2019-nCoV & SARS-CoV-2: Fluid Response
At Fluid Numerics we value community and view assistance that benefits the health and wellbeing of cohabitants on our planet as an opportunity to grow holistically. Instead of retreating from the compounding issues that are directly affecting our world we are leaning in to understand how we can support and are proud to stand by our resource partner, Google, in offering to help accelerate analysis, research and synthesis of current coronavirus study.
Google has partnered with the Harvard Global Health Institute to fund companies, government agencies, non-profit organizations and academic institutions working on COVID-19 research. Researchers in approved countries are eligible to apply for COVID-19 related research credits.
The fluid-slurm-gcp solution can scale globally across all Google Cloud regions. Fluid Numerics is currently putting together images with VirusSeeker-Virome and other virology toolkits that interface with GenBank and the NCBI databases which collaborate international research efforts.
Our HPC team is available to help organizations and their team members use GCP to accelerate coronavirus research or share this effort where you feel it may be relevant to someone that is currently fighting to understand this virus and it's potential.
National Institute of Health has made access to the dataset related to 2019-nCoV readily available and are also accepting submissions to the dataset from labs and institutions. NIH has made access to the dataset related to SARS-CoV2 readily available.
Let us know how we can help.
What we are doing:
- Built and deployed a partition for Fluid-Slurm-GCP that can host Folding@home Work Units for teams looking to provide more compute resources to F@H.
- Repository publicly available here: https://bitbucket.org/fluidnumerics/folding-at-home-slurm_gcp/src/master/
- Publishing an image and a package installation repository to rapidly deploy the toolkit for the workflows we have available to run on Fluid-Slurm-GCP that will install many of the packages involved in the viral metagenomics workflows commonly being practiced and published.
- Repository publicly available here: https://bitbucket.org/fluidnumerics/fluid-slurm-gcp-virology/src/master/
Resources we have referenced within our research:
China National Center for Bioinformation: 2019 Novel Coronavirus Resource (2019nCoVR)https://bigd.big.ac.cn/ncov/?lang=en
SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) Sequenceshttps://www.ncbi.nlm.nih.gov/genbank/sars-cov-2-seqs/
Get Rapid Access to Novel Coronavirus (2019-nCoV) Sequence Data from NLM’s GenBank®https://www.nlm.nih.gov/news/coronavirus_genbank.html
COVID-19 Open Research Dataset (CORD-19) on semanticscholar.orghttps://pages.semanticscholar.org/coronavirus-research
COVID-19 Open Research Dataset Challenge (CORD-19)https://www.kaggle.com/allen-institute-for-ai/CORD-19-research-challenge
VirusSeeker, a computational pipeline for virus discovery and virome composition analysis.https://www.ncbi.nlm.nih.gov/pubmed/28110145
Vipie: web pipeline for parallel characterization of viral populations from multiple NGS sampleshttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5430618/
Department of Pathology & Immunology : Washington University School of Medicinehttps://wupathlabs.wustl.edu/virusseeker/
Folding @ Home : COVID-19 Updatehttps://foldingathome.org/2020/03/10/covid19-update/
XSEDE COVID-19 HPC Consortium Request Informationhttps://www.xsede.org/c/journal/view_article_content?cmd=view&groupId=1477968&articleId=2421324&version=6.0