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<h1 id="pathogen-detection-resources-at-">Pathogen Detection Resources at Google Cloud Platform <a href="/pathogens/pathogens_help/"><img alt="Main documentation page" src="/core/assets/pathogens/images/arrowup_blue.gif"/></a></h1>
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<p>NCBI Pathogen Detection provides data at Google Cloud Platform in two places: The <a href="/pathogens/pathogens_help/#microbigge">MicroBIGG-E</a> and <a href="/pathogens/pathogens_help/#isolates-browser">Isolates Browser</a> tables are in <a href="https://cloud.google.com/bigquery/docs/">Google BigQuery</a> and MicroBIGG-E sequences FASTA format are in <a href="https://cloud.google.com/storage/docs/">Google Cloud Storage</a>.</p>
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<h3 id="pathogen-detection-resources-ava">Pathogen Detection Resources available on the Google Cloud</h3>
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<ul>
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<li><a href="/pathogens/docs/gcp/">Pathogen Detection Resources at Google Cloud Platform</a></li>
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<li><a href="/pathogens/docs/microbigge_gcp/#getting-started-with-bigquery">Getting started with BigQuery</a></li>
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<li><a href="/pathogens/docs/microbigge_gcp/">MicroBIGG-E table in BigQuery</a></li>
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<li><a href="/pathogens/docs/microbigge_gcp/#contig-sequences">MicroBIGG-E contig sequences in Google Storage buckets</a></li>
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<li><a href="/pathogens/docs/microbigge_gcp/#protein-sequences">MicroBIGG-E protein sequences in Google Storage buckets</a></li>
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||
<li><a href="/pathogens/docs/ast_gcp/">AST Browser in BigQuery</a></li>
|
||
<li><a href="/pathogens/docs/isolates_gcp/">Isolates Browser table in BigQuery</a></li>
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<li><a href="/pathogens/docs/isolates_gcp/#isolate_exceptions">Isolate Exceptions table in BigQuery</a></li>
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<li><a href="/pathogens/docs/bioproject_hierarchy_gcp/">BioProject Hierarchy in BigQuery</a>
|
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<!-- asdf_ -->
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</li>
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</ul>
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<h2 id="documentation-for-pathogen-detec">Documentation for Pathogen Detection resources at Google Cloud</h2>
|
||
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||
<ul>
|
||
<li>YouTube video <a href="https://ncbiinsights.ncbi.nlm.nih.gov/event/ncbi-pathogen-detection-in-cloud-03-2023/">NCBI minute: Introduction to NCBI Pathogen Detection and antimicrobial resistance data in Google BigQuery</a> and <a href="https://www.ncbi.nlm.nih.gov/pathogens/docs/ncbi_minute_230329/">links to materials and information</a> </li>
|
||
<li><a href="/pathogens/docs/getting_started_bigquery">Getting started with Google BigQuery</a> - Information about how to use Google BigQuery for accessing NCBI Pathogen Detection data in BigQuery tables.</li>
|
||
<li><a href="/pathogens/docs/isolates_gcp/">Isolates browser at GCP</a> - The data from the <a href="/pathogens/isolates/">Isolates Browser</a> </li>
|
||
<li><a href="/pathogens/docs/microbigge_gcp/">MicroBIGG-E at GCP</a> - The data from the Microbial Browser for the Identification of Genetic and Genomic Elements (<a href="/pathogens/microbigge/">MicroBIGG-E</a>) - Information about, and contig and protein seqeunces for genes and point mutations identified in Pathogen Detection isolates by AMRFinderPlus.</li>
|
||
<li><a href="/pathogens/docs/bioproject_hierarchy_gcp/">BioProject Hierarchy at GCP</a> - All data BioProjects for isolates in the Pathogen Detection browsers as well as any parent umbrella BioProjects they are children of.</li>
|
||
<li><a href="/pathogens/docs/ast_gcp/">AST data at GCP</a> - Submitted Antimicrobial Susceptibility Test results. </li>
|
||
<li>Email us with questions or feedback at <a href="mailto:pd-help@ncbi.nlm.nih.gov">pd-help@ncbi.nlm.nih.gov</a></li>
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</ul>
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|
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<h4 id="asm-ngs-2024-workshop">ASM NGS 2024 Workshop</h4>
|
||
|
||
<p>The first portion of the workshop covered Pathogen Detection and BigQuery. See https://github.com/ncbi/workshop-asm-ngs-2024/wiki for presentations and exercises.</p>
|
||
|
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<h4 id="asm-ngs-2022-workshop">ASM NGS 2022 Workshop</h4>
|
||
|
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<p>We participated in a <a href="https://github.com/ncbi/workshop-asm-ngs-2022/wiki">workshop</a> at <a href="https://asm.org/Events/ASM-NGS/Home">ASM NGS 2022</a> which included some projects that demonstrate how to use our resources in the cloud. See the <a href="https://github.com/ncbi/workshop-asm-ngs-2022/wiki/Setup">Workshop Setup</a>, <a href="https://github.com/ncbi/workshop-asm-ngs-2022/wiki/Project-1">Project 1: Use BigQuery to search MicroBIGG-E and Isolates data</a>, <a href="https://github.com/ncbi/workshop-asm-ngs-2022/wiki/Project-2">Project 2: Generate tree of KPC alleles to examine evolution of size variants</a>
|
||
, and <a href="https://github.com/ncbi/workshop-asm-ngs-2022/wiki/Project-3">Project 3: Selection analysis on 293-aa blaKPC genes</a> for examples of how to use NCBI Pathogen Detection data in the cloud.</p>
|
||
|
||
<h2 id="update-frequency">Update frequency</h2>
|
||
|
||
<p>Pathogen Detection data at Google Cloud Platform is updated daily, so updated results may lag behind results presented in the browsers or on FTP by up to one day.</p>
|
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|
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<h2 id="additional-related-resources">Additional related resources</h2>
|
||
|
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<h4 id="tools">Tools</h4>
|
||
|
||
<ul>
|
||
<li><a href="https://www.ncbi.nlm.nih.gov/sra/docs/sra-cloud/">SRA in the cloud</a> SRA metadata in Google BigQuery and AWS Athena</li>
|
||
<li><a href="https://blast.ncbi.nlm.nih.gov/doc/elastic-blast/">ElasticBLAST</a> Parallelized BLAST for the cloud</li>
|
||
</ul>
|
||
|
||
<h4 id="google-docs">Google docs</h4>
|
||
|
||
<ul>
|
||
<li><a href="https://cloud.google.com/docs/get-started">Getting Started with Google Cloud</a></li>
|
||
<li><a href="https://cloud.google.com/compute/docs/create-linux-vm-instance">Create a Linux VM instance in Compute Engine</a></li>
|
||
</ul>
|
||
|
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<h2 id="dont-have-a-cloud-account">Don't have a cloud account?</h2>
|
||
|
||
<p>NIH <a href="https://datascience.nih.gov/strides">Science and Technology Research Infrastructure for Discovery,
|
||
Experimentation, and Sustainability (STRIDES) Initiative</a> has launched a new NIH
|
||
Cloud Lab program that lets you experiment with using cloud for your research.
|
||
You can request a GCP or AWS account, and will receive $500 and three months,
|
||
in addition to access to biomedical tutorials that walk you through common
|
||
cloud-based research use cases. This is available to intramural researchers
|
||
currently but expect it to be ready for extramural researchers in the coming
|
||
months. Learn more via this link- <a href="https://cloud.nih.gov/resources/cloudlab/">https://cloud.nih.gov/resources/cloudlab/</a></p>
|
||
|
||
<hr/>
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<p><strong>If you have any questions or issues or anything that you need let us know at <a href="mailto:pd-help@ncbi.nlm.nih.gov">pd-help@ncbi.nlm.nih.gov</a></strong></p>
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