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Apollo bosc-2018

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https://github.com/GMOD/Apollo
http://genomearchitect.org/

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Apollo bosc-2018

  1. 1. Nathan A. Dunn1, Deepak Unni1, Eric Yao2, Robert Buels2, Ian Holmes2, Christine G. Elsik3 and Suzanna E. Lewis1 (1) Lawrence Berkeley National Laboratory, Berkeley, CA, (2) Department of Bioengineering, Berkeley, CA, (3) Division of Animal Sciences, University of Missouri, Columbia, MO, Community Annotation with Apollo: Engaging the Collective in a Genome Annotation Workflow https : //g ithub. org /G M O D /A pollo/ http: //ge nom e arc hite c t. org / Poster: B28
  2. 2. ge nom e arc hite c t. org Example Genome Analysis Workflow 2 Experimental design, sampling Comparative analyses Curated Gene Set Manual Annotation Sequencing Synthesis & dissemination Create Assembly FGENESH Automated Annotation
  3. 3. ge nom e arc hite c t. org 3 Consensus Gene Set Synthesis & dissemination FGENESH Create Assembly Manual Annotation Automated Annotation Experimental design, sampling Comparative analyses Analysis Requires High Quality Data Sequencing
  4. 4. ge nom e arc hite c t. org 4 Consensus Gene Set Synthesis & dissemination FGENESH Create Assembly Manual Annotation Automated Annotation Experimental design, sampling Comparative analyses Analysis Requires High Quality Data Sequencing •Share Error
  5. 5. ge nom e arc hite c t. org 5 Consensus Gene Set Synthesis & dissemination FGENESH Create Assembly Manual Annotation Automated Annotation Experimental design, sampling Comparative analyses Analysis Requires High Quality Data Sequencing •Understand Error •Reduce Error
  6. 6. ge nom e arc hite c t. org Explosion of Sequencing Data 6 Experimental design, sampling Comparative analyses Curated Gene Set Manual Annotation Sequencing Synthesis & dissemination FGENESH Automated Annotation Create Assembly
  7. 7. New Genome Annotation Tool Requirements • Can assist when assemblies are poor • Support collaborators who are geographically dispersed • Intuitive user interface • Easy to install and configure to suit any lab’s sequencing workflow
  8. 8. ge nom e arc hite c t. org Automated Identification is not Perfect 8 Automated Annotation Generation of Gene Models Find ORFs, multiple rounds of gene prediction Annotation of Gene Models
 Predicting function, expression patterns, metabolic network memberships • Assembly errors can cause fragmented annotations • Limited coverage makes precise identification difficult Manual Annotation
  9. 9. ge nom e arc hite c t. org Human Analysis Automated Annotation Manual Annotation Refines Genome 9 Experimental Evidence cDNAs, HMM domain searches, RNAseq, genes from other species. Manual Annotation • Additional analysis is dynamic • Make use of the researcher’s expertise • Integrate all underlying evidence
  10. 10. New Genome Annotation Tool Requirements • Can assist when assemblies are poor • Support collaborators who are geographically dispersed • Intuitive user interface • Easy to install and configure to suit any lab’s sequencing workflow
  11. 11. ge nom e arc hite c t. org 11 Annotators Apollo Google Web Toolkit (GWT) / Bootstrap Apollo is a Tool for Collaborative Annotation Annotators Apollo Google Web Toolkit (GWT) / Bootstrap Annotators Apollo Google Web Toolkit (GWT) / Bootstrap Biology is a team sport Manual tasks require more hands
  12. 12. New Genome Annotation Tool Requirements • Can assist when assemblies are poor • Support collaborators who are geographically dispersed • Intuitive user interface • Easy to install and configure to suit any lab’s sequencing workflow
  13. 13. ge nom e arc hite c t. org Apollo Overview Evidence Viewer Annotator Panel Genome Annotation Editor
  14. 14. ge nom e arc hite c t. org 1 - Evidence Viewer / Genome Browser 14 Evidence Transcripts (GFF3, GBK) BAM Reads Transcripts (GFF3, GBK) BigWig XY BigWig HeatMap Themes (dark/light) Color CDS Frame Automated Annotation Manual Annotation
  15. 15. ge nom e arc hite c t. org 1 - Evidence Viewer (Genome Browser) 15 Dynamically Open Configure Multiple Tracks addStores={"url":{"type":"JBrowse/Store/SeqFeature/ GFF3","urlTemplate":"http://host/genes.gff"}} &addTracks=[{"label":"genes","type":"JBrowse/View/ Track/CanvasFeatures","store":"url"}] Append via URL Statically Configure • BAM • BigWig • GFF • GTF • GBK • VCF • FASTA • FASTAi • SPARQL • custom types (e.g., REST end- point) https://gmod.github.io/jbrowse-registry/Customizable Views
  16. 16. ge nom e arc hite c t. org Sashimi Plot – Converts RNA-seq BAM files into intron support coverage features. Multi Variant Viewer – Multi-VCF viewer 1000 Genomes JBrowse Plugin Registry https://gmod.github.io/jbrowse-registry/ 44 registered plugins Lollipop, SVG Tracks with MyVariants.info plugin @cmdcolin
  17. 17. ge nom e arc hite c t. org JBrowse / JBServer DATABASE Any DB: MySql, Postgre, MongoDB, Redis, … JBServer Hooks (Plugins) Client & Server Plugins Apache, Nginx, … Client Only – HTTP (Traditional) JBrowse REST API / HTTP Socket.io (WebSockets) Waterline ORM Client Traditional JBrowse Plugins … JBServer Or Custom Workflows Workflow Service Ie: JBlast … JBConnect @enuggetry JBrowse Server Queueing (e.g., JBlast) Connect to Remote (e.g., Galaxy)
 and Local Servers
  18. 18. ge nom e arc hite c t. org 2 - Genome Annotation Editor 18 Transcripts (GFF3, GBK) BAM Reads Transcripts (GFF3, GBK) BigWig XY BigWig HeatMap Automated Annotation Manual Annotation Exported Refined Genomic Elements
  19. 19. ge nom e arc hite c t. org 19 Alignments shown in red Annotate other genomic types with drop-down Create Annotation Add Annotation by Dragging a Genomic Element
  20. 20. ge nom e arc hite c t. org 20 Create Variant Annotation (2.1.0) Add Variant Annotation by Dragging a Genomic Element Or by a Right-click @deepakunni3 Copy / Edit Properties Export VCF
  21. 21. ge nom e arc hite c t. org Edit Annotation Structure 21 Adjust exon by dragging
  22. 22. ge nom e arc hite c t. org Editing Annotations 22 Edit Additional Structural Data (right-click popup) Edit Associations • PubMed / dbxref • Gene Ontology • Metadata • key/value • status • comments Change Annotation Type History of Structural Edits
  23. 23. ge nom e arc hite c t. org Annotation Structure History 23 Revertible History of Structural Operations Highlighted row shown Current position
  24. 24. ge nom e arc hite c t. org Annotate Reference Sequence Alterations 24 Alteration Reflected
  25. 25. ge nom e arc hite c t. org 25 Collapsible 3 - Annotator Panel Link to Location Navigate Sequence and Organism
  26. 26. ge nom e arc hite c t. org 26 Search View / Edit Details List / Navigate Vertically Annotations
  27. 27. ge nom e arc hite c t. org Reference Sequence - Search and Export 27 Search Navigation Export Annotations
  28. 28. ge nom e arc hite c t. org Organism (Admin) 28 Import JBrowse directory Share “Public” organisms Genome Res. 2009 Sep;19(9):1630-8. doi: 10.1101/gr.094607.109 Create JBrowse tracks from FASTA / GFF3 / BAM / BigWig
  29. 29. ge nom e arc hite c t. org Users and Groups (Admin) Add / Search Users Edit User Permission Use Groups to Manage Bulk Permissions • Edit user permissions • Create / edit organisms Added Instructor Role to Manage Organisms http://gonramp.wustl.edu/ @Yating-L
  30. 30. ge nom e arc hite c t. org Admin 30 Predefine Curation Terms Reports
  31. 31. ge nom e arc hite c t. org Summary of Features Evidence Viewer Annotator Panel Customizable Multiple data types Easy to navigate Fast Visual Feedback History Alternate view of data Simplified administration Structural + Functional Genome Annotation Editor
  32. 32. ge nom e arc hite c t. org Reviewing and correcting feature set • exons, introns, UTRs • repeat regions • transposable elements • ncRNAs • tRNA, snRNA, snoRNA, miRNA, ncRNA, rRNA 32
  33. 33. ge nom e arc hite c t. org Apollo Server - Grails Security Architecture 33 Web Services Client Perl, Shell, Groovy, PHP, etc. Annotators Apollo Google Web Toolkit (GWT) / BootstrapJBrowse DOJO / jQuery WebSocket JDBC File System Apollo Client(s) Server REST
  34. 34. New Genome Annotation Tool Requirements • Can assist when assemblies are poor • Support collaborators who are geographically dispersed • Intuitive user interface • Easy to install and configure to suit any lab’s sequencing workflow
  35. 35. ge nom e arc hite c t. org Scriptable Web Services • Examples: Groovy, Perl, shell, Python • Autogenerated REST API doc in Apollo 35 curl -d "{ 'operation': 'get_features', ‘track':'Group1.10','username':'ndunn@me.c om','password':'demo'}" http://localhost: 8080/apollo/AnnotationEditorService Create Organisms and Tracks on the Fly @erasche @deepakunni3
  36. 36. ge nom e arc hite c t. org Track and Variant Services 36 https://github.com/GMOD/GenomeFeatureComponent D3
  37. 37. ge nom e arc hite c t. org Python API 37 https://pypi.org/project/apollo/ @erasche @luke-c-sargent @Yating-L http://gonramp.wustl.edu/ @abretaud https://github.com/galaxy-genome-annotation/python-apollo Automated Annotations Manual Annotation GFF3 FASTA BAM, etc GFF3 FASTA CHADO VCF
  38. 38. ge nom e arc hite c t. org Integration into Workflow and Tools 38 • Over 100 organizations refine annotation • Multiple genomes per organization NCBI Ensemble Refined Annotations Distributed to Public
  39. 39. ge nom e arc hite c t. org Summary AnnotApollo Google Web Toolkit (GWT) / Bootstrap Apollo Google Web Toolkit (GWT) / Bootstrap Apollo Google Web Toolkit (GWT) / Bootstrap Real-time collaborative Researchers refine genome annotations Integrates within workflow FGE Visual evidence and feedback
  40. 40. • Berkeley Bioinformatics Open-source Projects (BBOP), Berkeley Lab: Apollo and Gene Ontology teams. Suzanna E. Lewis (PI). • § Christine G. Elsik (PI). University of Missouri. • * Ian Holmes (PI). University of California Berkeley. • Apollo was supported by NIH grants 5R01GM080203 from NIGMS, and 5R01HG004483 from NHGRI. • Thanks to you and the Apollo and GMOD Communities Apollo Nathan Dunn Deepak Unni JBrowse* Eric Yao Robert Buels “Galaxy” Eric Rasche Anthony Bretaudeau Yating Lui Luke Sargent BBOP Apollo: http://genomearchitect.org https://github.org/GMOD/Apollo/ Thank You Alumni Monica Munoz- Torres Colin Diesh* Gene Ontology Chris Mungall Seth Carbon Poster: B28
  41. 41. ge nom e arc hite c t. org Future? • Improved widget integration • Tapering support, Collaborators? • Further integrations • Micro-attributions • Phenotypes • Variant Effect • ??? • apollo@lbl.gov (tomorrow) • There *was* a JB birds of a feather today • JBrowse Collaboration Fest Friday-Sunday • https://gitter.im/GMOD/jbrowse Activities Poster: B28 Questions? http://genomearchitect.org GMOD/Apollo Getting Apollo
  42. 42. Extra Slides
  43. 43. ge nom e arc hite c t. org https://hub.docker.com/r/jbrowse/gmod-jbrowse/ Desktop Electron App @cmdcolin Getting JBrowse https://www.npmjs.com/package/@gmod/jbrowse @erasche http://jbrowse.org @rbuels
  44. 44. ge nom e arc hite c t. org Annotation 44 Structural Annotation • exons, introns, UTRs • repeat regions • transposable elements • tRNA, snRNA, snoRNA, miRNA, ncRNA, rRNA Functional Annotation • metabolic pathways / functions • Gene Ontology • molecular function • biological process • cellular component • expression • gene families http://geneontology.org Photo Credit: Alex Wild at http://www.alexanderwild.com/
  45. 45. ge nom e arc hite c t. org • Configure apollo-config.groovy • Grails plugin • JBrowse plugin • Database • Fork • Ask • Web services Integration Strategies 45 https : //g ithub. org /G M O D /A pollo/ apollo@ lists.lbl. gov Perl, Shell, Groovy, PHP, etc.
  46. 46. ge nom e arc hite c t. org Example 46 Automated Annotations Manual Annotation GFF3 FASTA BAM, etc GFF3 FASTA CHADO VCF Public Data Next Workflow https://github.com/galaxy-genome-annotation/
  47. 47. ge nom e arc hite c t. org 47 Automated Annotations JBrowse GFF3 FASTA BAM, etc GFF3 FASTA CHADO TRIPAL Next Workflow Manual Annotation 47 Summary
  48. 48. ge nom e arc hite c t. org Apollo Server - Grails Security Architecture 48 Web Services Client Perl, Shell, Groovy, PHP, etc. Annotators Apollo Google Web Toolkit (GWT) / BootstrapJBrowse DOJO / jQuery WebSocket JDBC File System Apollo Client(s) Server REST
  49. 49. ge nom e arc hite c t. org Apollo Server - Grails Security Architecture 49 Web Services Client Perl, Shell, Groovy, PHP, etc. Annotators Apollo Google Web Toolkit (GWT) / BootstrapJBrowse DOJO / jQuery WebSocket JDBC File System Apollo Server Client(s) REST
  50. 50. ge nom e arc hite c t. org Apollo Server - Grails Security Architecture 50 Web Services Client Perl, Shell, Groovy, PHP, etc. Annotators Apollo Google Web Toolkit (GWT) / BootstrapJBrowse DOJO / jQuery WebSocket JDBC File System Apollo Server Client(s) REST
  51. 51. ge nom e arc hite c t. org Tracks 51 Search

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