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

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

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Example Genome Analysis Workflow
2
Experimental design,
sampling
Comparative analyses
Curated
Gene Set
Manual
Annotation
Sequencing
Synthesis &
dissemination
Create
Assembly
FGENESH
Automated
Annotation

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Consensus
Gene Set
Synthesis &
dissemination
FGENESH
Create
Assembly
Manual
Annotation
Automated
Annotation
Experimental design,
sampling
Comparative analyses
Analysis Requires High Quality Data
Sequencing

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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

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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

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Explosion of Sequencing Data
6
Experimental design,
sampling
Comparative analyses
Curated
Gene Set
Manual
Annotation
Sequencing
Synthesis &
dissemination
FGENESH
Automated
Annotation
Create
Assembly

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

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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

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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. 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

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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. 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

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Apollo Overview
Evidence Viewer
Annotator Panel
Genome Annotation Editor

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1 - Evidence Viewer / Genome Browser
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Evidence
Transcripts
(GFF3, GBK)
BAM Reads
Transcripts
(GFF3, GBK)
BigWig XY
BigWig
HeatMap
Themes
(dark/light)
Color CDS Frame
Automated
Annotation
Manual Annotation

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1 - Evidence Viewer (Genome Browser)
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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

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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

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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

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2 - Genome Annotation Editor
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Transcripts
(GFF3, GBK)
BAM Reads
Transcripts
(GFF3, GBK)
BigWig XY
BigWig
HeatMap
Automated
Annotation
Manual Annotation
Exported Refined
Genomic Elements

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Alignments shown in red
Annotate other genomic
types with drop-down
Create Annotation
Add Annotation by
Dragging a Genomic Element

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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

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Edit Annotation Structure
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Adjust exon by dragging

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Editing Annotations
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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

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Annotation Structure History
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Revertible History of Structural Operations
Highlighted row shown
Current position

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Annotate Reference Sequence Alterations
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Alteration Reflected

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Collapsible
3 - Annotator Panel
Link to
Location
Navigate Sequence and Organism

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Search
View / Edit Details
List / Navigate Vertically
Annotations

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Reference Sequence - Search and Export
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Search
Navigation
Export Annotations

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Organism (Admin)
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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

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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

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Admin
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Predefine Curation Terms
Reports

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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

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Reviewing and correcting feature set
• exons, introns, UTRs
• repeat regions
• transposable elements
• ncRNAs
• tRNA, snRNA, snoRNA, miRNA, ncRNA, rRNA
32

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Apollo Server - Grails
Security
Architecture
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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. 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

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Scriptable Web Services
• Examples: Groovy, Perl, shell, Python
• Autogenerated REST API doc in Apollo
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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

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Track and Variant Services
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https://github.com/GMOD/GenomeFeatureComponent
D3

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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

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Integration into Workflow and Tools
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• Over 100 organizations refine annotation
• Multiple genomes per organization
NCBI Ensemble
Refined Annotations Distributed to Public

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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. • 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

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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. Extra Slides

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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

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Annotation
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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/

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• Configure apollo-config.groovy
• Grails plugin
• JBrowse plugin
• Database
• Fork
• Ask
• Web services
Integration Strategies
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https : //g ithub. org /G M O D /A pollo/
apollo@ lists.lbl. gov
Perl, Shell, Groovy, PHP, etc.

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Example
46
Automated Annotations
Manual Annotation
GFF3 FASTA BAM, etc
GFF3 FASTA CHADO VCF
Public Data
Next Workflow
https://github.com/galaxy-genome-annotation/

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Automated Annotations
JBrowse
GFF3 FASTA BAM, etc
GFF3 FASTA CHADO
TRIPAL
Next Workflow
Manual Annotation
47
Summary

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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

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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

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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

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Tracks
51
Search