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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. | ||
| − | + | 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 | |
| − | * [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://www.codevscovid19.org/ 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 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. | |
| − | |||
| − | + | * [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) | ||
| − | + | 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://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] | ||
| − | + | == Distributed Computing == | |
| − | + | ||
| − | + | The distributed computing projects are to enable people to help COVID-19 analysis by their computer resources. | |
| − | + | ||
| − | + | * [https://foldingathome.org/ FOLDING@HOME] | |
| − | + | * [https://boinc.bakerlab.org/rosetta/ Rosetta@home] | |
| − | + | * [https://setiathome.berkeley.edu/ SETI@home] | |
| + | |||
| + | == 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 |
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.
Contents
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 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