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Apollo: Improving Collaborative Genome Curation
Apollo is a web-based genome annotation tool designed to enhance collaborative efforts among researchers by allowing real-time editing and evidence integration for gene model refinement. It supports multiple organisms, integrates curation pipelines, and extends user functionalities through permissions management and group collaborations. The platform is developed using technologies like Google Web Toolkit and offers a structured, scalable environment for genomic analysis and curation.
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Apollo: Improving Collaborative Genome Curation
- 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 : //github. 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 SequencingCreate Assembly Synthesis & dissemination Example Genome Analysis Workflow Many tools • Many people • Lots of data • Many Iterations Annotation FGENESH
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- 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.
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- 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
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- 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
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- 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
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- 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