Free Software Directory:COVID-19 Response Team

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Free Software Foundation COVID-19 Response Team.png

About the Covid-19 Medical Group

Team Captain: David Hedlund

Participants:

Free 3D-printing files

Data

Free software

Category/Use/fighting-coronavirus

  • GNU Health
  • https://nextstrain.org/, https://github.com/nextstrain
  • OpenTrace
  • https://libreplanet.org/wiki/HACKERS_and_HOSPITALS#Software - thomzane's work on covid-19 resources
  • 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
    • 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.
    • 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.
    • 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.
    • 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.
    • 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.
    • 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

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.

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Further reading



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