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Enhancements and Features of the Trellis DAS/2 Framework for Enhanced Data Access

The Trellis DAS/2 Framework aims to improve upon DAS1 with a RESTful approach utilizing HTTP transport and URL queries for efficient data retrieval. Key enhancements include support for alternative data formats, improved HTTP functionalities (like caching and authentication), and the ability to handle complex feature hierarchies. The framework facilitates seamless integration with existing databases through unique URIs for various data types, while offering robust client implementations such as the Integrated Genome Browser. With deployment options on cloud services like Amazon EC2, Trellis DAS/2 is positioned as a versatile tool for genomic data access and processing.

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Enhancements and Features of the Trellis DAS/2 Framework for Enhanced Data Access

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  1. Trellis DAS/2 Server Framework Gregg Helt

  2. DAS/2 Overview • Same goal and overall strategy as DAS1 • HTTP transport, URL queries, XML responses • RESTful approach to Web Services • Tries to address many issues with DAS1 • Enhancements • Alternative Data Formats (potentially much more efficient) • URIs for all assemblies, sequences, features, feature types • Feature Hierarchies • Enhanced use of HTTP (caching, authentication, etc.) • Enhanced use of XML (arbitrary XML, xml:base, etc.) • Writeback • Current Implementations • Servers • Genometry (Java, in-memory object database) • BioPackages (Perl, GMOD-Chado database) • Clients: IGB -- Integrated Genome Browser (Java WebStart) • Validator: Dasypus (Python) • Trellis Framework • Current deployments • Public • Affymetrix • TransVar (UNC Charlotte) • Huntsman Cancer Institute (U.Utah) • Trellis Cloud Deployments • Private

  3. Trellis DAS/2 Framework • Abstract DAS/2 data model • Basic Server implementation of data model • Translation from DAS HTTP requests to data model (URL  API) • Translation from data models to DAS HTTP responses (API  XML) • Basic DAS/2 servlet • Add data source plugin(s) for fully functional DAS/2 server • Open source • http://code.google.com/p/genomancer/ • Test deployments on Amazon EC2 cloud

  4. Trellis DAS/2 Server Trellis Framework Servlet Data Source Capabilities Plugin DAS/2 Client DAS/2 Data Model URL/HTTP Request to Model Model to Data Source Query Model to XML/HTTP Response Data Source to Model Response

  5. Trellis DAS2 Data Model

  6. Ivy DAS1DAS2 Proxy Trellis Framework Servlet Ivy DAS1DAS2 Plugin DAS/1 Server DAS1 Client DAS/2 Client DAS1 HTTP request DAS1 Data Model DAS2 to DAS1 query model DAS2 Data Model DAS1 to DAS2 response model DAS1 HTTP response

  7. Ivy DAS1 Data Model

  8. DAS1 / DAS2 Feature Comparison

  9. Ivy DAS1DAS2 Proxy • Test deployment on the Amazon EC2 cloud • Proxying for DAS1 Sanger Registry • http://www.genomancer.org/das2/das1_proxy/sources • Supported DAS 1.53/1.6 queries: • sources • segments • types • features • Queries not yet supported • dsn • dna • 1.53e extensions • Alignments • Etc.

  10. Vine DAS2DAS2 Proxy Trellis Framework Servlet Ivy DAS1DAS2 Plugin DAS/2 Server DAS/2 Client DAS2 Client DAS2 Data Model DAS2 HTTP request DAS2 HTTP response

  11. Poka: DAS2 UCSC Genome Database Server • Test deployment on the Amazon EC2 cloud • http://www.genomancer.org:9095/das2/ucsc/genome/sources • Current release: alpha • Supports roughly half of UCSC annotation tracks • Latest human genome: • 1724 total tracks in hg18 genome database • Poka can serve up 878 as DAS2 types/features • Next release: beta • Adds support for wiggle/wib tracks

  12. Demo

  13. Trellis Enhancements • Caching • Caching Injection • Sources Capability Injection • Format Injection • Tranformational DAS Proxy

  14. Sources Capability Injection

  15. Caching Injection

  16. Source/Type Transformations

  17. Format Injection • Trellis supports format plugins • Add format plugin to Trellis, then server can support alternative format even though data source plugin does not • Current: bed • Soon: gff, psl, bps, bgn, bar, wiggle • BigWig?

  18. Format Injection Trellis Framework Servlet URL/HTTP Request to Model Data Source Capabilities Plugin DAS/2 Client Model to DASXML HTTP Response DAS/2 Data Model Model to Data Source Query Model to JSON HTTP Response Data Source to Model Response Model to BED HTTP Response Model to ProtoBuf HTTP Response

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