Medical/COVID-19

This page is Fedora Medical SIG's COVID-19 page.

As the COVID-19 is of many people's interest, the page is created for people who want to contribute or do RPM packaging.

Analysis

Focusing projects

We list up the COVID-19 analysis focusing projects. This is a a top-down approach to find the areas.

• COVID19 Virtual Biohackathon 2020: Wiki Home Learning, Kick-off meeting video, Wrap-up meeting video.
• CodeVsCovid19

Projects used in COVID-19

We list up the projects used in the COVID-19. This is a bottom-up approach to find the areas.

nf-core

nf-core is a collection of analysis pipelines built using Nextflow. We refer it to see the actual analysis workflow to identify the used bio tools projects. Podman is supported as one of the container workflows according to this page.

Talking people in the project, the following nf-core/nanoseq, nf-core/artic and nf-core/viralrecon are the COVID-19 analyis pipelines.

• nf-core/nanoseq
• nf-core/artic (in development)
• nf-core/viralrecon (in development)

Following pipelines could be certainly relevant.

• Single-cell analysis: nf-core/scrnaseq, nf-core/smartseq2
• Whole-genome sequencing analysis: nf-core/sarek
• Meta-genomics analysis: nf-core/mag
• Investigations into the immune response: nf-core/bcellmagic

As almost any molecular biology technique can be used to look into some aspect of COVID-19, virtually all the nf-core pipeline can be relevant.

Packages list

• Debian Med COVID-19 packages
• Elixir bio.tools COVID-19 Coronavirus tools list

Distributed Computing

The distributed computing projects are to enable people to help COVID-19 analysis by their computer resources.

• FOLDING@HOME
• Rosetta@home
• SETI@home

Open Hardware

According to this article, there are open source hardware projects related to

• Ventilator
• Llabware, consumables, reagents
• Polymerase chain reaction (PCR) device