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 provides priority access for projects relating to COVID-19
  • CSC (ELIXIR-FI) has prioritised access to its cloud services for COVID-19 research
  • e-INFRA CZ (ELIXIR-CZ) 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 is contributing EMBASSY Cloud resources as detailed on the European Open Science Cloud, EOSC Marketplace
  • SIB (ELIXIR-CH) is providing a ready-to-use slurm workload manager with a scientific software stack via the ExPASy SIB Portal
  • ELIXIR-CH and ELIXIR-FI are working together to provide a common Virtual Machine (VM) that contains key resources in a single directory for e.g. collaborative teams and hackathon type events. This helps lower technical barriers and get more people involved more quickly.
  • IFB (ELIXIR France) is providing a federated set of high performance compute and cloud resources including national and regional servers

• 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)