One of the comments from the hackathon was to include version numbers of installed software packages that were tried and tested.

Since you have the "legends" for the data sources at the top, no need to repeat them in the entries of the published playbooks.

Several components, in particular those developed without access to the main UI could use a UI revamp.

It would be great if there was an optional way to add a short description or a title that describes the GMT file that you upload.

We can store the sets intersection regions

Either say that "No workflow was constructed yet" or disable the button.

https://playbook-partnership.dev.maayanlab.cloud/graph/e911fe95-bd9e-c578-6cc8-8982c0d92fab

https://playbook-partnership.maayanlab.cloud/graph/7006b674-1b23-8cd9-498c-595e1774ace0

The prompt is:

It is known that Clonidine and Propranolol cause a mysterious hypertension. Using the L1000 data, we want to find genes that are up- or down-regulated by these drugs and see if any of these drugs overlap with genes that are known to be associated with hypertension from GWAS Catalog, mouse phenotypes, and HPO.

• mean scored values are not resorted
• playbooks & community playbooks should be jointly searchable
• search functionality for published vs community behaves differently
• tsvector oddities
• case sensitivity in community catalog search
• missing description for use case 8
• email re-sign in not working (?)
• not detecting user browser preference for dark mode

This is necessary for Google OAuth to work for users besides test users

Timeouts were added to make sure slow processes don't keep the connection open, useSWR will actually retry periodically even if a timeout occurs. We should handle this soft-error so that the user doesn't leave the page thinking it's broken (in most cases a refresh will show the content).

https://playbook-partnership.dev.maayanlab.cloud/graph/f37a887d-e364-0c00-d38f-4d7b160960c1

https://playbook-partnership.maayanlab.cloud/graph/c75388fc-3301-3580-a68d-3dec91819ad5/node/fb3240e9-9e38-6256-14a9-8a666c8e9412

How do you compare two gene sets after you identify them?

@u8sand mentioned in the last meeting on 12/01/22 that he would provide an example JSON file for the workflow manifest for BCO conversion. Could you attach it here when it is ready?

What LICENSE are we meant to use?

This playbook for a diabetes use case is not working: https://playbook-partnership.dev.maayanlab.cloud/graph/49219e6e-e333-a156-f64b-3cfd761d8883

SyntaxError: Unexpected token < in JSON at position 0

Original: For a side effect and a drug, I would like to know if there are genes from the LINCS L1000 experiments that are up or down-regulated by the drugs that are also known to be involved with the side effect based on literature co-mentions or GWAS. I would like to know if such overlap is statistically significant. I would also like the results to be visualized using a SuperVenn diagram.

Suggestion: For a side effect and a drug, find differentially expressed genes from the LINCS L1000 resource that are up- or down-regulated by the drug, and are also associated with the side-effect based on literature co-mentions or GWAS. If overlapping genes are found, compute whether such overlap is statistically significant and visualize the results with a supervenn diagram.

https://playbook-workflow-builder.cloud/graph/1cd19811-6766-c46d-64c7-5928d71a4c86/node/33d371f7-467b-8007-0ad3-c61e4d38422b

• Though prompts hold up execution, the indicators don't make that obvious
• Graph mode has no real indicators

The BCO Contributors should include all authors which contributed to the nodes in the workflow that is built and the logged in user.

Sometimes executions fail, maybe an API was down or something, or maybe things changed. Deleting a "Resolved" entry is safe and will trigger a re-execution, this should certainly be doable in dev and maybe even prod.

We can put a link to the KLF4 use case there

The current registered API for Protein Products is no longer functioning:

curl -XGET https://api.glygen.org/directsearch/protein/?query=ACE2

Returns:

<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
<title>404 Not Found</title>
<h1>Not Found</h1>
<p>The requested URL was not found on the server. If you entered the URL manually please check your spelling and try again.</p>

https://playbook-partnership.dev.maayanlab.cloud/graph/0c59a3d5-052d-64ed-78fe-f05e40f8f3b0

Right now you can restart by clicking on the title, but a restart button might be useful. Also, a warning about restarted might be useful...

Replaces #87 for the one remaining feedback item