Free Software Directory:COVID-19 Response Team
About the Covid-19 Medical Group
Team Captain: David Hedlund
- Summary: An incident response team dedicated work on medical software relevant to COVID-19, and COVID-19 3D printing files.
Free 3D-printing files
- https://github.com/jakobzhao/virus/ - https://hgis.uw.edu/virus/
- https://www.arcgis.com/apps/opsdashboard/index.html#/bda7594740fd40299423467b48e9ecf6 - https://github.com/CSSEGISandData/COVID-19
- 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
- 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.
- 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.
- 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.
- TreeTime provides routines for ancestral sequence reconstruction and inference of molecular-clock phylogenies, i.e., a tree where all branches are scaled such that the positions of terminal nodes correspond to their sampling times and internal nodes are placed at the most likely time of divergence.To optimize the likelihood of time-scaled phylogenies, TreeTime uses an iterative approach that first infers ancestral sequences given the branch length of the tree, then optimizes the positions of unconstrained nodes on the time axis, and then repeats this cycle. The only topology optimization are (optional) resolution of polytomies in a way that is most (approximately) consistent with the sampling time constraints on the tree. The package is designed to be used as a stand-alone tool on the command-line or as a library used in larger phylogenetic analysis work-flows.
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