Medical/COVID-19: Difference between revisions

Latest revision as of 17:57, 17 May 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.

Bio tools used in COVID-19 analysis

We list up the bio tools projects used in the COVID-19 analysis. 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 the pipelines to look into the actual analysis workflows to identify the used bio tools projects.

Nextflow is the workflow software such as Workflow Description Language (WDL) and Common Workflow Language (CWL). The Podman container workflow is supported by Nextflow according to this page.

Pipeline	Description	Relevant level	Status
nf-core/nanoseq	Nanopore DNA/RNA sequencing analysis	Essential (High)	Stable
nf-core/artic	COVID-19 sequencing analysis. Reimplementation of the ARTIC field bioinformatics pipeline	Essential (High)	In development
nf-core/viralrecon	COVID-19 sequencing anaysis. Variant calling for viral samples.	Essential (High)	In development
nf-core/scrnaseq	Single-cell analysis	Certainly relevant (Middle)	Stable
nf-core/smartseq2	Single-cell analysis	Certainly relevant (Middle)	Stable
nf-core/sarek	Whole-genome sequencing analysis	Certainly relevant (Middle)	Stable
nf-core/mag	Meta-genomics analysis	Certainly relevant (Middle)	Stable
nf-core/bcellmagic	Investigations into the immune response	Certainly relevant (Middle)	Stable

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.

This information comes from the hearing in the nf-core community.

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 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 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]
+=== Bio tools used in COVID-19 analysis ===
-* [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 bio tools projects used in the COVID-19 analysis. This is a bottom-up approach to find the areas.
+==== nf-core ====
+[https://nf-co.re/ nf-core] is a collection of analysis pipelines built using [https://www.nextflow.io/ Nextflow]. We refer the pipelines to look into the actual analysis workflows to identify the used bio tools projects.
+Nextflow is the workflow software such as [https://openwdl.org/ Workflow Description Language (WDL)] and [https://www.commonwl.org/ Common Workflow Language (CWL)]. The Podman container workflow is supported by Nextflow according to [https://www.nextflow.io/docs/edge/podman.html this page].
-* [https://fevermap.net/ fevermap]: [https://gitlab.com/fevermap/fevermap Source]
+{| class="wikitable"
+|-
+! Pipeline !! Description !! Relevant level !! Status
+|-
+| [https://nf-co.re/nanoseq nf-core/nanoseq] || Nanopore DNA/RNA sequencing analysis || Essential (High) || Stable
+|-
+| [https://nf-co.re/artic nf-core/artic] || COVID-19 sequencing analysis. Reimplementation of [https://github.com/artic-network/fieldbioinformatics the ARTIC field bioinformatics pipeline] || Essential (High) || In development
+|-
+| [https://nf-co.re/viralrecon nf-core/viralrecon] || COVID-19 sequencing anaysis. Variant calling for viral samples. || Essential (High) || In development
+|-
+| [https://nf-co.re/scrnaseq nf-core/scrnaseq] || Single-cell analysis || Certainly relevant (Middle) || Stable
+|-
+| [https://nf-co.re/smartseq2 nf-core/smartseq2] || Single-cell analysis || Certainly relevant (Middle) || Stable
+|-
+| [https://nf-co.re/sarek nf-core/sarek] || Whole-genome sequencing analysis || Certainly relevant (Middle) || Stable
+|-
+| [https://nf-co.re/mag nf-core/mag] || Meta-genomics analysis || Certainly relevant (Middle) || Stable
+|-
+| [https://nf-co.re/bcellmagic nf-core/bcellmagic] || Investigations into the immune response || Certainly relevant (Middle) || Stable
+|}
-* [https://www.ibm.org/OpenPandemics OpenPandemics]
+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.
-* [https://www.worldcommunitygrid.org/discover.action WorldCommunityGrid]
-== Software projects used in COVID-19 ==
+This information comes from the hearing in the nf-core community.
-We list up the projects used in the COVID-19. This is a bottom-up approach to find the areas.
+==== 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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