JBrowse within the Arabidopsis Information Portal - PAG XXIII

Araport integrates JBrowse visualization software from GMOD. In order to support diverse sets of locally and remotely sourced tracks, the “ComboTrackSelector” JBrowse plugin was developed to enable the capability to partition metadata rich tracks in the “Faceted” selector while using the default “Hierarchical” selector for everything else.

A dynamic sequence viewer add-on, “SeqLighter”, was developed using the BioJS framework (http://biojs.net/), configured offer end-users with the capability to view the genomic sequence underlying the gene models (genic regions plus customizable flanking regions), highlight sub-features (like UTRs, exons, introns, start/stop codons) and export the annotated output in various formats (SVG, PNG, JPEG).

Presentation regarding JBrowse plugin development and its adoption by the Araport project, made at GMODs workshop the on 14 Jan 2015, conducted at PAG XXIII in San Diego, CA.

Presented by Vivek Krishnakumar

Transcript

1. araport.org @araport JBrowse within the Arabidopsis Information Portal Vivek Krishnakumar J. Craig Venter Institute 01/14/2015 GMOD PAG XXIII, San Diego, CA
2. araport.org @araport Overview • About Araport • Extensions to JBrowse – Hybrid track selector plugin – Sequence viewer widget • Araport on GitHub • Useful tidbits for JBrowse users
3. araport.org @araport About Araport • Objectives – Develop community web interface • sustainable, fundable and community-extensible • hosts analysis modules, visualization tools, user data spaces – Practice data federation • integrate diverse data sets from distributed sources • consume and expose data via RESTful web services – Maintain “gold standard” Col-0 annotation • assemble tissue-specific transcripts from publicly available RNA-seq datasets • incorporate novel coding and non-coding genes
4. araport.org @araport Araport https://www.araport.org • Explore data • ThaleMine • JBrowse • Science Apps • Search data • Quick Search • BLAST • Raw data downloads • Community • News & Events • Ask a question • Job Postings • Useful Links
5. araport.org @araport Araport Architecture External programs Portal (www.araport.org) API (api.araport.org) Agave Core meta data user profile ADAMA service manage service enroll a b c d e f CGI Computing Storage Databases ThaleMine JBrowse Authentication, metering, logging, versioning, HTTPS, CORS a b c d e f Apps Jobs Systems CGI InterMine Others CoGe SOAP CGI REST Science Apps
6. araport.org @araport Track selection in standard JBrowse installations Hierarchical selector Faceted selector
7. araport.org @araport Tracks at Araport • Combination of local and remotely located datasets • Local tracks generated from flat-files converted to JSON (In the near future, will be served by InterMine JBrowse web services) – Assembly, annotation, expression, similarity and variation related data – Normally associated with only a single unit of metadata (e.g. citation or text describing how data was generated) • Remote tracks are federated from CoGe via their RESTful API infrastructure – Epigenomics datasets collated from the EPIC project – Each dataset is associated with rich set of metadata tag/value pairs (such as experiment name, technique, conditions, etc.)
8. araport.org @araport Using the JBrowse plugin architecture ComboTrackSelector Hierarchical selector Faceted selector
9. araport.org @araport Configuring and enabling the plugin ComboTrackSelector Hierarchical selector Faceted selector • Uses the standard configuration file, trackList.json • Usually generated programmatically using loading scripts like flatfile-to-json.pl, etc. • Adding below plugin config stanza enables dual selectors: "plugins" : { "location" : "./plugins/ComboTrackSelector", "name" : "ComboTrackSelector" }, • Relies on a new configuration file, trackList2.json • Requires supporting comma-separated configuration file with metadata about the data • Both files above are either hand curated or programmatically generated
10. araport.org @araport Annotated sequence viewers TAIR SeqViewer
11. araport.org @araport Sequence viewer in JBrowse • JBrowse feature details windows shows region sequence and subfeatures separately • Members of the Arabidopsis community were used to working with TAIR SeqViewer and GBrowse2. But, Araport promotes usage of JBrowse over GBrowse2 • Users of our portal were missing this functionality at Araport and made requests during our portal “Preview” phase
12. araport.org @araport Developing a sequence viewer for JBrowse • Since JBrowse is client side application, widget would need to be lightweight JS for ease of integration • BioJS (http://biojs.net) library of reusable JS components was the perfect fit • Wide variety of components, not limited to: – Sequence, Chromosome karyotype – Tree, KEGGViewer – Cytoscape, Interaction Table
13. araport.org @araport Sequence viewer widget for JBrowse SeqLighter • Can be configured as a right click menu option for any track providing gene structure features "menuTemplate" : [ … { ”label" : "View Sequence", "iconClass" : "dijitIconDatabase", "action": "contentDialog", "content": "function(track,feature,div ){ return SequenceViewer(track,feature,div)}" }, … • Allows toggling annotation of various gene features (exon, intron, start/stop, UTR) • Flanking region sequences can be added (0.5 to 4 KB) • Results can be exported to SVG, PNG and JPG
14. araport.org @araport Araport on GitHub • GitHub organization: https://www.github.com/Arabidopsis-Information-Portal • Relevant repositories: – GMOD/jbrowse (fork) – jbrowse-contrib (track config)
15. araport.org @araport Tidbit (1) Generate screenshots programmatically • JBrowse does not currently have feature analogous to gbrowse_img to generate an image of desired region and set of tracks • It is possible however to disable nav/tracklist/ruler elements from the view, by setting appropriate URL parameters • Example: http://path/to/jbrowse/?tracks=A,B,C&nav= 0&tracklist=0&overview=0
16. araport.org @araport • Possible to do so, with server side JavaScript technology, nodejs (http://nodejs.org) and a headless webkit browser, PhantomJS (http://phantomjs.org) • Wrapped in command line toolkit, pageres • Install easily via Node Package manager, npm $ npm install pageres • Run simple command to generate PNG screenshots $ pageres <url> <resolution> $ pageres –d 15 \ "http://path/to/jbrowse/?tracks=A,B,C&nav=0&tracklist=0&o verview=0" 1024x768 Tidbit (1) Generate screenshots programmatically
17. araport.org @araport Tidbit (2) Streaming data files from iPlant • iPlant Data Store (iDS) provides cloud storage to researchers (initial allocation 100GB) • Several methods can be used to transfer data to and from iDS https://pods.iplantcollaborative.org/wiki/display/DS/Storing+and+Accessing+Your+Data+in+the+Data+Store – Discovery Environment web interface http://de.iplantc.org – iDrop GUI toolkit – iCommands command line interface • Instructions on wiki page describing method used to generate link(s) to BAM/BAI, VCF, GFF file on the iDS https://pods.iplantcollaborative.org/wiki/display/DEmanual/Sending+Genome+Files+to+the+Genome+Browser
18. araport.org @araport Tidbit (2) Streaming BAM files from iPlant
19. araport.org @araport Acknowledgements • JCVI Team Members – Engineers: Maria Kim – Analysts: Chia-Yi Cheng, Benjamin Rosen • Awesome dev community! • Matt Bomhoff, Eric Lyons from CoGe • iPlant Collaborative • Funding Agencies
20. araport.org @araport Chris Town, PI Lisa McDonald Education and Outreach Coordinator Chris Nelson Project Manager Jason Miller, Co-PI JCVI Technical Lead Erik Ferlanti Software Engineer Vivek Krishnakumar Bioinf. Engineer Svetlana Karamycheva Bioinf Engineer Eva Huala Project lead, TAIR Bob Muller Technical lead, TAIR Gos Micklem, co-PI Sergio Contrino Software Engineer Matt Vaughn co-PI Steve Mock Advanced Computing Interfaces Rion Dooley, Web and Cloud Services Matt Hanlon, Web and Mobile Applications Maria Kim Bioinf Engineer Ben Rosen Bioinf Analyst Joe Stubbs, API Developer Platform Walter Moreira API Developer Federation Chris Jordan Database Manager Eleanor Pence Intern Chia-Yi Cheng Bioinf Analyst Seth Schobel Bioinf. Engineer Araport Team Irina Belyaeva Software Engineer
21. araport.org @araport THANK YOU!