Update spatialomics page with Spatial2Galaxy project details - #1481
Update spatialomics page with Spatial2Galaxy project details#1481pavanvidem wants to merge 20 commits into
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Added SpatialData section with tools and references for handling spatial omics data.
Expanded the introduction to include collaboration details and contributions. Added sections for Spatial2Galaxy Partners and Supporters with relevant information. Added S2G logo.
Removed the 'Other tools' section from the document.
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| subdomain: spatialomics | |||
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| # Welcome to the Spatial OMICS Galaxy subdomain server | |||
| # Welcome to the Spatial OMICS Galaxy server | |||
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| # Welcome to the Spatial OMICS Galaxy server | |
| # Welcome to the Spatial Omics Galaxy Lab |
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I don't think we should call it a lab :) It is not created around a Galaxy community. Unlike labs, this page is only applies to EU server as Galaxy Europe is part of it. I also did not use any Galaxy Labs engine to make this page. It has been written manually.
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Then just "Spatial Omics Galaxy"? Or "Galaxy for Spatial Omics"?
Server is kind of an "unfriendly" name, I feel.
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or Spatial Omics Galaxy Portal?
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Let's decide this in the upcoming meeting
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
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| # Supporters | ||
| This Galaxy Lab is a joint project between different groups from the [Spatial2Galaxy ELIXIR Commissioned Service](https://elixir-europe.org/how-we-work/scientific-programme/science/cmr/spatial2){:target="_blank"} and the [Goecks Laboratory](https://www.goeckslab.org/). |
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| This Galaxy Lab is a joint project between different groups from the [Spatial2Galaxy ELIXIR Commissioned Service](https://elixir-europe.org/how-we-work/scientific-programme/science/cmr/spatial2){:target="_blank"} and the [Goecks Laboratory](https://www.goeckslab.org/). | |
| This is a joint project between different groups from the [Spatial2Galaxy ELIXIR Commissioned Service](https://elixir-europe.org/how-we-work/scientific-programme/science/cmr/spatial2){:target="_blank"} and the [Goecks Laboratory](https://www.goeckslab.org/). |
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| The SpatialOMICS Galaxy subdomain serves as a hub for all tools related to the analysis of highly-multiplexed image analysis. This server currently features the individual components of the [MCMICRO](https://mcmicro.org/) pipeline, including [BaSiC](https://github.com/ohsu-comp-bio/basic-illumination) for illumination correction, [ASHLAR](https://github.com/ohsu-comp-bio/ashlar) for stitching and registration, [Coreograph](https://github.com/ohsu-comp-bio/UNetCoreograph) to dearray tissue microarrays (TMAs), [UnMICST](https://github.com/ohsu-comp-bio/UnMicst) to create cell or nucleai probability maps, [S3segmenter](https://github.com/ohsu-comp-bio/S3segmenter) for nucleai and cell segmentation and [MCQuant](https://github.com/ohsu-comp-bio/quantification) for feature quantification. More tools for image analysis outside the MCMICRO ecosystem will be added in the future. | ||
| The Spatial Omics Galaxy Lab is a hub for all tools related to the analysis of highly multiplexed image-based spatial analysis. This is a collaborative effort by the Spatial2Galaxy project and the Goecks Laboratory members. We welcome any suggestions or requests for making tools related to Spatial Omics analysis available on this Galaxy instance. We also welcome contributions to the development of new tools, workflows or trainings! |
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Once we decide on a name, we need it to change it here as well.
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@itisAliRH please watch this PR. I guess we will merge this one at some point and then you migrate it to the hub? Or should we move this PR to the Hub already? |
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@bgruening I think we should move this to the Hub. The spatialomics bare page is already migrated in galaxyproject/galaxy-hub#3934, but this PR contains newer Spatial2Galaxy content that is not in the Hub yet. Merging it into the old website first would create another migration delta. Better path: port this PR’s content/assets into the Hub spatialomics page, resolve the naming there, then close this old-website PR with a pointer to the Hub PR. |
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I moved all the changes manually and created a new PR here galaxyproject/galaxy-hub#3984 |
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| - [Jeremy Goecks](https://github.com/jgoecks) | |||
| - [Cameron Watson](https://github.com/CameronFRWatson) | |||
| - [Allison Creason](https://github.com/alliecreason) | |||
| - [Amirhossein Nilchi](https://github.com/nilchia) | |||
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| - [Amirhossein Nilchi](https://github.com/nilchia) | |
| - [Amirhossein Naghsh Nilchi](https://github.com/nilchia) |
5 participants
Added new tools S2G partners etc