Resources

Resources

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

General

• 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: http://covid.wikipathways.org

Pandemic & science

• COVID-19 Research in Brief: 20 March to 27 March, 2020 in Nature Medicine
• 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)
• Elsevier's Coronavirus Information center Website

Data resources

Repositories and Standards useful for COVID-19

• FAIRsharing contains manually curated metadata on registries, knowledgebases, models and formats, terminologies, reporting guidelines and identifier schema. Please help us curate a special COVID-19 collection either by adding your own resources (you will need a FAIRsharing account to do this) or adding to our curation spreadsheet.

Sequencing/molecular data

• 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
• 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/.
• Genexa provides a huge amount of bioinformatics resources. This includes assemblies, an MSA, kmers unique to SARS-Cov-2 and a Kraken2 index.

Epidemiological data

• 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

Literature data

• COVID-19 Open Research Dataset (CORD-19) description and landing page.
  • CORD-19 Explorer is a quick and easy way to search the CORD-19 corpus.
  • COVID-19 Open Research Dataset Literature Corpus (CORD-19) and also additional resources
• 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
• SciBite Literature resources

Ontologies and Metadata standardization

• MIDAS COVID-19 modeling data CSV data downloads with structured metadata
• schema.org CovidTestingFacility type

Drug development and test assays

• Tracking test results in USA
• List of available test assays
• Why not to get excited about chloroquine just yet

Related Efforts

• 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
• Collection of efforts in the German Medical Informatics community, in German language only

Literature resources

• https://pages.semanticscholar.org/coronavirus-research
• LitCovid
• Compilation of resources by librarians around the world

Software resources

• 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

Workflows and pipelines

• Initial analysis of SARS-CoV-2 data using Galaxy and BioConda
  • Best practices for the analysis of SARS-CoV-2 data: Genomics and Cheminformatics
• nextstrain phylogeny analysis using data from GISAID
• ViReport analysis using data from GISAID
• Artic Nanopore workflow

Cloud computing

• ELIXIR Compute Platform Resources ELIXIR Nodes run computing services that can be accessed by research projects. Many additional computing resources have been made available to support COVID-19 research projects including:

  • Access to Docker Orchestrators including Mesos and OpenStack access, Kubernetes/OKD and potentially GPUs where needed. For access request & other queries please join #elixir-resourcesslack channel
  • de.NBI cloud, ELIXIR-Germany provides priority access for projects relating to COVID-19
  • CSC (ELIXIR-Finland) has prioritised access to its cloud services for COVID-19 research
  • e-INFRA CZ (ELIXIR-Czech) offer relaxed access conditions to supercomputer resources, storage services and distributed compute resources
  • A specific Galaxy COVID-19 instance for genomic analysis is available through Laniakea, ELIXIR Italy’s on-demand platform
  • EMBL-EBI located in the UK is contributing EMBASSY Cloud resources as detailed on the European Open Science Cloud, EOSC Marketplace
  • IFB (ELIXIR France) is providing a federated set of high performance compute and cloud resources including national and regional servers
  • ELIXIR-Swiss and ELIXIR-Finland have provided a common Virtual Machine (VM) that contains key resources in a single directory for the Gene Expression and this could be extended into e.g. other collaborative teams for this and other hackathon type events. This helps lower technical barriers and get more people involved more quickly.

• Common Workflow Language (CWL) execution via the Arvados platform

  • https://biohackathon.curii.com/ (Free, courtesy of Curii, Inc. and Amazon AWS

• Google Cloud Platform(?)

HPC and supercomputing

• COVID-19 HPC offers resources for research. See COVID-19 HPC
• Some ELIXIR supercomputing resources also available via Cloud Resources (see above)

Other

• No raw data, no science: another possible source of the reproducibility crisis Molecular Brain volume 13, Article number: 24 (2020)