1 / 12

WebApollo extending JBrowse to support DAS & genomic annotation editing

WebApollo extending JBrowse to support DAS & genomic annotation editing. Gregg Helt, Ed Lee, Nomi Harris, Mitch Skinner, Suzanna Lewis, Ian Holmes Lawrence Berkeley National Laboratory & UC Berkeley. Main Goal of WebApollo. Provide an interactive visual editor for

avital
Download Presentation

WebApollo extending JBrowse to support DAS & genomic annotation editing

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. WebApolloextending JBrowse to support DAS &genomic annotation editing Gregg Helt, Ed Lee, Nomi Harris, Mitch Skinner, Suzanna Lewis, Ian Holmes Lawrence Berkeley National Laboratory & UC Berkeley

  2. Main Goal of WebApollo Provide an interactive visual editor for genome annotation and curation, that anyone can use via a standard web browser

  3. Build on existing infrastructure • For front end start with current version of JBrowse (AJAX-based genome browser) • Port visual editing features of Apollo (Java-based genome curation tool) to JBrowse • For access to non-editable annotations, do whatever it takes to enable WebApolloto access as many types of genomic data as efficiently as possible (DAS?) • Data access implementations and ideas from Integrated Genome Browser (IGB) and Trellis DAS framework • For back end to editable annotations and curations, start with current Apollo backends (mostly GMOD Chado databases) • Evolve later to allow more back end flexibility (DAS writeback?)

  4. JBrowse • Mitch Skinner & Ian Holmes, UC Berkeley • JavaScript Genome Browser • Version 1.2 just released • CSS & DIV based rendering for interval data • Tiled Images for quantitative data • Nested Containment Lists for speedy interval queries • jbrowse.org • WebApollo uses and extends Jbrowse code base

  5. Apollo • Suzi Lewis, Nomi Harris, Ed Lee, etc., LBNL • Desktop Genome Annotation Editor • Implemented in Java • GMOD Chado database back end • WebApollo using revised back end GBOL (Java model of Chado schema)

  6. Whatever it takes to enable WebApolloto access as many types of genomic data as possible • More practically, efficient access to public data from UCSC, Ensembl,and GMOD Chado databases • Unified strategy like DAS is preferred • Leverage efficient JBrowse JSON data formats and nested containment lists • Solution: Trellis, a modular DAS2 server that supports alternative content formats • Trellis plugins to proxy for other DAS servers • Poka Trellis plugin for direct UCSC database access

  7. Alternative Content Format Support(Format Injection) Trellis Framework Servlet URL/HTTP Request to Model JBrowse Client Data Source Capabilities Plugin Model to DASXML HTTP Response DAS Data Model Model to Data Source Query Model toNCList JSON HTTP Response Data Source to Model Response Model to BED HTTP Response Model to ProtoBuf HTTP Response

  8. DAS JBrowse ProxyIvy Plugin + Trellis + Format Injection Trellis Framework Servlet Ivy DAS Plugin DAS Server JBrowseClient DAS Data Model DAS HTTP request with alt content param DAS HTTP request DAS HTTP response NCList etc. JSON format

  9. UCSC JBrowse ProxyPokaplugin + Trellis + format injection Trellis Framework Servlet UCSC MySQL Genome database PokaPlugin JBrowseClient DAS Data Model DAS HTTP Request w/alt content param DAS Model to UCSC MySQL Model to NCListetc. JBrowse MySQL response to DAS Model

  10. WebApollo Demo

  11. WebApollo Demo2

  12. All open source • Client Code on GitHub: berkeleybop/jbrowse • Server Code all over the place • Trellis: http://code.google.com/p/genomancer/ • GBOL: http://code.google.com/p/gbol/ • WebApollo-specific server bits: • http://code.google.com/p/apollo-web/ • Etc.

More Related