Details
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Type:
Epic
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Epic Name:Connect Integrated Genome Browser and CyVerse
Description
Starting January 2019, we began creating Web site middleware to let Integrated Genome Browser users visualize data using CyVerse resources. By connecting the rich client IGB with cloud resources managed by the CyVerse project, we can give IGB users more power to execute compute-intensive visual analytics algorithms "in the cloud" and then visualize the results within IGB.
Our first idea was to build the CyVerse access component into IGB itself as an IGB App. However, after looking into the challenges, we realized that a far better approach would be to create an intermediary, a Web site, that would manage interactions with the CyVerse resources on behalf of the user.
Key features of the site:
- It will manage user logins using OAuth, ensuring that our site gains no knowledge of a user's password. Our site will learn their user name, but that is all. All user account management will occur using CyVerse resources only.
- The site will be lightweight, requiring minimal resources, and will be easy to deploy.
- The site will enable users to launch compute-intensive visual analytics functions, including: creating scaled coverage graphs to enable visual inspection of differential gene expression across samples and sample types, a function that is currently very difficult and inconvenient for user's to execute on their own, using their personal computer
- The site will enable users to store data in the cloud, in their CyVerse accounts, but still be able to visualize the data within IGB, running on the user's personal computer
- The site will enable users to annotate data, adding information about the genome version (if relevant) and information about how the data should appear when loaded into IGB. These attributes will enable other users looking at the same data to see what the data's owners also see.
This work is funded by an R01 grant to Ann Loraine: Linking Integrated Genome Browser and CyVerse
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| Workflow | Loraine Lab Workflow [ 18198 ] | Fall 2019 Workflow Update [ 18930 ] |
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| Summary | Open CyVerse files in IGB via BioViz bridge | Open CyVerse files in IGB |
| Epic Name | Open CyVerse files in IGB via BioViz bridge | Open CyVerse files in IGB |
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| Workflow | Fall 2019 Workflow Update [ 18930 ] | Revised Fall 2019 Workflow Update [ 21056 ] |
| Status | Open [ 1 ] | In Progress [ 3 ] |
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| Assignee | Ann Loraine [ aloraine ] |
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| Epic Status | To Do [ 10001 ] | Done [ 10003 ] |
| Summary | Open CyVerse files in IGB | Connect CyVerse to IGB |
| Summary | Connect CyVerse to IGB | Connect Integrated Genome Browser and CyVerse |
| Epic Name | Open CyVerse files in IGB | Connect Integrated Genome Browser and CyVerse |
| Description |
Starting January 2019, we began creating Web site middleware to let Integrated Genome Browser users visualize data using CyVerse resources. By connecting the rich client IGB with cloud resources managed by the CyVerse project, we can give IGB users more power to execute compute-intensive visual analytics algorithms "in the cloud" and then visualize the results within IGB.
Our first idea was to build the CyVerse access component into IGB itself as an IGB App. However, after looking into the challenges, we realized that a far better approach would be to create an intermediary, a Web site, that would manage interactions with the CyVerse resources on behalf of the user. *Key features of the site*: * It will manage user logins using OAuth, ensuring that our site gains no knowledge of a user's password. Our site will learn their user name, but that is all. All user account management will occur using CyVerse resources only. * The site will be lightweight, requiring minimal resources, and will be easy to deploy. * The site will enable users to launch compute-intensive visual analytics functions, including: creating scaled coverage graphs to enable visual inspection of differential gene expression across samples and sample types, a function that is currently very difficult and inconvenient for user's to execute on their own, using their personal computer * The site will enable users to store data in the cloud, in their CyVerse accounts, but still be able to visualize the data within IGB, running on the user's personal computer * The site will enable users to annotate data, adding information about the genome version (if relevant) and information about how the data should appear when loaded into IGB. These attributes will enable other users looking at the same data to see what the data's owners also see. |
| Description |
Starting January 2019, we began creating Web site middleware to let Integrated Genome Browser users visualize data using CyVerse resources. By connecting the rich client IGB with cloud resources managed by the CyVerse project, we can give IGB users more power to execute compute-intensive visual analytics algorithms "in the cloud" and then visualize the results within IGB.
Our first idea was to build the CyVerse access component into IGB itself as an IGB App. However, after looking into the challenges, we realized that a far better approach would be to create an intermediary, a Web site, that would manage interactions with the CyVerse resources on behalf of the user. *Key features of the site*: * It will manage user logins using OAuth, ensuring that our site gains no knowledge of a user's password. Our site will learn their user name, but that is all. All user account management will occur using CyVerse resources only. * The site will be lightweight, requiring minimal resources, and will be easy to deploy. * The site will enable users to launch compute-intensive visual analytics functions, including: creating scaled coverage graphs to enable visual inspection of differential gene expression across samples and sample types, a function that is currently very difficult and inconvenient for user's to execute on their own, using their personal computer * The site will enable users to store data in the cloud, in their CyVerse accounts, but still be able to visualize the data within IGB, running on the user's personal computer * The site will enable users to annotate data, adding information about the genome version (if relevant) and information about how the data should appear when loaded into IGB. These attributes will enable other users looking at the same data to see what the data's owners also see. |
Starting January 2019, we began creating Web site middleware to let Integrated Genome Browser users visualize data using CyVerse resources. By connecting the rich client IGB with cloud resources managed by the CyVerse project, we can give IGB users more power to execute compute-intensive visual analytics algorithms "in the cloud" and then visualize the results within IGB.
Our first idea was to build the CyVerse access component into IGB itself as an IGB App. However, after looking into the challenges, we realized that a far better approach would be to create an intermediary, a Web site, that would manage interactions with the CyVerse resources on behalf of the user. *Key features of the site*: * It will manage user logins using OAuth, ensuring that our site gains no knowledge of a user's password. Our site will learn their user name, but that is all. All user account management will occur using CyVerse resources only. * The site will be lightweight, requiring minimal resources, and will be easy to deploy. * The site will enable users to launch compute-intensive visual analytics functions, including: creating scaled coverage graphs to enable visual inspection of differential gene expression across samples and sample types, a function that is currently very difficult and inconvenient for user's to execute on their own, using their personal computer * The site will enable users to store data in the cloud, in their CyVerse accounts, but still be able to visualize the data within IGB, running on the user's personal computer * The site will enable users to annotate data, adding information about the genome version (if relevant) and information about how the data should appear when loaded into IGB. These attributes will enable other users looking at the same data to see what the data's owners also see. This work is funded by an R01 grant to Ann Loraine: [Linking Integrated Genome Browser and CyVerse |https://reporter.nih.gov/project-details/9750774] |
| Description |
Starting January 2019, we began creating Web site middleware to let Integrated Genome Browser users visualize data using CyVerse resources. By connecting the rich client IGB with cloud resources managed by the CyVerse project, we can give IGB users more power to execute compute-intensive visual analytics algorithms "in the cloud" and then visualize the results within IGB.
Our first idea was to build the CyVerse access component into IGB itself as an IGB App. However, after looking into the challenges, we realized that a far better approach would be to create an intermediary, a Web site, that would manage interactions with the CyVerse resources on behalf of the user. *Key features of the site*: * It will manage user logins using OAuth, ensuring that our site gains no knowledge of a user's password. Our site will learn their user name, but that is all. All user account management will occur using CyVerse resources only. * The site will be lightweight, requiring minimal resources, and will be easy to deploy. * The site will enable users to launch compute-intensive visual analytics functions, including: creating scaled coverage graphs to enable visual inspection of differential gene expression across samples and sample types, a function that is currently very difficult and inconvenient for user's to execute on their own, using their personal computer * The site will enable users to store data in the cloud, in their CyVerse accounts, but still be able to visualize the data within IGB, running on the user's personal computer * The site will enable users to annotate data, adding information about the genome version (if relevant) and information about how the data should appear when loaded into IGB. These attributes will enable other users looking at the same data to see what the data's owners also see. This work is funded by an R01 grant to Ann Loraine: [Linking Integrated Genome Browser and CyVerse |https://reporter.nih.gov/project-details/9750774] |
Starting January 2019, we began creating Web site middleware to let Integrated Genome Browser users visualize data using CyVerse resources. By connecting the rich client IGB with cloud resources managed by the CyVerse project, we can give IGB users more power to execute compute-intensive visual analytics algorithms "in the cloud" and then visualize the results within IGB.
Our first idea was to build the CyVerse access component into IGB itself as an IGB App. However, after looking into the challenges, we realized that a far better approach would be to create an intermediary, a Web site, that would manage interactions with the CyVerse resources on behalf of the user. *Key features of the site*: * It will manage user logins using OAuth, ensuring that our site gains no knowledge of a user's password. Our site will learn their user name, but that is all. All user account management will occur using CyVerse resources only. * The site will be lightweight, requiring minimal resources, and will be easy to deploy. * The site will enable users to launch compute-intensive visual analytics functions, including: creating scaled coverage graphs to enable visual inspection of differential gene expression across samples and sample types, a function that is currently very difficult and inconvenient for user's to execute on their own, using their personal computer * The site will enable users to store data in the cloud, in their CyVerse accounts, but still be able to visualize the data within IGB, running on the user's personal computer * The site will enable users to annotate data, adding information about the genome version (if relevant) and information about how the data should appear when loaded into IGB. These attributes will enable other users looking at the same data to see what the data's owners also see. This work is funded by an R01 grant to Ann Loraine: [Linking Integrated Genome Browser and CyVerse|https://reporter.nih.gov/project-details/9750774] |
Article has been published. Closing ticket.
https://www.frontiersin.org/articles/10.3389/fbinf.2022.764619/full
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
We wrote an article describing the site, which we named BioViz Connect. Drafts of the article are available in BioRxiv, a preprint server.