Difference between revisions of "Free Software Directory:COVID-19 Response Team"

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[[File:Free Software Foundation COVID-19 Response Team.png|200px]]
 
[[File:Free Software Foundation COVID-19 Response Team.png|200px]]
 
The COVID-19 Response Team gathers free software resources to help slow the spread of COVID-19.
 
  
 
==About the Covid-19 Medical Group==
 
==About the Covid-19 Medical Group==
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* [[User:Craigt|Craigt]]
 
* [[User:Craigt|Craigt]]
 
* '''Summary''': An [https://en.wikipedia.org/wiki/Incident_response_team incident response team] dedicated work on medical software relevant to COVID-19, and COVID-19 3D printing files.
 
* '''Summary''': An [https://en.wikipedia.org/wiki/Incident_response_team incident response team] dedicated work on medical software relevant to COVID-19, and COVID-19 3D printing files.
 
==HACKERS and HOSPITALS==
 
* [https://libreplanet.org/wiki/HACKERS_and_HOSPITALS/ HACKERS and HOSPITALS] is a related effort on the LibrePlanet wiki to coordinate Hackers with Hospitals during an immediate time of need.
 
* We need to help coordinate the medical needs of hospitals with local area fabricators. We have a large number of healthcare professionals, hackers, makers, engineers, biomedical innovators, and crafters. If we can all work together, we can save lives.
 
  
 
==Free 3D-printing files==
 
==Free 3D-printing files==
 
See [https://libreplanet.org/wiki?title=HACKERS_and_HOSPITALS#Resources the Resources section of HACKERS and HOSPITALS].
 
 
==Data==
 
* [https://www.gisaid.org/ Global Initiative on Sharing All Influenza Data (GISAID)]
 
  
 
==Free software==
 
==Free software==
[[Category/Use/fighting-coronavirus]]
+
* https://libreplanet.org/wiki/HACKERS_and_HOSPITALS#Software - thomzane's work on covid-19 resources
 
 
* [[GNU Health]]
 
* https://nextstrain.org/, https://github.com/nextstrain
 
* [https://github.com/OpenTrace-community OpenTrace]
 
* https://joinup.ec.europa.eu/collection/digital-response-covid-19/open-source-solutions
 
* https://joinup.ec.europa.eu/collection/open-source-observatory-osor
 
* https://spectrum.ieee.org/static/covid19-ieee-resources
 
* https://spectrum.ieee.org/tag/COVID-19
 
* https://standards.ieee.org/covid-19/index.html
 
 
* https://www.gezapig.nl/covid.html - list put together by bendikker on health related free software
 
* https://www.gezapig.nl/covid.html - list put together by bendikker on health related free software
** [[BioRuby]]<br>BioRuby comes with a comprehensive set of free development tools and libraries for bioinformatics and molecular biology, for the Ruby programming language. BioRuby has  components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports many widely used data formats and provides easy access to databases, external programs and public web services, including BLAST, KEGG, GenBank, MEDLINE and GO.BioRuby comes with a tutorial, documentation and an interactive environment, which can be used in the shell, and in the web browser.BioRuby is supported by the Open Bioinformatics Foundation or O|B|F.
+
** BioRuby comes with a comprehensive set of free development tools and libraries for bioinformatics and molecular biology, for the Ruby programming language. BioRuby has  components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports many widely used data formats and provides easy access to databases, external programs and public web services, including BLAST, KEGG, GenBank, MEDLINE and GO.BioRuby comes with a tutorial, documentation and an interactive environment, which can be used in the shell, and in the web browser.BioRuby is supported by the Open Bioinformatics Foundation or O|B|F.
** [[Cwltool]]<br>The Common Workflow Language (CWL) is an open standard for describing analysis workflows and tools in a way that makes them portable and scalable across a variety of software and hardware environments, from workstations to cluster, cloud, and high performance computing (HPC) environments. CWL is designed to meet the needs of data-intensive science, such as Bioinformatics, Medical Imaging, Astronomy, High Energy Physics, and Machine Learning.
+
*** https://directory.fsf.org/wiki/BioRuby
** [[Pydicom]], [[Orthanc]]<br>DICOM (Digital Imaging in Medicine) is the bread and butter of medical image datasets, storage and transfer.  
+
** The Common Workflow Language (CWL) is an open standard for describing analysis workflows and tools in a way that makes them portable and scalable across a variety of software and hardware environments, from workstations to cluster, cloud, and high performance computing (HPC) environments. CWL is designed to meet the needs of data-intensive science, such as Bioinformatics, Medical Imaging, Astronomy, High Energy Physics, and Machine Learning.
** [[Drmaa]]<br>Distributed Resource Management Application API. This is a Python implementation of the Distributed Resource Management (DRM) Application API (DRMAA). It provides all high- level functionality necessary to consign a job to a DRM system (e.g. Sun Gridengine), including common operations on jobs, such as termination or suspension.  
+
** Dicom (Digital Imaging in Medicine) is the bread and butter of medical image datasets, storage and transfer.
** [[Genometools]]<br>The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt. It is based on a C library named “libgenometools” which consists of several modules.
+
*** https://directory.fsf.org/wiki/Pydicom
** [[ImageJ]]<br>ImageJ is a public domain Java image processing program inspired by NIH Image for the Macintosh. It runs, either as an online applet or as a downloadable application, on any computer with a Java 1.4 or later virtual machine.
+
*** https://directory.fsf.org/wiki/Cwltool
** [[PyNAST]]<br>Alignment of short DNA sequences. The package provices a reimplementation of the Nearest Alignment Space Termination tool in Python. It was prepared for next generation sequencers.Given a set of sequences and a template alignment, PyNAST will align the input sequences against the template alignment, and return a multiple sequence alignment which contains the same number of positions (or columns) as the template alignment. This facilitates the analysis of new sequences in the context of existing alignments, and additional data derived from existing alignments such as phylogenetic trees. Because any protein or nucleic acid sequences and template alignments can be provided, PyNAST is not limited to the analysis of 16s rDNA sequences.
+
** The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt. It is based on a C library named “libgenometools” which consists of several modules.
** [[PyNN]]<br>Simulator-independent specification of neuronal network models. PyNN allows for coding a model once and run it without modification on any simulator that PyNN supports (currently NEURON, NEST, PCSIM and Brian). PyNN translates standard cell- model names and parameter names into simulator-specific names.  
+
*** https://directory.fsf.org/wiki/Genometools
** [[Pysam]]<br>Pysam is a python module for reading, manipulating and writing genomic data sets.Pysam is a wrapper of the htslib C-API and provides facilities to read and write SAM/BAM/VCF/BCF/BED/GFF/GTF/FASTA/FASTQ files as well as access to the command line functionality of the samtools and bcftools packages. The module supports compression and random access through indexing.This module provides a low-level wrapper around the htslib C-API as using cython and a high-level, pythonic API for convenient access to the data within genomic file formats.
+
** ImageJ is a public domain Java image processing program inspired by NIH Image for the Macintosh. It runs, either as an online applet or as a downloadable application, on any computer with a Java 1.4 or later virtual machine.
** [[Open Source Ventilator Remote Monitor Project]]<br>Remote monitoring interface for low-cost rapidly-manufactured ventilators.Our goal is to quickly develop a remote monitoring interface for low-cost rapidly-manufactured ventilators currently being developed to provide emergency relief in the Covid-19 Pandemic. We strive for a lightweight, interoperable, and reliable interface. Currently the interface provides ventilator remote monitoring only (no control).This software is not approved to be used in a medical setting.
+
*** https://directory.fsf.org/wiki/ImageJ
 
+
** Pysam is a python module for reading, manipulating and writing genomic data sets.Pysam is a wrapper of the htslib C-API and provides facilities to read and write SAM/BAM/VCF/BCF/BED/GFF/GTF/FASTA/FASTQ files as well as access to the command line functionality of the samtools and bcftools packages. The module supports compression and random access through indexing.This module provides a low-level wrapper around the htslib C-API as using cython and a high-level, pythonic API for convenient access to the data within genomic file formats.
===Android apps===
+
*** https://directory.fsf.org/wiki/Pysam
Normally we don't list Android apps. This is an exception (like the [[Collection:Replicant|Replicant]] free software replacement list) specifically to fight COVID-19.
 
 
 
* [https://www.tracetogether.gov.sg/ TraceTogether]
 
 
 
==Categories==
 
* [[Category/Use/fighting-coronavirus]]
 
* [[Category/Hobbies/health]]
 
* [[Category/Biology/health-and-medicine]]
 
  
==Further reading==
 
* [https://en.wikipedia.org/wiki/COVID-19_apps COVID-19 apps] (Wikipedia)
 
* [https://www.fsf.org/blogs/community/hackers-and-hospitals-how-you-can-help HACKERS and HOSPITALS: How you can help — Free Software Foundation — working together for free software]
 
* [https://libreplanet.org/wiki/HACKERS_and_HOSPITALS HACKERS and HOSPITALS - LibrePlanet]
 
* [https://libreplanet.org/wiki/Remote_Communication Remote Communication - LibrePlanet]
 
* [https://joinup.ec.europa.eu/collection/ehealth/news/tackling-beast-using-gnu-health-help-fight-against Tackling the beast: Using GNU Health to help the fight against the | Joinup]
 
  
 
[[Category:Project Team]]
 
[[Category:Project Team]]

Revision as of 14:44, 10 April 2020

Free Software Foundation COVID-19 Response Team.png

About the Covid-19 Medical Group

Team Captain: David Hedlund

Participants:

Free 3D-printing files

Free software

  • https://libreplanet.org/wiki/HACKERS_and_HOSPITALS#Software - thomzane's work on covid-19 resources
  • https://www.gezapig.nl/covid.html - list put together by bendikker on health related free software
    • BioRuby comes with a comprehensive set of free development tools and libraries for bioinformatics and molecular biology, for the Ruby programming language. BioRuby has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports many widely used data formats and provides easy access to databases, external programs and public web services, including BLAST, KEGG, GenBank, MEDLINE and GO.BioRuby comes with a tutorial, documentation and an interactive environment, which can be used in the shell, and in the web browser.BioRuby is supported by the Open Bioinformatics Foundation or O|B|F.
    • The Common Workflow Language (CWL) is an open standard for describing analysis workflows and tools in a way that makes them portable and scalable across a variety of software and hardware environments, from workstations to cluster, cloud, and high performance computing (HPC) environments. CWL is designed to meet the needs of data-intensive science, such as Bioinformatics, Medical Imaging, Astronomy, High Energy Physics, and Machine Learning.
    • Dicom (Digital Imaging in Medicine) is the bread and butter of medical image datasets, storage and transfer.
    • The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt. It is based on a C library named “libgenometools” which consists of several modules.
    • ImageJ is a public domain Java image processing program inspired by NIH Image for the Macintosh. It runs, either as an online applet or as a downloadable application, on any computer with a Java 1.4 or later virtual machine.
    • Pysam is a python module for reading, manipulating and writing genomic data sets.Pysam is a wrapper of the htslib C-API and provides facilities to read and write SAM/BAM/VCF/BCF/BED/GFF/GTF/FASTA/FASTQ files as well as access to the command line functionality of the samtools and bcftools packages. The module supports compression and random access through indexing.This module provides a low-level wrapper around the htslib C-API as using cython and a high-level, pythonic API for convenient access to the data within genomic file formats.


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