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Client Applications
3rd-Party Web Applications
Mosaic integrates with a number of external web applications that can be securely launched directly from Mosaic. In the left sidebar, the applications link will slide up a modal that displays the web applications that are available for a given page. If you are looking at a single sample, then only web applications that accept a single sample will be displayed. If you are looking at multiple samples, then only web applications that accepts multiple samples will be displayed.
Single Sample Web Applications
Web applications that accept a single sample:
Gene.iobio
Analyze genomic variants in realtime with lots of annotations (clinvar, vep, gnomAD allele frequency, etc).
Links:
Clin.iobio
Workflow and reporting for iobio variant analysis pipeline.
Links:
Bam.iobio
View metrics & statistics for your alignement data (BAM/CRAM).
Links:
Vcf.iobio
View metrics & statistics for your variant data (VCF).
Links:
IGV
BAM and VCF browser.
Coverage Explorer
Identify & confirm that a gene or list of genes has sufficient coverage for a sample or pedigree.
Multi Sample Web Applications
Web applications that accept multiple samples:
Multibam
Quality control for up to thousands of BAM/CRAM files. Visualize numerous metrics and statistics for all the selected samples (up to the entire project).
Links:
Add Web Applications
New web applications can easily be added to Mosaic. To learn more, contact us to explore an enterprise plan.
Deploy Web Application Internally
Mosaic can make it easier to deploy internal web applications to your organization. You can use Mosaic's authentication, authorization, role-based access, and Oauth support to get started much more quickly. New applications can be made accessible to only a subset of your entire organization. To learn more, contact us to hear about an enterprise plan.
Launch with filters (i.e. launch with a specific cohort)
When you launch a web application the input will be the samples that are currently passing any active filters. In this way you can generate a cohort on-the-fly and then launch out to a web application for further analysis on that cohort.
Saving an analysis
When launching a stateless third party application from Mosiac, it's useful to be able to re-launch an analysis without manually entering all of the launch steps. For this reason, Mosaic can save an analysis customized to each application.
API Endpoint
When saving an analysis from a client application to Mosaic, the client should pass a payload parameter which is a JSON blob. This could be the params used to generate the analysis like the sample ID and gene or it could be the raw data the client app generates. See https://mosaic.frameshift.io/api/#api-Project_Analyses-CreateProjectAnalysis for the API documentation.
Launching from Mosaic
When launching a saved analysis from Mosaic, Mosaic will add the analysis_id query parameter to the launch url. The client app can then use that parameter to retrieve the JSON and recreate the previous client app state. See https://mosaic.frameshift.io/api/#api-Project_Analyses-GetProjectAnalysis for the API documentation.