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Resources
Robert Hoehndorf edited this page Mar 25, 2020
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This page lists relevant links for the COVID-19 Biohackathon 2020. See https://github.com/virtual-biohackathons/covid-19-bh20 or we are putting the band back together
- slack: https://join.slack.com/t/virtualbiohac-xt62674/shared_invite/zt-cuur40oj-wdrVz50NocwVrH7vgKTdPg
- News category
- Wikipedia/wikidata is tracking the pandemic both internationally and locally
- What does a pandemic mean for the USA and others following the Italian model
- Popular article 'Act today or people will die' on COVID-19 and its spread
- Live maps from Bing
- The Economist has an interesting article on COVID-19 drug development - unfortunately it is paywalled but a copy resides here
- Wikidata: SARS-CoV-2, COVID-19 (and this book with a growing list of queries)
- WikiPathways: https://www.wikipathways.org/index.php/Pathway:WP4846
- WHO pandemic phase descriptions and actions
- Fighting COVID-19 with AI: efforts and lessons from China
- COVID-19 resource center from The Lancet
- A human monoclonal antibody blocking SARS-CoV-2 infection PDF
- March 16: models on hospital bed use and deaths in UK and USA, see Imperial College study
- March 23: UK announces a research project to track and map COVID-19 using next generation sequencing Announcement
- GISAID has the most complete sequence data collection of SARS-CoV-2. But GISAID has lots of restrictions on releasing data.
- NCBI Reference sequence Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome
- NCBI SRA has a growing amount of public raw data for science - but note the usage licenses! We may be able to redistribute with appropriate metadata.
- Other SARS-CoV-2 sequence data from NCBI
- SRP250294 This is a set of Illumina and Oxford Nanopore data depleted of host sequences and other contaminating sequences.
- sequencing data and structures from EMBL-EBI https://www.ebi.ac.uk/ena/pathogens/covid-19
- COVID-19 Open Research Dataset Literature Corpus (CORD-19) and also additional resources
- CNCB has raw data of corona viridae: ftp://download.big.ac.cn/Genome/Viruses/Wuhan_seafood_market_pneumonia_virus/ and ftp://download.big.ac.cn/Genome/Viruses/Coronaviridae/genome/.
- ZB MED COVID Hub, genome browser and links to related information
- CORD-19, CORD-19-on-FHIR -- Semantics for COVID-19 Discovery.
- Annotated CORD-19 data set, sentence co-occurrences and Coronavirus vocabs
- Global coronavirus (COVID-19) data tracking the number of confirmed cases, deaths, and recoveries, by location, updated daily https://aws.amazon.com/marketplace/pp/Global-Coronavirus-COVID-19-Data-Johns-Hopkins/prodview-rmk3gahdzo3tg#overview
- MIDAS COVID-19 modeling data CSV data downloads with structured metadata
- schema.org CovidTestingFacility type
- Tracking test results in USA
- List of available test assays
- Why not to get excited about chloroquine just yet
- The OpenCovid19 Initiative
- COVID-19 Open Research Dataset Challenge (CORD-19)
- HackSeq, now to May 21
- We vs virus / Wir vs Virus, in German only, 20-22 March
- https://pages.semanticscholar.org/coronavirus-research
- LitCovid
- Compilation of resources by librarians around the world
- Erik Garrison on assembly of nanopore.
- Galaxy efforts
- Rami Krispin's coronavirus package in R -- also dataset
- PyCOVID Python library by Sudharshan Ashok -- also dataset
- Initial analysis of SARS-CoV-2 data using Galaxy and BioConda
- nextstrain phylogeny analysis using data from GISAID
- ViReport analysis using data from GISAID
- Artic Nanopore workflow
- OpenStack(?)
- Google Cloud Platform(?)
- COVID-19 HPC offers resources for research. See COVID-19 HPC