Merge pull request #6 from mblue9/maria-edits-2024

add 2024 news
Bioconductor · Dec 16, 2024 · d560cd2 · d560cd2
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diff --git a/inst/RJournal/dec-2024/bioc.qmd b/inst/RJournal/dec-2024/bioc.qmd
@@ -1,6 +1,6 @@
 ---
-title: "Bioconductor Notes, Winter 2024"
-date: "2023-02-24"
+title: "Bioconductor Notes, December 2024"
+date: "2024-12-31"
 abstract: >
   We discuss general project news.
 author:
@@ -37,85 +37,75 @@ nwkfl = 30
 nbooks = 5
 ```
 
-The current Bioconductor release is [3.20](https://bioconductor.org/news/bioc_3_20_release/). It is
+Bioconductor [3.20](https://bioconductor.org/news/bioc_3_20_release/), released in October 2024, is now available. It is
 compatible with R `r curR` and consists of `r nsoft` software packages, `r nexp`
 experiment data packages, `r nanno` up-to-date annotation packages, `r nwkfl`
 workflows, and `r nbooks` books. [Books](https://bioconductor.org/books/release/) are
 built regularly from source and therefore fully
 reproducible; an example is the
 community-developed [Orchestrating Single-Cell Analysis with Bioconductor](https://bioconductor.org/books/release/OSCA/).
 
-## Bioconductor in Python!
 
-We're excited to introduce [BiocPy](https://www.github.com/biocpy), a project aimed at enabling Bioconductor workflows in Python. Analysts today use a variety of languages in their workflows, including R/Bioconductor for statistical analysis and Python for imaging or machine learning tasks. BiocPy aims to facilitate interoperability between R and Python by providing standardized data structures based on existing Bioconductor data structures. These include genomic ranges for interval based operations, summarized experiments and other derivatives for analyzing genomic experiments. To learn more, visit the [BiocPy](https://github.com/biocpy) GitHub organization.
+# Core Team and Infrastructure Updates
 
-# Core team updates
+TODO [Core team]: What's new?
 
-What's new for core?
 
-## Partnering with Outreachy
+# Community and Impact
 
-Bioconductor will also participate in Outreachy's FIXME
-internship round to offer internships with Bioconductor community projects.
+## Publications and Preprints
 
+In October 2024, two notable preprints were published by Bioconductor contributors:
 
-# Conferences
+- [Eleven quick tips for writing a Bioconductor package](https://osf.io/preprints/osf/wxjky)
+Authors: Charlotte Soneson, Lori Shepherd, Marcel Ramos, Kevin Rue-Albrecht, Johannes Rainer, Hervé Pagès, and Vincent J. Carey (Bioconductor Core Team and collaborators).
+This preprint provides concise, practical advice for developing high-quality Bioconductor packages.
+
+- [Learning and teaching biological data science in the Bioconductor community](https://arxiv.org/abs/2410.01351)
+Authors: Bioconductor Training Committee and others.
+This preprint explores the Bioconductor community’s role in advancing biological data science education and training.
 
-Links on conferences?
+## Outreachy Internships
 
-# Blog
+TODO[Jen]
 
-New blog entries to mention?
+## ELIXIR BioHackathon Europe 2024
+Bioconductor participated in this collaborative event (November 4–8), held in Barcelona, to advance interoperability and innovation in life sciences. Key contributions included projects focused on EDAM-bio.tools and training infrastructure.
 
-# Boards updates
+## Training Domain Launch
 
-## Community Advisory Board
+Bioconductor is developing [training.bioconductor.org](https://training.bioconductor.org/), a centralised website for accessing and organising high-quality Bioconductor training materials. This work is still in progress, with the Training Committee actively discussing ways to restructure existing resources and improve their discoverability. A key focus is supporting community-driven tutorials and emphasising pedagogical quality to better serve learners.
 
-Update?
+## Bioconductor Carpentry Single-Cell Module
 
-<!--
-- The [Community Advisory Board](https://bioconductor.org/about/community-advisory-board/) (CAB) are voting in new members. Outgoing members are Susan Holmes, Leonardo Collado-Torres, Yagoub A. I. Adam, Matt Ritchie, Benilton Carvalho, we gratefully thank them for their service.
+Bioconductor now features an official [single-cell RNA sequencing (scRNA-seq) module](https://carpentries-incubator.github.io/bioc-scrnaseq/) in the Carpentries Incubator. This module, renamed from the Orchestrating Single-Cell Analysis (OSCA) curriculum, provides a structured introduction to scRNA-seq analysis with Bioconductor and is aimed at both learners and educators.
 
-- There is a Call for Bioconductor Community-Led events supported by the CAB.
-Apply in [this form](https://forms.gle/oTHp26TG3eP9q4eE7)
--->
+## Bioconductor Joins Bluesky
 
+In October 2024, Bioconductor expanded its social media presence by joining Bluesky. This move reflects Bioconductor's commitment to engaging with its global community across diverse platforms. We invite you to [follow us](https://bsky.app/profile/bioconductor.bsky.social) to stay updated on the latest news, events, and community highlights.
 
-# Committees and Working groups updates
+# Conferences
 
-If you are interested in becoming involved with one of these groups please contact the group leader(s).
+## BioCAsia2024
+Held in Sydney, Australia (November 7–8), the Bioconductor Asia meeting fostered collaboration and knowledge sharing among regional and global Bioconductor users and developers. For more details, visit the [BioCAsia2024 website](https://biocasia2024.bioconductor.org/).
 
-Updates?
+## Galaxy and Bioconductor Community Conference
+Announced in September 2024, the first Galaxy and Bioconductor Community Conference (GBCC 2025) is scheduled for June 23–26, 2025, at Cold Spring Harbor Laboratory, New York. The conference aims to showcase the integration of Galaxy and Bioconductor tools, promoting reproducible workflows and community-driven development. For more details, see the [blog post](https://blog.bioconductor.org/posts/2024-09-03-gbcc2025-announcement/).
 
-<!--
 
-- [Cloud Methods](https://workinggroups.bioconductor.org/currently-active-working-groups-committees.html#cloud-methods)
-  held their first meeting Feb 2023. The working group will meet monthly to
-  develop standards and tools for the Bioconductor community related to the
-  cloud.
+# Boards and Working Groups Updates
 
-- [Social media working group](https://workinggroups.bioconductor.org/currently-active-working-groups-committees.html#social-media).
-  A new group, started in Feb 2023, have set up
-  [Bioconductor Mastodon acccount](https://genomic.social/@bioconductor).
+## New Board Members
 
-- [Teaching Committee](https://workinggroups.bioconductor.org/currently-active-working-groups-committees.html#education)
-    - Are planning a hackathon for the
-      [Bioconductor Carpentries RNA-seq lesson](https://carpentries-incubator.github.io/bioc-rnaseq/).
-    - Will be participating in
-      [Galaxy Training Smorgasbord 2023](https://gallantries.github.io/video-library/events/smorgasbord3/),
-      a free online global event, May 22-26.
+- The [Community Advisory Board](https://bioconductor.org/about/community-advisory-board/) (CAB) welcomes new members Zahraa Alsafwani, Jasmine Daly, Tobilola Ogunbowale, and Lluis Revilla. We extend our gratitude to outgoing members Daniela Cassol, Estefania Mancini, Jordana Muwanguzi, and Mike Smith for their service.
 
-- [Website working group]([https://workinggroups.bioconductor.org/currently-active-working-groups-committees.html#website)
-  are planning the redesign of [bioconductor.org](bioconductor.org).
+- The [Technical Advisory Board](https://bioconductor.org/about/technical-advisory-board/) (TAB) welcomes new members Michael Lawrence and Jacques Serizay. Outgoing members Sean Davis and Michael Love are also warmly thanked for their contributions.
 
--->
+## Code of Conduct Committee Elections
 
-# Other
+In October 2024, Bioconductor sought new members to join its Code of Conduct (CoC) Committee, which plays a vital role in maintaining the integrity and safety of our community. The CoC meets 3–4 times annually to address important issues. Applications are now closed, but you can learn more about the committee and its work on the Code of Conduct page.
 
-- Summer school *"Statistical Data Analysis for Genome-Scale Biology"* [CSAMA 2023](https://csama2023.bioconductor.eu/) in Bressanone-Brixen, Italy, June 11-16 2023. Application deadline May 15. 
-- Course *"Statistical Analysis of Genome Scale Data"* at [CSHL](https://meetings.cshl.edu/courses.aspx?course=C-DATA&year=23) in New York, USA, June 30 - July 13 2023. Application deadline March 15. 
-- Workshop *"Opportunities for Bioconductor and ELIXIR communities to co-develop training infrastructure"* accepted for the [ELIXIR All Hands meeting](https://elixir-europe.org/events/elixir-all-hands-2023) in Dublin, Ireland, June 5-8 2023.
-- Workshop *"Orchestrating Large-Scale Single-Cell Analysis with Bioconductor"* accepted for [ISMB/ECCB 2023](https://www.iscb.org/ismbeccb2023-programme/tutorials#ip4) in Lyon, France, July 23 2023.
+If you are interested in becoming involved with any [Bioconductor working group](https://workinggroups.bioconductor.org/currently-active-working-groups-committees.html) please contact the group leader(s).
 
 
 # Using Bioconductor
@@ -153,7 +143,7 @@ Key resources include:
 for peer-reviewed Bioconductor workflows as well as conference contributions.
 - The [Bioconductor YouTube](https://www.youtube.com/user/bioconductor)
      channel includes recordings of keynote and talks from recent 
-     conferences including BioC2022, EuroBioC2022, and BiocAsia2021, in addition to 
+     conferences, in addition to 
      video recordings of training courses. 
 - Our [package submission](https://github.com/Bioconductor/Contributions)
   repository for open technical review of new packages.
@@ -169,3 +159,5 @@ and adopts practices (such as a
 project-wide [Code of Conduct](https://bioconductor.org/about/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](https://slack.bioconductor.org) workspace or by emailing [email protected].
diff --git a/inst/RJournal/jun-2024/bioc.qmd b/inst/RJournal/jun-2024/bioc.qmd
@@ -0,0 +1,143 @@
+---
+title: "Bioconductor Notes, June 2024"
+date: "2024-06-30"
+abstract: >
+  We discuss general project news.
+author:
+  - name: Maria Doyle, Bioconductor Community Manager
+    affiliation: University of Limerick
+  - name: Bioconductor Core Developer Team
+    affiliation: Dana-Farber Cancer Institute, Roswell Park Comprehensive Cancer Center, City University of New York, Fred Hutchinson Cancer Research Center, Mass General Brigham
+execute: 
+  echo: false
+  warning: false
+  message: false
+---
+
+
+# Introduction 
+
+[Bioconductor](https://bioconductor.org) 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.
+
+# Software
+
+```{r lkdat,results="hide",echo=FALSE}
+curR = "4.4"
+nsoft = 2289
+nexp = 431
+nanno = 928
+nwkfl = 30
+nbooks = 5
+```
+
+Bioconductor [3.19](https://bioconductor.org/news/bioc_3_19_release/), released in May 2024, is now available. It is
+compatible with R `r curR` and consists of `r nsoft` software packages, `r nexp`
+experiment data packages, `r nanno` up-to-date annotation packages, `r nwkfl`
+workflows, and `r nbooks` books. [Books](https://bioconductor.org/books/release/) are
+built regularly from source and therefore fully
+reproducible; an example is the
+community-developed [Orchestrating Single-Cell Analysis with Bioconductor](https://bioconductor.org/books/release/OSCA/).
+
+
+# Core Team and Infrastructure Updates
+
+TODO [Core team]: What's new?
+
+
+# Community and Impact
+
+## CZI EOSS6 Grants Announcement
+
+In June 2024, the Chan Zuckerberg Initiative (CZI) announced funding for five Bioconductor projects as part of the EOSS Cycle 6. These projects focus on advancing training accessibility, developer support, GPU computing, resource tagging with ontologies, and the expansion of Tidyomics tools. For more details on each project and its collaborators, see the blog post [here](https://blog.bioconductor.org/posts/2024-07-12-czi-eoss6-grants/).
+
+
+## CZI Open Science Meeting Highlights
+
+On June 12–14, 2024, Bioconductor members attended the Chan Zuckerberg Initiative (CZI) Open Science Meeting in Boston. This gathering provided an opportunity for current CZI Open Science grantees to connect and share their progress. Bioconductor was recognised as one of the top open-source software projects in the CZ Software Mentions dataset. For more details, see the blog post [here](https://blog.bioconductor.org/posts/2024-07-24-czi-os-meeting-highlights/).
+
+## Outreachy Internships
+
+TODO [Jen]: Bioconductor will also participate in Outreachy's FIXME
+internship round to offer internships with Bioconductor community projects.
+
+## CSAMA 2024: Biological Data Science Summer School
+
+The 20th edition of [CSAMA (Computational Statistics for Biological Data Analysis) Summer School](https://csama2024.bioconductor.eu/) took place in Bressanone-Brixen, Italy, from June 23–28, 2024. This intensive course covered advanced analysis of molecular data using the R/Bioconductor ecosystem. Faculty included Robert Gentleman, co-founder of R and Bioconductor, and Vince Carey, current Bioconductor lead, highlighting Bioconductor's role in open-source training. 
+
+# Conferences
+
+## BioC2024 Reminder
+
+The annual Bioconductor Conference (BioC2024) is fast approaching! This year’s event will be held in Grand Rapids, Michigan, from July 24–26, 2024. Featuring keynote talks, interactive workshops, and ample opportunities for community engagement, BioC2024 is a must-attend event for Bioconductor users and developers alike. Visit the [conference website](https://www.bioc2024.bioconductor.org/) to register and learn more.
+
+## EuroBioC2024 Reminder
+
+Planning is well underway for EuroBioC2024, the European Bioconductor Conference, scheduled for September 4–6, 2024, in Oxford, UK. Like BioC2024, EuroBioC2024 will include keynote presentations, hands-on workshops, and plenty of opportunities for networking with members of the Bioconductor community. For details and updates, visit the [conference website](https://eurobioc2024.bioconductor.org/).
+
+# Boards and Working Groups Updates
+
+TODO  - Updates?
+
+If you are interested in becoming involved with any [Bioconductor working group](https://workinggroups.bioconductor.org/currently-active-working-groups-committees.html) please contact the group leader(s).
+
+
+# Using Bioconductor
+
+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](https://bioconductor.org/packages/SingleCellExperiment), with
+```
+  BiocManager::install("SingleCellExperiment")
+```
+[Docker](https://bioconductor.org/help/docker/)
+images provides a very effective on-ramp for power users to rapidly
+obtain access to standardized and scalable computing environments.
+Key resources include:
+
+
+- [bioconductor.org](https://bioconductor.org) to install,
+  learn, use, and develop Bioconductor packages.
+- A list of [available software](https://bioconductor.org/packages)
+  linking to pages describing each package.
+- A question-and-answer style
+  [user support site](https://support.bioconductor.org) and
+  developer-oriented [mailing list](https://stat.ethz.ch/mailman/listinfo/bioc-devel).
+- A community slack workspace ([sign up](https://slack.bioconductor.org))
+   for extended technical discussion.
+- The [F1000Research Bioconductor gateway](https://f1000research.com/gateways/bioconductor)
+for peer-reviewed Bioconductor workflows as well as conference contributions.
+- The [Bioconductor YouTube](https://www.youtube.com/user/bioconductor)
+     channel includes recordings of keynote and talks from recent 
+     conferences, in addition to 
+     video recordings of training courses. 
+- Our [package submission](https://github.com/Bioconductor/Contributions)
+  repository for open technical review of new packages.
+
+Upcoming and recently completed events are browsable at our
+[events page](https://bioconductor.org/help/events/).
+
+The [Technical](https://bioconductor.org/about/technical-advisory-board/)
+and and [Community](https://bioconductor.org/about/community-advisory-board/)
+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](https://bioconductor.org/about/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](https://slack.bioconductor.org) workspace or by emailing [email protected].