We discuss general project news.
Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. The project has entered its twentieth year, with funding for core development and infrastructure maintenance secured through 2025 (NIH NHGRI 2U24HG004059). Additional support is provided by NIH NCI, Chan-Zuckerberg Initiative, National Science Foundation, Microsoft, and Amazon. In this news report, we give some updates on core team and project activities.
In May 2024, Bioconductor 3.19 was released*. It is compatible with R 4.4 and includes 2300 software packages, 430 experiment data packages, 926 up-to-date annotation packages, 30 workflows, and 5 books. Books are built regularly from source, ensuring full reproducibility; an example is the community-developed Orchestrating Single-Cell Analysis with Bioconductor.
*Note: Bioconductor 3.20 was subsequently released in October 2024. For details on the latest release, visit the Bioconductor website.
We participated in the May-August 2024 Outreachy Internship program, during which intern Scholastica Urua contributed to the Microbiome Study Curation project. Scholastica reflected on her experience in a blog post, available here. Her work was recognized with the award for best Microbiome Virtual International Forum MicroTalk. The recording of her talk can be viewed on YouTube.
In July 2024, Beatriz Calvo-Serra was honoured as the inaugural recipient of the Bioconductor Athena Award. Beatriz was a passionate contributor to computational biology and an active member of the Bioconductor community. For more details, see this blog post.
The annual BioC conference was held July 24-26 2024 at the Van Andel Institute in Grand Rapids, Michigan. Over 350 participants took part, with 116 attending in person and 240 joining virtually, allowing participants from regions as far away as Latin America, Africa, and Asia to be part of the event. This year’s conference also marked our first time in the Mid-West US, highlighting the expanding reach and diversity of our community. See recap blog post here
The European Bioconductor Conference (EuroBioC2024), held in Oxford in September 2024, welcomed over 100 in-person attendees. Highlights included keynote talks and workshops. Community-driven events like EuroBioC continue to foster collaboration and innovation. See recap blog post here.
Registration for BioCAsia 2024 is now open! The conference will take place on November 7–8, 2024, in Sydney, Australia, fostering collaboration among the bioinformatics community in the Asia-Pacific region. A Conference Access Award is available to assist presenters and participants with registration fees.
In July 2024, Bioconductor opened its annual call for nominations to the Community Advisory Board (CAB) and Technical Advisory Board (TAB). These boards play a vital role in guiding Bioconductor’s technical development, community outreach, and long-term viability. The nomination period closed on August 31, 2024, and we thank everyone who applied or shared the call within their networks. For more information on the CAB and TAB, visit:
If you are interested in becoming involved with any Bioconductor working group please contact the group leader(s).
Start using Bioconductor by installing the most recent version of R and evaluating the commands
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install()Install additional packages and dependencies, e.g., SingleCellExperiment, with
BiocManager::install("SingleCellExperiment")Docker images provides a very effective on-ramp for power users to rapidly obtain access to standardized and scalable computing environments. Key resources include:
Upcoming and recently completed events are browsable at our events page.
The Technical and and Community Advisory Boards provide guidance to ensure that the project addresses leading-edge biological problems with advanced technical approaches, and adopts practices (such as a project-wide Code of Conduct) that encourages all to participate. We look forward to welcoming you!
We welcome your feedback on these updates and invite you to connect with us through the Bioconductor Slack workspace or by emailing community@bioconductor.org.
Text and figures are licensed under Creative Commons Attribution CC BY 4.0. The figures that have been reused from other sources don't fall under this license and can be recognized by a note in their caption: "Figure from ...".
For attribution, please cite this work as
Manager & Team, "Bioconductor Notes, September 2024", The R Journal, 2024
BibTeX citation
@article{RJ-2024-3-bioconductor,
author = {Manager, Maria Doyle, Bioconductor Community and Team, Bioconductor Core Developer},
title = {Bioconductor Notes, September 2024},
journal = {The R Journal},
year = {2024},
note = {https://journal.r-project.org/news/RJ-2024-3-bioconductor},
volume = {16},
issue = {3},
issn = {2073-4859},
pages = {198-200}
}