for each machine appears at the bottom of their node info reports. Both amarone and kakapo1 use a BBS-like container based on Nvidia’s CUDA container available to maintainers.

Additionally, a biocViews term GPU has been added.

How to take advantage of new GPU support

GPU_reliance: optional

GPU_reliance: required

“Task views”, starting with CRAN

CRAN task views are a bonanza for practicing data scientists. Introduced in 2005, “[t]hey provide guidance about which CRAN packages are relevant for tasks related to a certain topic, and can also facilitate automatic installation of all corresponding packages (Zeileis et al. (2023)).

library(rvest)
read_html("https://cran.r-project.org/web/views/Omics.html") |> 
  html_elements("h3") |> html_text()

 [1] "Annotation and databases"    "Genomics"                   
 [3] "Transcriptomics"             "Proteomics"                 
 [5] "Metabolomics"                "Other omics"                
 [7] "Multiple omics"              "Specific tasks"             
 [9] "Specific application fields" "CRAN packages"              
[11] "Related links"               "Other resources"            

biocViews: a graph is all you get

The biocViews has a badge indicating that it has been in Bioconductor for 19 years. Briefly, the intent was to emulate CRAN task views, with a vocabulary and curation of packages using topics relevant to genomic data science. Figure 1 gives a basic idea of the vocabulary and its structure. There are 497 terms in a directed graph with root “BiocViews”.

The mapping from biocViews terms to packages is specified in each package’s DESCRIPTION file. For a given release of Bioconductor, the BiocPkgTools includes the mapping from each package to the list of biocViews terms chosen by the package developer to characterize package capabilities. All packages map to at least one term. The average number of terms for software packages is 9, and the maximum number of terms in use for any package is 45, for roastgsa.

EDAM: Formal ontology for bioinformatics

Summary

This project began with the notion that an ad hoc enumeration of concepts used to tag Bioconductor packages (biocViews) could be “replaced” with a more systematic ontology (EDAM). It turns out that biocViews has purposes beyond package “tagging” for discovery support, and modifications to the vocabulary have ramifications in other domains of the Bioconductor software ecosystem. It is also clear that EDAM “lacks” concepts that are used in biocViews, and will need to be updated. This is a formal process requiring review and consensus among EDAM maintainers. See this pull request for an example arising from this project.

Ultimately we believe that tooling related to that provided in the biocEDAM package will help propose term assignments for Bioconductor packages (and other artifacts useful in genomic data science) that developers and content creators can adopt as they see fit. This will lead to gains in resource discoverability and will provide values for organizing ecosystems and workflow collections like Bioconductor and bio.tools.

For a broader view of Bioconductor’s future direction, see Vince Carey’s recent opinion piece in Patterns: https://doi.org/10.1016/j.patter.2025.101319.

We welcome feedback and contributions — especially from those working on package metadata. If you’d like to try the biocEDAM tooling, see Tip 1 above.

Acknowledgments

This work was supported in part by a Chan-Zuckerberg Initiative Essential Open Source Software project EOSS6-0000000067, “Ontological resource tagging and discovery for Bioconductor”. Important milestones were reported in a BioHackathon Europe 2024 preprint. A Bioconductor Technical Advisory Board Working Group is currently engaged with these activities.

References

Gonçalves, R. S. et al. (2024). The text2term tool to map free-text descriptions of biomedical terms to ontologies. arXiv: 2407.02626 [cs.DB]. URL: https://arxiv.org/abs/2407.02626.

Zeileis, A. et al. (2023). CRAN Task Views: The Next Generation. arXiv: 2305.17573 [stat.CO]. URL: https://arxiv.org/abs/2305.17573.

🗓 Event Details

• Date: Monday, 28 July 2025
  
• Time: 17:00–18:00 CEST
  
• Location: Online – see details below.
• Add to calendar: Download .ics file

📋 Agenda

• 40 minutes – R + Rust: extendr
  
• 20 minutes – Rust in bioinformatics

🎤 Speakers

• Sun Wenjie Website
  
• Mossa Merhi Reimert: GitHub
  
• Josiah Parry: LinkedIn | Website | GitHub

This session is open to all developers interested in bridging R and Rust, especially those working on packages for Bioconductor and CRAN.

📍 Location

• Zoom link: https://us06web.zoom.us/j/83712090308?pwd=DuNbDvPaLkJAHC7a2HebwLWyl8U9Qw.1
  
• Meeting ID: 837 1209 0308
  
• Passcode: 877331

The joining link is now available above. We’ll also share updates in the #events channel on Bioconductor Zulip.

☑️ Please note: By attending, you agree to abide by the Bioconductor Code of Conduct.
📹 The session will be recorded and may be shared on the Bioconductor YouTube channel.

💬 Questions or suggestions? Reach out in the Bioconductor Zulip.

🔍 Workshop Highlights

Students especially enjoyed sessions on:

• Taxonomic assignment
  
• Community similarity
  
• Data visualization

The course followed best practices in data science education, inspired by the Carpentries model, and was led by two Bioconductor Carpentries instructors. Both Professor Leo Lahti and Izabela Mamede were among the 31 instructors trained over the past two years as part of this initiative. Read more in the Bioconductor Carpentries update.

A big thank you to everyone who made this event possible, especially the Bioinformatics program heads, Professors Flávia Aburjaile and Raquel Minardi, Professor Glória R. Franco who helped set up and organize the workshop, the co-instructors João Paulo P. de Almeida and Izabela Mamede, the participants, and Professor Leo Lahti who traveled all the way from Finland to Brazil to teach the course. The event, as well as the disseminated methodology, was supported by the European Union’s Horizon 2020 research and innovation programme FindingPheno (grant 952914).

We hope this workshop serves as a stepping stone for future collaborations and research in microbiome data analysis in Brazil and beyond.

💬 Continue the Conversation on Zulip!

To stay connected and continue the conversation:

• Join the #miaverse channel, dedicated to the framework we used in the course (like (Tree)SummarizedExperiment for microbiome). This directly fits the course methodology and is a good place for specific questions and shared learning.
• Join the #microbiome_metagenome channel for broader microbiome discussions. This is more useful for general community building and connecting with researchers beyond the course cohort.

👉 You can join the conversation at https://chat.bioconductor.org