Apollo enables collaborative, real-time curation (akin to Google Docs) of genomic elements using both structural and experimental information. Built on top of the JBrowse framework, Apollo is composed of a web-based client, an annotation-editing engine, and a server-side data service. Users can visualize gene models, protein alignments, and expression and variant data to conduct structural and/or functional annotations. In our most recent release, version 2.0.x, the improved architecture allows users to more easily query data and build extensions, supports multiple organisms per server, and allows additional types of sequence annotations based on the Sequence Ontology. The new, removable side-dock offers detailed view of annotations, sequences, and organisms, a new reporting structure, and WebSocket support to improve real-time communication. The new Grails framework (Spring / Hibernate / Groovy) in the server more robustly scales a single server over multiple organisms while better supporting additional curators. Apollo’s entire secure REST API is exposed, allowing genomic features to be injected into Apollo from an automated curation process or organization-specific metadata to be extracted directly from Apollo using a SQL query or REST. The new version offers improved features, including the ability to bring together 2 or more scaffolds in order to annotate genes split across them, and increases the ability to customize and integrate Apollo into modern curation pipelines. During this demonstration we will introduce the new architecture, highlight advantages for users, and detail our future plans. Project Website: http://genomearchitect.org/ Source Code: https://github.com/GMOD/Apollo License: Berkeley Software Distribution (BSD) License at https://github.com/GMOD/Apollo/blob/master/LICENSE.md

1. Nathan A Dunn
1
, Monica C. Munoz-Torres
1
, Colin
Diesh
2
, Deepak Unni
2
, Eric Yao
3
, Ian Holmes
3
,
Christine G. Elsik
2
and Suzanna Lewis
1
(1) Lawrence Berkeley National Laboratory, Berkeley, CA, (2) Division of Animal Sciences,
University of Missouri, Columbia, MO, (3) Department of Bioengineering, Berkeley, CA
Apollo: Improving Collaborative
Genome Annotation
https : //g ithub. org / G M O D /A pollo/
http: //ge nom e arc hite c t. org /

2. Genome Annotation
Structural Annotation
• exons, introns, UTRs
• repeat regions
• transp elements
• molecular evolution
• sequence conservation
Functional Annotation
• Gene Ontology
• molecular function
• biological process
• cellular component
• expression
• metabolic pathways / functions
• gene families

3. Experimental
design, sampling
Comparative
analyses
Consensus
Gene Set
Manual
Annotation
Automated
Annotation
Sequencing Create
Assembly
Synthesis &
dissemination
Example Genome Analysis Workflow
Many tools • Many people • Lots of data • Many Iterations
Annotation
FGENESH

4. Automated Identification of Genomic Features
Automated
Annotation
Generation of Gene Models
find ORFs, multiple rounds of gene
prediction, etc.
Annotation of Gene Models
Describing function, expression patterns,
metabolic network memberships
• Assembly errors can cause fragmented annotations
• Limited coverage makes precise identification difficult
Manual
Annotation

5. Human Analysis
Automated
Annotation
Manual Annotation Refines Features
Experimental Evidence
cDNAs, HMM domain searches, RNAseq,
genes from other species.
• Additional data
• Biological knowledge
• Curator experience
Manual
Annotation

6. Annotators
Apollo
Google Web Toolkit
(GWT) / Bootstrap
What is Apollo?
Annotators
Apollo
Google Web Toolkit
(GWT) / Bootstrap
Annotators
Apollo
Google Web Toolkit
(GWT) / Bootstrap
• Web-based Genome Editor
• JBrowse
• Real-time collaborative
• Automatic Save
Photo Credits: i5K; Alex Wild at http://www.alexanderwild.com/: leaf cutter ant, ensign wasp; Leo Bukeboom:
Nasonia vitripennis jewel wasp; Wikimedia Commons: Apis mellifera honey bee; Mike MacNeil USDA/ARS Fort
Keogh LARRL: Bos taurus cow.

7. Apollo Genome Editor
Navigation
User Annotations
Evidence
Transcripts
(GFF3, GBK)
BAM Reads
Transcripts
(GFF3, GBK)
BigWig XY
BigWig
HeatMap
Create Annotation
by Dragging /
Right-click
Custom Color
Schemes
Color CDS Frame

8. How to Edit Data?
Sequence Alterations
Edit Structure by Dragging
or Popup Menu
History, Undo/Redo
Edit Functional Data
• PubMed / xdbref
• Gene Ontology
• Metadata
• key/value
• status
• comments

9. Navigate while Viewing Genome
• Allows users an alternate dimensions to navigate and edit
• Well-established paradigm for “editing” in applications
Resizable / Closeable
Shareable Links

10. Search Annotations and Discover Details
Search
Navigation
View / Edit Details

11. Explore and Export Sequences
Search
Navigation

12. Add and Share Organisms
Add organisms from existing JBrowse directory
Specify “Public” organisms
that do not require a login

13. Manage Who Sees What
Add / Search Users
Edit User Organism
Permission
User Can “Admin”
an Organism

14. Work with Lots of Users and Organisms
Add User to Groups
with Permissions
Set Bulk User
Permissions
using Groups

15. How to get Apollo into your WorkFlow?
Reports
Data
Input
Data
Output
Analysis
Authentication
BLAT
(built-in)
Remote BLAST
Example Workflow

16. Server Criteria
Apollo Server
File
System
e Directories
Security
• Quick setup and easy to deploy
• Plugins (websockets, security, etc.)
• Scaleable
• Rapid Application Development
• Integrated testing
• Bonus: Minimal changes
• Mature and well-supported DataStore
• Thread-safe
transactions
• Transparent / Queryable
• Structured
• Simple Setup
REST
WebSocket
Considerations
• Node.js
• Ruby on Rails
• Grails
• Struts, Spring MVC, etc.
• Django, Php, etc.
JBrowse
Clients

17. Grails Server
Apollo Server - Grails
JDBC
File
System
ectories
Security
• Quick Setup
• Plugins
• Scaleable (Spring / Hibernate / JVM)
• Rapid Application Development
• Integrated testing
• Existing JBrowse tracks
DataStore
• Thread-safe transactions
• POJO (No XML)
• Multiple DB support
• Structured
REST
WebSocket
JBrowse
Clients

18. • Integrate with JBrowse
• Uses exposed REST
• Build your own interface
• Build Complex UI
• Well-supported
• Is JavaScript at some level
Sidebar Client Criteria
Of the Million Available Options
• Angular + Bootstrap
• jQuery all the way
• GWT + Bootstrap
• Dojo
• Other Ideas: React, Polymer, etc.
Annotators
Apollo
Google Web Toolkit
(GWT) / BootstrapJBrowse
DOJO / jQuery
Apollo
JBrowse
REST
WebSocket

19. GWT
• Java -> JS Optimized Cross-Compiler
• Google uses for Complex UI (Gmail,
Sheets, Adwords)
• Uses exposed REST
• Build your own interface (more here)
• Can still use JS / HTML wherever
GWT Sidebar Client
JBrowse Genomic Viewer
• Websockets improved
reliability / performance
Annotators
Apollo
Google Web Toolkit
(GWT) / BootstrapJBrowse
DOJO / jQuery
Apollo
JBrowse
REST
WebSocket

20. Scriptable Web Services
• Examples: Groovy, Perl, shell
• Autogenerated API-doc in Apollo
curl -d "{ 'operation': 'get_features',
‘track':'Group1.10','username':'ndunn@me.c
om','password':'demo'}" http://localhost:
8080/apollo/AnnotationEditorService

21. Apollo Server - Grails
Security
JBrowse Directories
Architecture
Web Services Client
Perl, Shell, Groovy, PHP, etc.
Annotators
Apollo
Google Web Toolkit
(GWT) / BootstrapJBrowse
DOJO / jQuery
REST
REST
WebSocket
JDBC
File
System
Apollo
JBrowse

22. • apollo-config.groovy
• Web services
• Grails plugin
• JBrowse plugin
• Database
• Fork
• Ask
• Hackathon (Jan 14, Scripps)
How to make changes and connect to Apollo
https : //g ithub. org /G M O D /A pollo/
apollo@ lists.lbl. gov

23. Example Integrations
Galaxy
Docker
GFF3 output, scriptsWeb services
VectorBase
iPlant
Collaborative

24. Manual Annotation with Apollo Improves
Gene Models
Improve annotations
• Multiple evidence sources
• Remote collaborators
• Work on multiple organisms
• Publish improved gene sets
Enable curators to do their job
• Manage multiple organisms
• Manage users and groups
• Integrate curation pipeline
• Extend Apollo to meet needs
Reports
Import
Evidence
(JBrowse) Export
Curated
Genome
Analysis
Curate
Edit
GFF3
BAM
BigWig
Explore

25. Group 20 Group 31
Future Work
Mavenize
Web Apollo
Desktop Apollo
DB backend, Sidebar,
Grails, Multi-
organism, WS
1.0
2.0
Projection2.1
2.2
Variant / phenotype
annotation
2.3
Human Data /
Client-side
Optimization
Collapse introns and space between features
Bring scaffolds together
View and link genes across scaffolds

26. • 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.
• Stephen Ficklin, GenSAS, Washington State University
• Apollo is supported by NIH grants 5R01GM080203 from
NIGMS, and 5R01HG004483 from NHGRI. Also supported
by the Director, Office of Science, Office of Basic Energy
Sciences, of the U.S. Department of Energy under Contract
No. DE-AC02-05CH11231
• Alex Wild at http://www.alexanderwild.com/: leaf cutter
ant, ensign wasp; Leo Bukeboom: Nasonia vitripennis jewel
wasp; Wikimedia Commons: Apis mellifera honey bee;
Mike MacNeil USDA/ARS
• Thanks to you and the Apollo / GMOD
Communities
Apollo
Monica Munoz-Torres
Nathan Dunn
Colin Diesh §
Deepak Unni §
JBrowse
Eric Yao
*Gene Ontology
Chris Mungall
Seth Carbon
Heiko Dietze
BBOP
Apollo: http://GenomeArchitect.org
https://github.org/GMOD/Apollo/
Questions?
NAL at USDA
Christopher Childers
Monica Poelchau
Mei-Ju Chen
Yu-Yu “Fish” Lin
Gary Moore
United States Department of Agriculture
National Institute of Food and Agriculture