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
   

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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
   

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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
   

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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
   

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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
   

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6. araport.org
   @araport
   Track selection in standard JBrowse
   installations
   Hierarchical selector Faceted selector
   

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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.)
   

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8. araport.org
   @araport
   Using the JBrowse plugin architecture
   ComboTrackSelector
   Hierarchical selector Faceted selector
   

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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
   

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10. araport.org
    @araport
    Annotated sequence viewers
    TAIR SeqViewer
    

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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
    

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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
    

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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
    

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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)
    

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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
    

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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
    $ pageres –d 15 \
    "http://path/to/jbrowse/?tracks=A,B,C&nav=0&tracklist=0&o
    verview=0" 1024x768
    Tidbit (1)
    Generate screenshots programmatically
    

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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
    

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18. araport.org
    @araport
    Tidbit (2)
    Streaming BAM files from iPlant
    

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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
    

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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
    

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21. araport.org
    @araport
    THANK YOU!
    

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