Pangenome Browser for Everyone's Aggregated Data

[Josiah Seaman]

Hello all,

It looks like there are some solid groups forming up around aggregating data, especially sequence.  I'd like to invite javascript developers to contribute to the Pantograph Pangenome Browser at graphgenome.org.  We'll be taking the sequences from other groups here, and compiling them into a Graph Genome that allows us to see all mutations and virus strains simultaneously.  This browser is a new design paradigm that will allow us to scale to thousands of individuals while still showing the full sequence.  This should allow us to track strains of the virus and ensure they cannot evade the vaccine or tests.  The same tool is also useful for haplotyping Human sequences for treatment recommendations from similar patients.

We need:

* Project Managers to coordinate volunteers

* Javascript

* React, Mobx-state-tree

* RDF for Graph Representation

* Linux, Docker, Devops for Graph Creation

* Python and C++ for updating existing tools in our pipeline

* R extending HaploBlocker to work with Viral genomes

Please sign up on the wiki and send me a private email at jos...@newline.us if you'd like to get involved.  I'll be doing this full-time until the surge is over (or I get really sick) so you can get started whenever you have availability.  https://github.com/virtual-biohackathons/covid-19-bh20/wiki/Pangenome-Browser

All the best,

Josiah Seaman

Bioinformatician and Data Visualization

Max Planck Institute, Kew Royal Botanic Gardens

[Josiah Seaman]

We've had two volunteers join the project so far in private replies.  I've started a Slack channel called Pangenome_Browser. To join the conversation please Join Virtual Biohackathon Slack: https://join.slack.com/t/virtualbiohac-xt62674/shared_invite/zt-cuur40oj-wdrVz50NocwVrH7vgKTdPg

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