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
- GNU Health
- https://nextstrain.org/, https://github.com/nextstrain
- 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.
- 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.
- 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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