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nextstrain / auspice

Web app for visualizing pathogen evolution
https://docs.nextstrain.org/projects/auspice/
GNU Affero General Public License v3.0
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Time series analysis of auspice data #1133

Open gurkhali opened 4 years ago

gurkhali commented 4 years ago

Context
Declarative queries that can be performed for specific event time range.

Description
Folks I have been working a side project to extend the capabilities of auspice and provide a researchers like yourself an extensible way to do declarative analysis for specific periods of time.

More details on the work can be found here

I have built a few dashboards that may be helpful in discussions such as ...

@trvrb discussion about spread in Louisiana

I have a mutation chart that maybe helpful on this

This should also help in @grubaughlab analysis

Please keep in mind that this is nights and weekend project and this is still a significant WIP and will likely have issues ranging from code bugs to my best effort at analysis. That said, I feel that I have implemented enough functionality to open it to you guys.

If you are interested I am happy to provide access to the running instance that you can use interactively.

I am inspired by your work and thanks @trvrb @jameshadfield @emmahodcroft @eharkins @huddlej for your dedication and effort

jameshadfield commented 4 years ago

This looks cool and we're always excited to see different techniques being used to interrogate the data! Having not used influxdb before, if you were to write a (short) tutorial for the repo then I'd be keen to try it out.

gurkhali commented 4 years ago

Here is a short video of the capability of the tool that I built. I would love to understand if this would be helpful to you guys. Let me know if you have any questions.