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This page is [[SIGs/Medical|Fedora Medical SIG]]'s COVID-19 page.
 
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.
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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 ==
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== Analysis ==
  
We list up the COVID-19 focusing projects. This is a a top-down approach to find the areas.
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=== 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]
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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://www.codevscovid19.org/ CodeVsCovid19]
  
* [https://covid19.galaxyproject.org/ COVID-19 analysis on using galaxy]: [https://github.com/galaxyproject/SARS-CoV-2 GitHub]
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== Projects used in COVID-19 ==
* [https://github.com/CDCgov/SARS-CoV-2_Sequencing SARS-CoV-2 Sequencing Resources]
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* [https://cbg-ethz.github.io/V-pipe/sars-cov-2/ V-pipe SARS-CoV-2]
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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]
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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]
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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 ==
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* [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]
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* Whole-genome sequencing analysis: [https://nf-co.re/sarek nf-core/sarek]
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* 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://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]
 
* [https://bio.tools/t?domain=covid-19 Elixir bio.tools COVID-19 Coronavirus tools list]
  
* nf-core
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== Distributed Computing ==
** [https://nf-co.re/nanoseq nf-core/nanoseq]
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** [https://nf-co.re/artic nf-core/artic] (in development)
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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)
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** single-cell analysis
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* [https://foldingathome.org/ FOLDING@HOME]
*** [https://nf-co.re/scrnaseq nf-core/scrnaseq]
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* [https://boinc.bakerlab.org/rosetta/ Rosetta@home]
*** [https://nf-co.re/smartseq2 nf-core/smartseq2]
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* [https://setiathome.berkeley.edu/ SETI@home]
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 +
== Open Hardware ==
  
== Hardware projects ==
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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
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* Ventilator
* https://opensourceventilator.ie/
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* Llabware, consumables, reagents
* https://github.com/jcl5m1/ventilator
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* Polymerase chain reaction (PCR) device

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.

Following pipelines could be certainly relevant.

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