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Update working groups #41

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146 changes: 46 additions & 100 deletions active_working_groups.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -5,20 +5,40 @@ order. If you are interested in becoming involved with one of these groups
please contact the group leader(s).


## BiocAsia

- Description: This group will primarily be involved with conference planning for the BiocAsia conference and seeks to formalise this as a Bioconductor Working Group
- Slack: #biocasia-conference-organization, #biocasia
- Leads: Stevie Pederson, Stefano Mangiola
- Current Members: Stevie, Stefano, Ellis Patrick, Peter Hickey, Kozo Nishida, Jiya Chaudhary, Manoj Wagle, Lori Shepherd

## BiocAwards

- Description: In 2020, Bioconductor established annual Bioconductor awards to
recognize outstanding contributions to the Bioconductor community. This
committee meets annually starting roughly 4-6 months before the annual
conference to conduct nominations and voting.
- Links: https://bioconductor.org/about/awards/
- Leads: Lori Shepherd <[email protected]> and Maria Doyle
- Current Members: Stevie Pederson, Johannes Rainer

## Code of Conduct

- Description: The Code of Conduct Committee reviews and revises the
Bioconductor Code of Conduct as needed. There is also a large effort to
translate the Code of Code to multiple languages.
- Links: https://github.com/Bioconductor/bioc_coc_multilingual
- Slack: private channel
- Leads: Saskia Freytag
- Current Members: Kevin Rue-Albrecht, Johannes Rainer
- Leads: Anna Quaglieri, Gerry Tonkin-Hill
- Current Members: Kevin Rue-Albrecht, Martin Davila-Cervantes, Federica
Gazzelloni, Michael Love, Federico Marini, Sowmya Parthiban, Shixiang Wang,
Lluis Revilla, Paulina Boadiwaa Mensah, Peace Sandy, Sinmisoluwa Adesanya,
Michella Savage

## Conference Planning

- Description: Organizes and Plans the Annual Conference.
- Slack: #bioc-conference-organization, #bioc-conference-web
- Slack: #bioc-conference-organization, #bioc-conference-everyone
- Leads: Levi Waldron, Erica Feick
- Current Members: Charlotte Soneson, Jenny D, Jenny S, Lori, Marc, Andrew, Daniela, Matt, Mikhail, Samuel, Krithika, Sean, Wes

Expand All @@ -31,17 +51,12 @@ please contact the group leader(s).
- Current Members: Levi Waldron, Marcel Ramos, Erdal Cosgun, Sridhar Srivatsan,
Brian Schilder, Vince Carey

## Developers Training
## EDAM collaboration

- Description: This group aims to help create and promote development
discussions and opportunities within the Bioconductor organization. This
includes organizing developer forum talks, collating material on the
Bioconductor YouTube channel, and monitoring the new developer mentorship
program.
- Links: [New Developer Training Program](http://bioconductor.org/developers/new-developer-program/), [Playlist on Bioconductor YouTube](https://www.youtube.com/watch?v=CcJgcDy2qEI&list=PLdl4u5ZRDMQQLMupAtEzm2y4gUIUm_1n6)
- Slack: #developers-mentorship, #developers-forum
- Leads: Mike Smith, Kevin Rue-Albrecht
- Current Members: Aedin Culhane, Lori Shepherd
- Description: This group unites EDAM and Bioconductor community members to explore indexing the Bioconductor ecosystem using the [EDAM ontology](https://edamontology.org/). Our working group's objectives include increasing the visibility of Bioconductor packages to a broader audience, including those not primarily using R, and expanding EDAM as a standard for annotating computational biology resources. Through this collaboration, we aim to synergize two large, international communities focused on open science. Future plans may include exploring connections with bio.tools, Bioschemas, and TeSS. If you're interested in contributing or want to learn more, join us on Slack.
- Slack: #edam-collaboration
- Leads: Claire Rioualen, Maria Doyle, Hervé Pagès
- Current Members: Vince Carey, Hervé Menager, Lori Shepherd, Johannes Rainer, Kozo Nishida, Matúš Kalaš

## Education

Expand All @@ -52,17 +67,6 @@ please contact the group leader(s).
- Founding Members: Laurent Gatto, Charlotte Soneson, Kevin Rue-Albrecht, Jenny Drnevich, Robert Castelo, Toby Hodges, Susan Holmes
- Current Members: Open to all. Join us! Details [here](https://www.bioconductor.org/help/education-training/).

## Governance

- Description: This group is re-evaluating with potential to restructure the
governance and organiztion of _Bioconductor_. This includes but not limited to
the current Scientific, Community, and Technical Boards as well as the
Bioconductor Foundation.
- Links:
- Slack: #biocoductor-governance
- Leads: Charlotte Soneson, Vince Carey
- Current Members: Levi Waldron, Aedin Culhane, Charlotte Soneson, Vince Carey, Lori Shepherd

## Mass Spectrometry for Proteomics and Metabolomics

- Description: The goal of this working group is to identify members of the
Expand All @@ -72,8 +76,7 @@ please contact the group leader(s).
- Links: https://github.com/lgatto/BiocMassSpecWorkingGroup
- Slack: #mass-spectrometry, #metabolomics, #proteomics
- Leads: Laurent Gatto (TAB) and Johannes Rainer (CAB)
- Current Members: Lauent, Johannes. A call for people interested to join will
be opened soon.
- Current Members: Lauent, Johannes.

## Multilingual

Expand All @@ -83,69 +86,18 @@ please contact the group leader(s).
- Leads: Leonardo Collado-Torres, Kozo Nishida, Daniela Cassol, Kevin Rue-Albrecht
- Current Members:

## Package Review

- Description: The package review working group was established to review and
revise the current review process for Bioconductor. It also was tasked with
updating Bioconductor package guidelines and package submission
documentation. Its current focus is to update, clean up, and reorganize the
material presented at http://contributions.bioconductor.org/. This is <b>not</b> the
group to volunteer to become a Bioconductor package reviewer. This group is to
refine the requirements for a Bioconductor package.
- Links: https://github.com/Bioconductor/pkgrevdocs, https://contribution.bioconductor.org
- Slack: #package-submission, #reviewers
- Leads: Lori Shepherd <[email protected]>
- Current Members: Lori Shepherd, Kayla Interdonato, Johannes Rainer, Yagoub
Adam, Kevin Rue-Albrecht, Estefania Mancini, Mike Smith, Daniela Cassol

## Privacy

- Description: Data privacy is an important topic to the Bioconductor project,
with its large community and many websites and services hosted by a variety of
organisations around the globe. This working group is engaged in making sure
that Bioconductor services meet both legal requirements and community
expectations regarding personal data privacy.
- Links:
- Leads:
- Current Members: Vince Carey, Mike Smith
- Past Members: Katermina Kechris

## Publication

- Description: Publication discussion with F1000R and other venues that enable publication of workflows, BioC material from workshops or package presentations. This working group is trying to make it easier and less expensive to publish papers on BioC advances that can be kept up to date while still providing DOI and valid publication metadata so that there is a citation and recognition mechanism. Highly interested in new Overlay publishing and using quarto for new publication models.
- Links:
- Leads: Susan Holmes
- Current Members: Susan, Sean Davis,

## Recommended classes and methods

- Description: Discussions arounnd Bioconductor 'official' classes and methods and how to articulate their benefits to increase their usage across the ecosystem, in particular in new contributions.
- Links: https://github.com/Bioconductor/BiocClassesWorkingGroup
- Leads: Laurent Gatto
- Current Members: Vince Carey, Laurent Gatto, Johannes Rainer, Lori Shepherd

## Spatial and Multi-omics

- Description:
- Links:
- Leads: Stephanie Hicks
- Current Members:

## Industry

- Description: Many Bioconductor users are from industry. Yet industry users aren't a large voice in the Bioconductor community. This working group is centered around collaborating and engaging with industry users. Topics of interest include: how to get more industry users participating with the community, what guidelines can be established to bolster the community relationship with industry, and much more.
- Links:
- Slack: #industry
- Leads: Nicole Ortogero, David Henderson
- Current Members: Michael Lawrence, Xiuwen Zheng, Wade Davis, Snehal Wani, Scott Chasalow
## Package Build Report Triage

## Website

- Description: The Website working group will create the list of requirements for the Bioconductor website redesign.
- Links:
- Slack: #biocwebsite
- Leads: Maria Doyle, Lori Shepherd, Aedin Culhane
- Current Members: Kevin Rue-Albrecht, Sean Davis, Susan Holmes, Vince Carey, Alex Mahmoud, Marcel Ramos, Hédia Thani, Shila Ghazanfar, Laurent Gatto, Jen Wokaty, Samuel Gamboa, Bob Shear, Matt Ritchie
- Description: This committee would be responsible for reaching out to ERRORing
package maintainers to fix their package and identify inactive packages for
deprecation. While we have autonotificaiton of failure, many (most)
maintainers ignore and are not good about checking the provided build
reports. The core team has found that sending personalized emails greatly
increases the likelihood of a maintainer to fix the package.
- Links: https://bioconductor.org/checkResults/
- Leads: Lori Shepherd <[email protected]>
- Current Members: Johannes Rainer, Kayla Interdonato. I need more members! Please if interested
please email or slack

## Social Media

Expand All @@ -155,23 +107,17 @@ expectations regarding personal data privacy.
- Leads: Maria Doyle
- Current Members: Laurent Gatto, Susan Holmes, Federica Gazzelloni, İrem Kahveci, Hamdi Furkan Kepenek, Xueyi Dong, Shixiang Wang, Kozo Nishida

## EDAM collaboration

- Description: This group unites EDAM and Bioconductor community members to explore indexing the Bioconductor ecosystem using the [EDAM ontology](https://edamontology.org/). Our working group's objectives include increasing the visibility of Bioconductor packages to a broader audience, including those not primarily using R, and expanding EDAM as a standard for annotating computational biology resources. Through this collaboration, we aim to synergize two large, international communities focused on open science. Future plans may include exploring connections with bio.tools, Bioschemas, and TeSS. If you're interested in contributing or want to learn more, join us on Slack.
- Slack: #edam-collaboration
- Leads: Claire Rioualen, Maria Doyle, Hervé Pagès
- Current Members: Vince Carey, Hervé Menager, Lori Shepherd, Johannes Rainer, Kozo Nishida, Matúš Kalaš

## TeSS

- Description: This group focuses on enhancing the connectivity and integration between the [TeSS (Training eSupport System)](https://tess.elixir-europe.org) portal and the Bioconductor project. Our objectives include implementing Bioschemas for Bioconductor training material and events to improve their discoverability and accessibility via TeSS (https://tess.elixir-europe.org/content_providers/bioconductor). We aim to strengthen the bridge between these platforms, facilitating easier access to Bioconductor training resources.
- Slack: #elixir. A TeSS-specific channel may be created based on interest and participation.
- Leads: Maria Doyle
- Current Members: Maria Doyle, Laurent Gatto (contact Maria on Slack if interested to join this initiative)

## BiocAsia
## Website

- Description: This group will primarily be involved with conference planning for the BiocAsia conference and seeks to formalise this as a Bioconductor Working Group
- Slack: #biocasia
- Leads: Stevie Pederson, Stefano Mangiola
- Current Members: Stevie, Stefano, Ellis Patrick, Peter Hickey, Kozo Nishida, Jiya Chaudhary, Manoj Wagle, Lori Shepherd
- Description: The Website working group will create the list of requirements for the Bioconductor website redesign.
- Links:
- Slack: #biocwebsite
- Leads: Maria Doyle, Lori Shepherd, Aedin Culhane
- Current Members: Kevin Rue-Albrecht, Sean Davis, Susan Holmes, Vince Carey, Alex Mahmoud, Marcel Ramos, Hédia Thani, Shila Ghazanfar, Laurent Gatto, Jen Wokaty, Samuel Gamboa, Bob Shear, Matt Ritchie
21 changes: 13 additions & 8 deletions inactive_working_groups.Rmd
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Expand Up @@ -4,12 +4,17 @@ These are legacy working groups that may have achieved their goals and now are
currently inactive. If you think there is a need to re-establish one of the
listed groups please contact the listed Lead and [email protected].

## BiocAwards
## Package Review

- Description: In 2020, Bioconductor established annual Bioconductor awards to
recognize outstanding contributions to the Bioconductor community. This
committee meets annually starting roughly 4-6 months before the annual
conference to conduct nominations and voting.
- Links: https://bioconductor.org/about/awards/
- Leads: Lori Shepherd <[email protected]> and Simone Bell
- Current Members: Lori Shepherd and Simone Bell
- Description: The package review working group was established to review and
revise the current review process for Bioconductor. It also was tasked with
updating Bioconductor package guidelines and package submission
documentation. Its current focus is to update, clean up, and reorganize the
material presented at http://contributions.bioconductor.org/. This is <b>not</b> the
group to volunteer to become a Bioconductor package reviewer. This group is to
refine the requirements for a Bioconductor package.
- Links: https://github.com/Bioconductor/pkgrevdocs, https://contribution.bioconductor.org
- Slack: #package-submission, #reviewers
- Leads: Lori Shepherd <[email protected]>
- Current Members: Lori Shepherd, Kayla Interdonato, Johannes Rainer, Yagoub
Adam, Kevin Rue-Albrecht, Estefania Mancini, Mike Smith, Daniela Cassol
66 changes: 54 additions & 12 deletions needed_working_groups.Rmd
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Expand Up @@ -10,15 +10,57 @@ active or listed here, you can either contact [email protected] or
submit a pull requested providing Description, Lead, Initial Members, and any
other relevent links.</p>

## Package Build Report Triage

- Description: This committee would be responsible for reaching out to ERRORing
package maintainers to fix their package and identify inactive packages for
deprecation. While we have autonotificaiton of failure, many (most)
maintainers ignore and are not good about checking the provided build
reports. The core team has found that sending personalized emails greatly
increases the likelihood of a maintainer to fix the package.
- Links: https://bioconductor.org/checkResults/
- Leads: Lori Shepherd <[email protected]>
- Current Members: Johannes Rainer. I need more members! Please if interested
please email or slack
## Developers Training

- Description: This group aims to help create and promote development
discussions and opportunities within the Bioconductor organization. This
includes organizing developer forum talks, collating material on the
Bioconductor YouTube channel, and monitoring the new developer mentorship
program.
- Links: [New Developer Training Program](http://bioconductor.org/developers/new-developer-program/), [Playlist on Bioconductor YouTube](https://www.youtube.com/watch?v=CcJgcDy2qEI&list=PLdl4u5ZRDMQQLMupAtEzm2y4gUIUm_1n6)
- Slack: #developers-mentorship, #developers-forum
- Leads: Mike Smith, Kevin Rue-Albrecht
- Current Members: Aedin Culhane, Lori Shepherd

## Industry

- Description: Many Bioconductor users are from industry. Yet industry users aren't a large voice in the Bioconductor community. This working group is centered around collaborating and engaging with industry users. Topics of interest include: how to get more industry users participating with the community, what guidelines can be established to bolster the community relationship with industry, and much more.
- Links:
- Slack: #industry
- Leads: Nicole Ortogero, David Henderson
- Current Members: Michael Lawrence, Xiuwen Zheng, Wade Davis, Snehal Wani, Scott Chasalow

## Privacy

- Description: Data privacy is an important topic to the Bioconductor project,
with its large community and many websites and services hosted by a variety of
organisations around the globe. This working group is engaged in making sure
that Bioconductor services meet both legal requirements and community
expectations regarding personal data privacy.
- Links:
- Leads:
- Current Members: Vince Carey, Mike Smith
- Past Members: Katermina Kechris

## Publication

- Description: Publication discussion with F1000R and other venues that enable publication of workflows, BioC material from workshops or package presentations. This working group is trying to make it easier and less expensive to publish papers on BioC advances that can be kept up to date while still providing DOI and valid publication metadata so that there is a citation and recognition mechanism. Highly interested in new Overlay publishing and using quarto for new publication models.
- Links:
- Leads: Susan Holmes
- Current Members: Susan, Sean Davis,

## Recommended classes and methods

- Description: Discussions arounnd Bioconductor 'official' classes and methods and how to articulate their benefits to increase their usage across the ecosystem, in particular in new contributions.
- Links: https://github.com/Bioconductor/BiocClassesWorkingGroup
- Leads: Laurent Gatto
- Current Members: Vince Carey, Laurent Gatto, Johannes Rainer, Lori Shepherd

## Spatial and Multi-omics

- Description:
- Links:
- Leads:
- Current Members:


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