From 35c4c612caf8d00ee7756d5b17bd59c378a9d2ad Mon Sep 17 00:00:00 2001 From: Wendi Bacon <44605769+nomadscientist@users.noreply.github.com> Date: Wed, 4 Oct 2023 23:06:44 +0200 Subject: [PATCH 1/8] created scCoP page --- content/projects/singlecell/index.md | 77 ++++++++++++++++++++++++++++ 1 file changed, 77 insertions(+) create mode 100644 content/projects/singlecell/index.md diff --git a/content/projects/singlecell/index.md b/content/projects/singlecell/index.md new file mode 100644 index 0000000000..98453d7ba9 --- /dev/null +++ b/content/projects/singlecell/index.md @@ -0,0 +1,77 @@ +--- +description: "Users, developers, and trainers providing feedback and energy to improve and expand the Galaxy single cell capabilities." +autotoc: true +title: "Galaxy Single Cell Community of Practice" +--- + +We are a mix of users, developers, and trainers providing feedback and energy to improve and expand the Galaxy single cell capabilities. Do you use Galaxy single cell tools for scRNA-seq or beyond? Do you have feedback for us? Want to be a tester of new resources? Want to impact the future of single cell in Galaxy? Are you a developer looking for a place to play? Are you developing Galaxy single cell materials and want to stay aware of what others are doing in this field? + +**Welcome to the Galaxy Single-Cell Community of Practice!** + +## I'm just trying to learn to analyse my data, how did I get here? +Hello user! You'll be interested in the following resources: + + - [Learning pathway for getting to grips with Galaxy and single cell](https://training.galaxyproject.org/training-material/learning-pathways/intro_single_cell.html) + - [Single cell training material](https://training.galaxyproject.org/training-material/topics/single-cell/) + - Galaxy instance: [Single cell instance](https://singlecell.usegalaxy.eu) or Human Cell Atlas instance](https://humancellatlas.usegalaxy.eu) + - [Matrix channel for asking for help](https://matrix.to/#/#Galaxy-Training-Network_galaxy-single-cell:gitter.im) + +Saying that, we'd absolutely love to have users feedback on their experiences to help us improve. You'd be very welcome to join the Community of Practice to help improve the Galaxy single cell space! + +# What are the goals of the single cell community of practice? + +🎯Goals +- Prevent work duplication +- Collaborate across pipeline, ensuring users feedback to developers +- Identify community needs +- Tool & tutorial development +- Testing +- Build & support user community + +# Who are we looking for? + +Anyone with energy! We love hearing from users, developers, trainers, and everyone in between who is using or developing Galaxy for single cell analysis. + +# How do we function? + +We meet every 3 weeks (alternating USA and AU time zones) for 1 hour. + +Our meeting agenda is: + - Random intro chatter & introductions + - Updates from Trello site (what people are working on / asking for help) + - 🐛Help/bugs + - Status reports & new stuff that’s happening + - Other cool stuff (example: Smorgasbord) + - Ongoing actions to send out + +We send out emails to the mailing list after each meeting, at the mid-way point between meetings, and the day before meetings as a reminder. + +We keep rolling notes on a googledoc and monitor our work on Trello. + +When people ask for help or are working across institutes, we set up chat sub-channels to bring them together. + +We have a chat forum to discuss news and ideas, and are represented in the Galaxy Community Reps chat group. + + + +# How can you join & other important links + +Start by joining our [💬Matrix channel](https://matrix.to/#/#usegalaxy-eu_single-cell-workflows) and introduce yourself! (Or you can just lurk there for a bit!) + + - 📪[Mailing list](https://lists.galaxyproject.org/lists/single-cell-cop.lists.galaxyproject.org/) + - ✅[Trello site](https://trello.com/invite/b/KLVgHvCB/ATTI53fe3f6ea71737e3aa6570e5ed148a528698CA27/sccop-tool-wrapping-tutorial-development) + - 🗓️[SC-CoP Google Calendar](https://calendar.google.com/calendar/embed?src=f6b4dbe4aa3d7076e740e4198aa482d6b92b52129c9f867cfb49f7ac40450796%40group.calendar.google.com&ctz=Europe%2FLondon) <-- Subscribe! + - 📝[Meeting Notes doc](https://docs.google.com/document/d/19W--oeFoEgfZbw9MWvky_A__554th-VG3ryOqtfmHSA/edit?usp=sharing) <--- There's a section here called 'New here?' that gives tips on how to start contributing as well! + - 🧑🏽‍🏫[User Matrix Channel](https://matrix.to/#/#Galaxy-Training-Network_galaxy-single-cell:gitter.im) + +## Key words + +Single-cell +Single cell +Single-cell RNA-Sequencing +Single-cell RNA-seq +scRNA-seq +snRNA-seq +10x +Single cell biology +Single cell multiomics From 4250295373280d246443f5d63c11ce20f8ab08a9 Mon Sep 17 00:00:00 2001 From: Wendi Bacon <44605769+nomadscientist@users.noreply.github.com> Date: Wed, 4 Oct 2023 23:10:44 +0200 Subject: [PATCH 2/8] fix link in communities of practice page --- content/community/practice/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/content/community/practice/index.md b/content/community/practice/index.md index cd840c07a9..48d27c6768 100644 --- a/content/community/practice/index.md +++ b/content/community/practice/index.md @@ -17,7 +17,7 @@ title: Communities of Practice | Small Scale Servers | Admins of small scale Galaxy servers. |[](https://lists.galaxyproject.org/lists/small-scale-admins.lists.galaxyproject.org/)| | [Machine Learning](https://ml.usegalaxy.eu/) | A comprehensive set of data preprocessing, machine learning, deep learning and visualisation tools, and consolidated workflows for end-to-end machine learning analysis. | [](https://training.galaxyproject.org/training-material/topics/statistics/) [](https://ml.usegalaxy.eu/) | | [Materials Science](https://materials.usegalaxy.eu/) | A Galaxy workbench with tools and workflows for materials science, including muon spectroscopy. | [](https://materials.usegalaxy.eu/) | -| Single cell
[Single-cell Workbench](https://singlecell.usegalaxy.eu) [Human cell atlas Workbench](https://humancellatlas.usegalaxy.eu)| Group of single cell tool developers, trainers and users to help connect outreach, user needs, and computationalists. | [](https://matrix.to/#/#usegalaxy-eu_single-cell-workflows:gitter.im) [](https://training.galaxyproject.org/training-material/topics/single-cell/) [](https://lists.galaxyproject.org/lists/single-cell-cop.lists.galaxyproject.org/) | +| [Single cell](content/projects/singlecell/index.md) | Group of single cell tool developers, trainers and users to help connect outreach, user needs, and computationalists. | [](https://matrix.to/#/#usegalaxy-eu_single-cell-workflows:gitter.im) [](https://training.galaxyproject.org/training-material/topics/single-cell/) [](https://lists.galaxyproject.org/lists/single-cell-cop.lists.galaxyproject.org/) | # Set up your own community From 88036082ed3a6b04f26348ac7a8d6dd74081a03c Mon Sep 17 00:00:00 2001 From: Wendi Bacon <44605769+nomadscientist@users.noreply.github.com> Date: Wed, 4 Oct 2023 23:58:01 +0200 Subject: [PATCH 3/8] update details section --- content/projects/singlecell/index.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/content/projects/singlecell/index.md b/content/projects/singlecell/index.md index 98453d7ba9..508aad1cbc 100644 --- a/content/projects/singlecell/index.md +++ b/content/projects/singlecell/index.md @@ -34,7 +34,7 @@ Anyone with energy! We love hearing from users, developers, trainers, and everyo # How do we function? -We meet every 3 weeks (alternating USA and AU time zones) for 1 hour. +**Meetings** We meet every 6 weeks (alternating USA and AU time zones) for 1 hour. Our meeting agenda is: - Random intro chatter & introductions @@ -44,13 +44,13 @@ Our meeting agenda is: - Other cool stuff (example: Smorgasbord) - Ongoing actions to send out -We send out emails to the mailing list after each meeting, at the mid-way point between meetings, and the day before meetings as a reminder. +**Emails** We send out emails to the mailing list after each meeting, at the mid-way point between meetings, and the day before meetings as a reminder. -We keep rolling notes on a googledoc and monitor our work on Trello. +**Notes** We keep rolling notes on a googledoc and monitor our work on Trello. -When people ask for help or are working across institutes, we set up chat sub-channels to bring them together. +**Collaborative Chat Forums** When people ask for help or are working across institutes, we set up chat sub-channels to bring them together. -We have a chat forum to discuss news and ideas, and are represented in the Galaxy Community Reps chat group. +**General Chat Forum** We have a chat forum to discuss news and ideas, and are represented in the Galaxy Community Reps chat group. From ab18ce2fad605500129a71c1bbd7352990160eba Mon Sep 17 00:00:00 2001 From: Wendi Bacon <44605769+nomadscientist@users.noreply.github.com> Date: Thu, 5 Oct 2023 09:19:33 +0200 Subject: [PATCH 4/8] triggering tests again Link said it failed but GTN hadn't updated so hopefully now fine? --- content/projects/singlecell/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/content/projects/singlecell/index.md b/content/projects/singlecell/index.md index 508aad1cbc..e73d26539c 100644 --- a/content/projects/singlecell/index.md +++ b/content/projects/singlecell/index.md @@ -8,7 +8,7 @@ We are a mix of users, developers, and trainers providing feedback and energy to **Welcome to the Galaxy Single-Cell Community of Practice!** -## I'm just trying to learn to analyse my data, how did I get here? +## I'm just trying to learn to analyse my data, how did I get here? Hello user! You'll be interested in the following resources: - [Learning pathway for getting to grips with Galaxy and single cell](https://training.galaxyproject.org/training-material/learning-pathways/intro_single_cell.html) From dae12f9353f02c64e639b914468bd75b7c2a5008 Mon Sep 17 00:00:00 2001 From: Wendi Bacon <44605769+nomadscientist@users.noreply.github.com> Date: Thu, 5 Oct 2023 15:52:17 +0200 Subject: [PATCH 5/8] Update content/projects/singlecell/index.md Co-authored-by: Pavankumar Videm --- content/projects/singlecell/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/content/projects/singlecell/index.md b/content/projects/singlecell/index.md index e73d26539c..c1fc10440a 100644 --- a/content/projects/singlecell/index.md +++ b/content/projects/singlecell/index.md @@ -8,7 +8,7 @@ We are a mix of users, developers, and trainers providing feedback and energy to **Welcome to the Galaxy Single-Cell Community of Practice!** -## I'm just trying to learn to analyse my data, how did I get here? +# I'm just trying to learn to analyse my data, how did I get here? Hello user! You'll be interested in the following resources: - [Learning pathway for getting to grips with Galaxy and single cell](https://training.galaxyproject.org/training-material/learning-pathways/intro_single_cell.html) From 8231085a8c82e375bf9ac9b72cf3522dfa81b86c Mon Sep 17 00:00:00 2001 From: Wendi Bacon <44605769+nomadscientist@users.noreply.github.com> Date: Thu, 5 Oct 2023 17:06:56 +0200 Subject: [PATCH 6/8] add more common terms --- content/projects/singlecell/index.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/content/projects/singlecell/index.md b/content/projects/singlecell/index.md index c1fc10440a..4c97b0c85d 100644 --- a/content/projects/singlecell/index.md +++ b/content/projects/singlecell/index.md @@ -8,7 +8,7 @@ We are a mix of users, developers, and trainers providing feedback and energy to **Welcome to the Galaxy Single-Cell Community of Practice!** -# I'm just trying to learn to analyse my data, how did I get here? +## I'm just trying to learn to analyse my data, how did I get here? Hello user! You'll be interested in the following resources: - [Learning pathway for getting to grips with Galaxy and single cell](https://training.galaxyproject.org/training-material/learning-pathways/intro_single_cell.html) @@ -75,3 +75,6 @@ snRNA-seq 10x Single cell biology Single cell multiomics +ScanPy +Seurat +AnnData From 7d3164e2e1a5c34c75ed5e9f8f7b3742357ba7dc Mon Sep 17 00:00:00 2001 From: Dannon Date: Thu, 5 Oct 2023 11:17:20 -0400 Subject: [PATCH 7/8] Update content/community/practice/index.md --- content/community/practice/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/content/community/practice/index.md b/content/community/practice/index.md index 48d27c6768..b6b9154e49 100644 --- a/content/community/practice/index.md +++ b/content/community/practice/index.md @@ -17,7 +17,7 @@ title: Communities of Practice | Small Scale Servers | Admins of small scale Galaxy servers. |[](https://lists.galaxyproject.org/lists/small-scale-admins.lists.galaxyproject.org/)| | [Machine Learning](https://ml.usegalaxy.eu/) | A comprehensive set of data preprocessing, machine learning, deep learning and visualisation tools, and consolidated workflows for end-to-end machine learning analysis. | [](https://training.galaxyproject.org/training-material/topics/statistics/) [](https://ml.usegalaxy.eu/) | | [Materials Science](https://materials.usegalaxy.eu/) | A Galaxy workbench with tools and workflows for materials science, including muon spectroscopy. | [](https://materials.usegalaxy.eu/) | -| [Single cell](content/projects/singlecell/index.md) | Group of single cell tool developers, trainers and users to help connect outreach, user needs, and computationalists. | [](https://matrix.to/#/#usegalaxy-eu_single-cell-workflows:gitter.im) [](https://training.galaxyproject.org/training-material/topics/single-cell/) [](https://lists.galaxyproject.org/lists/single-cell-cop.lists.galaxyproject.org/) | +| [Single cell](/projects/singlecell/) | Group of single cell tool developers, trainers and users to help connect outreach, user needs, and computationalists. | [](https://matrix.to/#/#usegalaxy-eu_single-cell-workflows:gitter.im) [](https://training.galaxyproject.org/training-material/topics/single-cell/) [](https://lists.galaxyproject.org/lists/single-cell-cop.lists.galaxyproject.org/) | # Set up your own community From 00c09ec2406236eeb6b85954f6991d0bec17810b Mon Sep 17 00:00:00 2001 From: Wendi Bacon <44605769+nomadscientist@users.noreply.github.com> Date: Thu, 5 Oct 2023 17:24:54 +0200 Subject: [PATCH 8/8] add benchmarking workflows --- content/projects/singlecell/index.md | 1 + 1 file changed, 1 insertion(+) diff --git a/content/projects/singlecell/index.md b/content/projects/singlecell/index.md index 4c97b0c85d..34e938a370 100644 --- a/content/projects/singlecell/index.md +++ b/content/projects/singlecell/index.md @@ -27,6 +27,7 @@ Saying that, we'd absolutely love to have users feedback on their experiences to - Tool & tutorial development - Testing - Build & support user community +- Benchmarking tools and workflows # Who are we looking for?