Custom Data-centric Portals and Pipelines
Do you need to automate passing data through a sequence of tools?
Manage and track user access to key datasets?
Present customized results to clients?
Example of Prior Work
A Comprehensive Genomic Variants Annotation Tool
Literature Curation Interface and the Variant Annotation Interface, ETL Processes, Admin Interface, GWAS/Bulk Data Processing, Ontology and External Databases Lookup System.
Patient Data Portal
A complex system of workflows to allow registered users annotate and manage clinical data for than 2500 patients including the following functionalities:
- Ingest data from outside resources
- Convert data, monitor changes
- Curate data using both third-party curation solution and automated workflows
- Validate data
- Convert data, monitor changes
- ETL data into tranSMART
- Modify tranSMART application to allow export of large studies
- Spin tranSMART containers to distribute load
- Configure setup to allow rapid spinning up of new instances using LXD
- Present data to users based on custom-build CRM
Compound Curation tool
Curation tool connected with scripts for Public Resource Data Mining/Crawling and Ontology Lookups.
Sample Management System
- Simple, Excel-like User Interface to manage sample data and metadata
- Data import from CSV and TSV
- Database backend
- Searching and filtering
- Field-specific ontology lookups and controlled vocabularies
- Bulk updates
- Dashboard with visualizations