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OmniBrowser #913

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kunpengliao1 opened this issue Apr 9, 2021 · 28 comments
Closed

OmniBrowser #913

kunpengliao1 opened this issue Apr 9, 2021 · 28 comments
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@kunpengliao1
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kunpengliao1 commented Apr 9, 2021 •
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Thank you for submitting a portal to the HCA DCP Methods Registry!

To expedite your portal's addition to https://data.humancellatlas.org/analyze,
please provide the following package metadata. You can easily edit this information later by clicking "Improve this page" at the bottom of your portal's detail page (example).

Required:

  • Tool title: OmniBrowser
  • Contact name: Analytical BioSciences
  • Contact email: [email protected]
  • Who to attribute: Analytical BioSciences Team
  • Portal URL: https://omnibrowser.abiosciences.com/
  • Short description:OmniBrowser is a comprehensive curated single cell data compendium with visualization and analysis capabilities that further empower and innovate drug discovery and development.

Optional:

  • Long description:OmniBrowser is a web portal for scRNA-seq data exploration, supported by a spectrum of commonly used tools for data visualization and analysis. The OmniBrowserTM toolset is designed with a special attention to support biologists with limited programming and analytical bandwidth or depth. The underlying database of OmniBrowser is currently the largest curated scRNA-seq dataset collection in the world, with >1850 datasets from >840 publications in publication consistency. To query such datasets, OmniBrowser provides a series of web-based tools, including gene expression query, dimensional reduction visualization, differential analysis & across-dataset comparison, similar gene search, association analysis with sample metadata, GO analysis.

Datasets are constantly updated on OmniBrowser in order to support the constantly growing demands from a board range of customers. As datasets and analytical functions continue to expand on the OmniBrowser platform, Analytical Biosciences will develop and distribute more collection of tools that will make the analyses of big data more efficient and effective in order to advance the biomedical R&D.

  • Logo or screenshot:

OmniBrowser
@github-actions github-actions bot added the canary Done by the Clever Canary label Apr 9, 2021
@NoopDog
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NoopDog commented Apr 15, 2021

Hi @kunpengliao1
Thank you for summiting the portal. We are reviewing and will be back to you shortly with any questions.

Cheers,
Dave Rogers

@NoopDog NoopDog self-assigned this Apr 20, 2021
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NoopDog commented Apr 20, 2021

Hi @kunpengliao1, is this an open-source project? This is required to be included in the listing.

Can you provide a link to the source code repository and indicate the license type?

Thank You,
Dave Rogers

@kunpengliao1
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kunpengliao1 commented Apr 20, 2021 via email

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NoopDog commented Apr 20, 2021

Hi @kunpengliao1 I have reached out internally to get clarification on the standards for acceptance regarding the portals. I will let you know when I hear back. Thanks again for your application and your patience. Cheers, D

frano-m pushed a commit that referenced this issue Apr 23, 2021
FASTGenomics. OmniBrowser. First pass. #540. #913.
085592b
frano-m pushed a commit that referenced this issue Apr 23, 2021
FASTGenomics. OmniBrowser. First pass. #540. #913.
074552c
NoopDog pushed a commit that referenced this issue Apr 23, 2021
@NoopDog
FASTGenomics. OmniBrowser. First pass. #540. #913.
3d21e20
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NoopDog commented Apr 23, 2021

Hi, @kunpengliao1 I am happy to report that OmniBrowser has been approved for posting on the analysis portals section of the site. Your listing is on our staging server here:

https://dev.singlecell.gi.ucsc.edu/analyze/methods/omnibrowser

Can you take a look and let us know if you feel any changes are required before going live?

Cheers and Thanks,
Dave Rogers

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kunpengliao1 commented Apr 23, 2021 via email

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NoopDog commented Apr 23, 2021

HI Kunpeng Liao,

I think GitHub issues is modifying the image. Can you make a PR against the data portal repo staging branch to upload your image here:

https://github.com/HumanCellAtlas/data-portal/tree/staging/content/analyze/_images/portals

This will get us the original image which will be downsampled to optimize download times but should result in an adequate resolution.

Cheers,
Dave

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kunpengliao1 commented Apr 23, 2021 via email

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NoopDog commented Apr 23, 2021

Hi Kunpeng Liao,

Would you be able to make a PR for this change? At the bottom of the page, you should see an "improve this page" link selecting it will take you to the file in GitHub in the staging branch. Can you PR your updates against staging?

Thanks!
Dave

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kunpengliao1 commented Apr 23, 2021 via email

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NoopDog commented Apr 23, 2021

Hi Hi Kunpeng Liao,

The "Improve this Page" link is at the bottom of this page:
https://dev.singlecell.gi.ucsc.edu/analyze/methods/omnibrowser

@kunpengliao1
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kunpengliao1 commented Apr 23, 2021 via email

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NoopDog commented Apr 23, 2021

Yes, please. This edits the actual markdown source of the file.

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kunpengliao1 commented Apr 23, 2021 via email

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NoopDog commented Apr 23, 2021

Hi, @kunpengliao1 we have updated the text as you requested and pushed the portal live.
https://data.humancellatlas.org/analyze/methods/omnibrowser

Please feel free to make a PR to update the listing by using the "Improve this Page" link at the bottom of your page.

Cheers, and thank you for submitting your portal to the registry,
D

@NoopDog NoopDog closed this as completed Apr 23, 2021
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kunpengliao1 commented Apr 25, 2021 via email

@lelewang111
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Hello David, glad to communicate with you, regarding our omnibrowser, we will update the information in the near future. I would like to confirm with you in advance where to update the information and upload pictures. What is the specific process? Thank you very much for your guidance and look forward to your reply!

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NoopDog commented Jun 2, 2022

Hi @lelewang111 yes, please use the "Improve this page" link at the bottom of the page to create a pull request with the desired updates.

https://data.humancellatlas.org/analyze/methods/omnibrowser

This will take you to the markdown page for omnibrowser here:
https://github.com/DataBiosphere/data-portal/blob/main/content/analyze/portals/analysis-portals/omnibrowser.md

Let me know if you have any questions.

Cheers,
D

@lelewang111
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Hello David, I have change it by edit. Please help to check whether I have done the right way. And could you please let me know when the information can be updated? Thank you so much!

@lelewang111
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Hello David, I have change it by edit. Please help to check whether I have done the right way. And could you please let me know when the information can be updated? Waiting for your kind reply! Thank you so much!

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NoopDog commented Jun 10, 2022

Hi @lelewang111 I am not seeing your pull request. Did you make a pull request against this repository? Thanks, D

@lelewang111
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I have click the Propose changes, What should I do after this step?

@lelewang111
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Hi David, I have make a pull request on last Friday, did you see that? Please let me know when it will be updated? Thanks !

@lelewang111
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Hi David，Sorry to bother you , I have check zhe omnibrowser:https://data.humancellatlas.org/analyze/methods/omnibrowser
It has not yet update, I want to know when this page will be updated? Thank you so much!

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NoopDog commented Jun 17, 2022 •
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Hi, @lelewang111 this is on prod now at https://data.humancellatlas.org/analyze/portals/omnibrowser
Looks like this was accidentally in the methods section before and it has now been properly moved to be with the other portals. Please make note of the updated link.

Cheers,
D

@lelewang111
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Hi David, about the previous omnibrowser link information(https://data.humancellatlas.org/analyze/methods/omnibrowser),whether it will be deleted, and just keep up-to-date information(https://dev.singlecell.gi.ucsc.edu/analyze/portals/omnibrowser), because we can see two link now, both have our omnibrowser information , and I want keep the lastest one. Thanks!

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NoopDog commented Jun 17, 2022

Hi @lelewang111

My mistake. I gave you the wrong link above the correct live link is:

New Live LInk - Please share this URL

https://data.humancellatlas.org/analyze/portals/omnibrowser

Testing LInk - for testing only - do not share

https://dev.singlecell.gi.ucsc.edu/analyze/portals/omnibrowser

The old link https://data.humancellatlas.org/analyze/methods/omnibrowser now displays a page not found.

Sorry for the confusion. Let me know if you have any additional questions.
Cheers,
D

@lelewang111
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Hi David, reveived with thanks!
Thank you so much for your help!

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