Medical/COVID-19: Difference between revisions

Revision as of 13:48, 24 April 2020

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.

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 Nextflow pipelines. We refer it to see the actual analysis workflow to identify the used bio tools projects.

Talking people in the project, nf-core/nanoseq, nf-core/artic and nf-core/viralrecon are primarily important.

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
Metagenomics 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

Distributed Computing

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

Open Hardware

According to [https://opensource.com/article/20/3/open-hardware-covid19

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

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

@@ Line 1: / Line 1: @@
 This page is [[SIGs/Medical|Fedora Medical SIG]]'s COVID-19 page.
-The COVID-19 is of many people's interest. So, this page is created for people who want to contribute or do RPM packaging.
+As the COVID-19 is of many people's interest, the page is created for people who want to contribute or do RPM packaging.
-== COVID-19 focusing projects ==
+== Analysis ==
-We list up the COVID-19 focusing projects. This is a a top-down approach to find the areas.
+=== Focusing projects
-* [https://github.com/virtual-biohackathons/covid-19-bh20 COVID19 Virtual Biohackathon 2020]: [https://www.youtube.com/watch?v=x-QTP5Z_WIU Kick-off meeting video]
+We list up the COVID-19 analysis focusing projects. This is a a top-down approach to find the areas.
+* [https://github.com/virtual-biohackathons/covid-19-bh20 COVID19 Virtual Biohackathon 2020]: [https://github.com/virtual-biohackathons/covid-19-bh20/wiki Wiki] [https://github.com/virtual-biohackathons/covid-19-bh20/wiki Home Learning], [https://www.youtube.com/watch?v=x-QTP5Z_WIU Kick-off meeting video], [https://www.youtube.com/watch?v=g5cQk8jIMwo Wrap-up meeting video].
 * [https://www.codevscovid19.org/ CodeVsCovid19]
-* [https://covid19.galaxyproject.org/ COVID-19 analysis on using galaxy]: [https://github.com/galaxyproject/SARS-CoV-2 GitHub]
+== Projects used in COVID-19 ==
-* [https://github.com/CDCgov/SARS-CoV-2_Sequencing SARS-CoV-2 Sequencing Resources]
-* [https://cbg-ethz.github.io/V-pipe/sars-cov-2/ V-pipe SARS-CoV-2]
+We list up the projects used in the COVID-19. This is a bottom-up approach to find the areas.
+=== nf-core ===
-* [https://fevermap.net/ fevermap]: [https://gitlab.com/fevermap/fevermap Source]
+nf-core is a collection of Nextflow pipelines. We refer it to see the actual analysis workflow to identify the used bio tools projects.
-* [https://www.ibm.org/OpenPandemics OpenPandemics]
+Talking people in the project, nf-core/nanoseq, nf-core/artic and nf-core/viralrecon are primarily important.
-* [https://www.worldcommunitygrid.org/discover.action WorldCommunityGrid]
-== Software projects used in COVID-19 ==
+* [https://nf-co.re/nanoseq nf-core/nanoseq]
+* [https://nf-co.re/artic nf-core/artic] (in development)
+* [https://nf-co.re/viralrecon nf-core/viralrecon] (in development)
-We list up the projects used in the COVID-19. This is a bottom-up approach to find the areas.
+Following pipelines could be certainly relevant.
+* Single-cell analysis: [https://nf-co.re/scrnaseq nf-core/scrnaseq], [https://nf-co.re/smartseq2 nf-core/smartseq2]
+* Whole-genome sequencing analysis: [https://nf-co.re/sarek nf-core/sarek]
+* Metagenomics analysis: [https://nf-co.re/mag nf-core/mag]
+* Investigations into the immune response: [https://nf-co.re/bcellmagic 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 ===
 * [https://blends.debian.org/med/tasks/covid-19 Debian Med COVID-19 packages]
 * [https://bio.tools/t?domain=covid-19 Elixir bio.tools COVID-19 Coronavirus tools list]
-* nf-core
+== Distributed Computing ==
-** [https://nf-co.re/nanoseq nf-core/nanoseq]
-** [https://nf-co.re/artic nf-core/artic] (in development)
+The distributed computing projects are to enable people to help COVID-19 analysis by their computer resources.
-** [https://nf-co.re/viralrecon nf-core/viralrecon] (in development)
-** single-cell analysis
+* [https://foldingathome.org/ FOLDING@HOME]
-*** [https://nf-co.re/scrnaseq nf-core/scrnaseq]
+* [https://boinc.bakerlab.org/rosetta/ Rosetta@home]
-*** [https://nf-co.re/smartseq2 nf-core/smartseq2]
+* [https://setiathome.berkeley.edu/ SETI@home]
+== Open Hardware ==
-== Hardware projects ==
+According to [https://opensource.com/article/20/3/open-hardware-covid19
+ this article], there are open source hardware projects related to
-* https://opensource.com/article/20/3/open-hardware-covid19
+* Ventilator
-* https://opensourceventilator.ie/
+* Llabware, consumables, reagents
-* https://github.com/jcl5m1/ventilator
+* Polymerase chain reaction (PCR) device

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