cdcgov / hantanet

Standalone Hantavirus visualization engine, powered by MicrobeTrace

HantaNet

The Visualization Multitool for Molecular Epidemiology and Bioinformatics - with focus on the Hanta Virus

Developed By (some folks at) CDC

Access Request, Repo Creation Request

• CDC GitHub Open Project Request Form [Requires a CDC Office365 login, if you do not have a CDC Office365 please ask a friend who does to submit the request on your behalf. If you're looking for access to the CDCEnt private organization, please use the GitHub Enterprise Cloud Access Request form.]

Related documents

• Open Practices
• Rules of Behavior
• Thanks and Acknowledgements
• Disclaimer
• Contribution Notice
• Code of Conduct

Overview

Describe the purpose of your project. Add additional sections as necessary to help collaborators and potential collaborators understand and use your project.

Public Domain

This project constitutes a work of the United States Government and is not subject to domestic copyright protection under 17 USC § 105. This project is in the public domain within the United States, and copyright and related rights in the work worldwide are waived through the CC0 1.0 Universal public domain dedication. All contributions to this project will be released under the CC0 dedication. By submitting a pull request you are agreeing to comply with this waiver of copyright interest.

License

The project utilizes code licensed under the terms of the Apache Software License and therefore is licensed under ASL v2 or later.

This program is free software: you can redistribute it and/or modify it under the terms of the Apache Software License version 2, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache Software License for more details.

You should have received a copy of the Apache Software License along with this program. If not, see http://www.apache.org/licenses/LICENSE-2.0.html

Privacy

This project contains only non-sensitive, publicly available data and information. All material and community participation is covered by the Surveillance Platform Disclaimer and Code of Conduct. For more information about CDC's privacy policy, please visit http://www.cdc.gov/privacy.html.

Contributing

Anyone is encouraged to contribute to the project by forking and submitting a pull request. (If you are new to GitHub, you might start with a basic tutorial.) By contributing to this project, you grant a world-wide, royalty-free, perpetual, irrevocable, non-exclusive, transferable license to all users under the terms of the Apache Software License v2 or later.

Before you get started, please read the Developer's Guide to MicrobeTrace.

All comments, messages, pull requests, and other submissions received through CDC including this GitHub page are subject to the Presidential Records Act and may be archived. Learn more at http://www.cdc.gov/other/privacy.html.

Records

This project is not a source of government records, but is a copy to increase collaboration and collaborative potential. All government records will be published through the CDC web site.

Notices

Please refer to CDC's Template Repository for more information about contributing to this repository, public domain notices and disclaimers, and code of conduct.

Adding custom symbols (png, jpg, and svg) to be used in the github web application - Collaborators only

1. Switch to the dev branch of this repo.
2. In the project, navigate to the img/custom-symbols folder.
3. Click "Add file" -> click "Upload files".
4. Add/Drag n Drop the desired img files and commit changes.
5. Within the same folder, click on the symbols.json to open it.
6. Click the edit (pencil) icon.
7. Add the new file names to the list in the same format as the current ones (i.e "custom-icon.png").
8. ENSURE to add commas after file names that are not the last one in the list. The last one should not have a comma.
9. Commit changes and give about 10-15 minutes for the webapp to build and check to see if the new symbols are available.

Adding custom symbols (png, jpg, and svg) to be used in the github web application - External Request

Email desired symbol files to Roxy Cintron ([email protected]) with request

hantanet's Issues

Update Map View

Restore MicrobeTrace basic functionality

Most MicrobeTrace features were removed in HantaNet but the client has requested to restore them.

The following new features are also of particular interest:

1. The client likes the fixed (default) filtering threshold applied to each gene module but would like to have the option of selecting the TN93 threshold since this will be useful to know which strain is closest to an unknown sequence if there's no match in the reference dataset

2. Add option to download each module's reference alignment

3. Add alignment viewer and editor to each gene module

4. Add user-provided alignment to the gene module and generate a cluster; in this case, the client would like to align their sequences against the gene module's reference alignment

5. Add map feature to visualize the geographic distribution of clusters/strains

tooltip bug

Hover over filtering threshold and see values in bars

Integrate Aggregation component with app

Filtering threshold

The client likes the fixed (default) filtering threshold applied to each gene module but would like to also have the option of selecting the TN93 threshold. This feature will be useful to match an unknown sequence to the closest strain if there's not an exact match in the reference dataset.

Shape icons change when adding new data

Add Polygon Controls, Labels and Colors

Add file download function

Users should be able to download the reference csv and fasta files if desired.

For example, the client would like to align new sequences against the reference fasta file to input the new alignment or distance matrix into HantaNet to classify the new sequences.

Go to File --> Add Data
The gene module csv and fasta files are listed but the download button isn't working in the three gene modules.

As a user, I want to drag the network in the 3D view

Create-IT translation of MT site

Need Evan on meeting with vendor

Update Starting Position in Map View

Establish Production & Dev Environments

Add process and instructions for adding custom icons to the application

Custom Shapes for Timeline

Ensure custom shapes remain the same in timeline.

Currently shapes flip back to original.

Integrate Aggregation component with app

Separate heatmap, phylo trees and sequences into a box in the view drop down since they are all sequence-related views

Bidirectionality

Colors change during timeline play

Integrate Bubbles component with app

Symbols may change during timeline play

Reveal Everything does not show all links + Should Reveal Link/Node Color Tables

I changed some thresholds on Global settings. I then hit the "Reveal Everything" button. 2 of the links (These were genetic links), disappeared). The epi ones remained

Separate heatmap, phylo trees and sequences into a box in the view drop down since they are all sequence-related views

Update Vulnerabilities from Dependabot

Fix Symbol Table Drag/Drop Functionality

Moving Cluster totals legend box

Update reference sequence repo

Moving cluster totals legend box

Create-IT manual collaboration