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APOLLO: Scalable and
collaborative genome curation
Monica Munoz-Torres, PhD | @monimunozto



Nathan Dunn, Colin Diesh*, Deepak Unni*, Seth Carbon, Heiko Dietze, Christopher
Mungall, Nicole Washington, Ian Holmes*, Christine Elsik*, and Suzanna E. Lewis



Berkeley Bioinformatics Open-Source Projects

Genomics Division, Lawrence Berkeley National Laboratory



8th International Biocuration Conference. Beijing, China. 24 April, 2015
OUTLINE

•  LAST	
  TIME	
  
where	
  we	
  le.	
  off	
  last	
  year	
  
	
  
•  IMPROVEMENTS	
  
architecture,	
  scalability,	
  features	
  
	
  
•  COLLABORATIONS	
  
JBrowse	
  &	
  GenSAS	
  
	
  
•  FUTURE	
  PLANS	
  
what	
  lies	
  on	
  the	
  horizon	
  
Apollo	
  Scalable	
  and	
  CollaboraJve	
  	
  
Genome	
  CuraJon	
  
2OUTLINE
APOLLO

genome annotation editing tool
3
v  Web	
  based,	
  integrated	
  with	
  JBrowse.	
  
v  Supports	
  real	
  Jme	
  collaboraJon!	
  
v  AutomaJc	
  generaJon	
  of	
  ready-­‐made	
  computable	
  data.	
  	
  
v  Supports	
  annotaJon	
  of	
  genes,	
  	
  pseudogenes,	
  tRNAs,	
  snRNAs,	
  
snoRNAs,	
  ncRNAs,	
  miRNAs,	
  TEs,	
  and	
  repeats.	
  
v  IntuiJve	
  annotaJon,	
  gestures,	
  and	
  pull-­‐down	
  menus	
  to	
  create	
  and	
  
edit	
  transcripts	
  and	
  exons	
  structures,	
  insert	
  comments	
  (CV,	
  freeform	
  
text),	
  GO	
  terms,	
  etc.	
  
INTRODUCTION
DETAILS FROM OUR LAST UPDATE

•  ~	
  100	
  insJtuJons	
  worldwide	
  	
  
•  >	
  60	
  genomes	
  across	
  the	
  tree	
  of	
  life:	
  	
  
•  from	
  plants	
  to	
  arthropods,	
  to	
  fungi,	
  	
  
to	
  fish	
  and	
  other	
  vertebrates	
  including	
  
human,	
  bovine	
  ca]le,	
  and	
  dog	
  
PREVIOUSLY WE LEARNED 4
©BroadInsJtute.org	
  	
  
Nature Rev Gen 2009
©alexanderwild.com
©alexanderwild.com
©outdooralabama.com
National
Agricultural
Library
LESSONS WE HAVE LEARNED

What	
  we	
  have	
  learned:	
  	
  
•  CollaboraJve	
  work	
  disJlls	
  invaluable	
  knowledge	
  
•  We	
  must	
  enforce	
  strict	
  rules	
  and	
  formats	
  
•  We	
  must	
  evolve	
  with	
  the	
  data	
  
•  A	
  li]le	
  training	
  goes	
  a	
  long	
  way	
  
•  NGS	
  poses	
  addiJonal	
  challenges	
  
PREVIOUSLY WE LEARNED 5
HIGHLIGHTED IMPROVEMENTS

scalability
SCALABILITY 6
•  Easier	
  deployment,	
  more	
  detailed	
  documentaJon	
  
•  Supports	
  mulJple	
  organisms	
  per	
  server,	
  improved	
  comparaJve	
  tools	
  
•  Easier	
  to	
  query	
  the	
  data	
  and	
  build	
  extensions	
  
	
  
•  More	
  flexible	
  user	
  interface	
  via	
  removable	
  side-­‐dock	
  with	
  customizable	
  tabs;	
  
be]er	
  search	
  funcJonality,	
  validaJon	
  checks,	
  and	
  ediJng	
  capability	
  
	
  
•  Allows	
  larger	
  set	
  of	
  sequence	
  annotaJons	
  based	
  on	
  the	
  Sequence	
  Ontology	
  
•  Offers	
  fine-­‐grained	
  user	
  and	
  group	
  level	
  permissions	
  
NEW APOLLO ARCHITECTURE

simpler, more flexible
ARCHITECTURE 7
Web-­‐based	
  client	
  +	
  annotaJon-­‐ediJng	
  engine	
  +	
  server-­‐side	
  data	
  service	
  
REST / JSON
Websockets
Annotation Engine (Server)
Shiro
LDAP
OAuth
JBrowse Data
Organism 2
Annotations
Security
Preferences
Organisms
Tracks
BAM
BED
VCF
GFF3
BigWig
Annotators
Google Web Toolkit (GWT) /
Bootstrap
JBrowse DOJO / jQuery JBrowse Data
Organism 1
Load genomic
evidence for
selected organism
Single Data Store
PostgreSQL, MySQL,
MongoDB, ElasticSearch
Apollo v2.0
NEW APOLLO ARCHITECTURE

simpler, more flexible
ARCHITECTURE 8
REST / JSON
Websockets
Annotation Engine (Server)
Shiro
LDAP
OAuth
JBrowse Data
Organism 2
Annotations
Security
Preferences
Organisms
Tracks
BAM
BED
VCF
GFF3
BigWig
Annotators
Google Web Toolkit (GWT) /
Bootstrap
JBrowse DOJO / jQuery JBrowse Data
Organism 1
Single Data Store
PostgreSQL, MySQL,
MongoDB, ElasticSearch
Apollo v2.0
Single Data Store
PostgreSQL, MySQL,
MongoDB, ElasticSearch
	
  	
  
Grails controllers (J2EE servlet) route
requests to the appropriate JBrowse
data directory for a given organismNEW!
Load genomic
evidence for
selected organism
NEW APOLLO ARCHITECTURE

simpler, more flexible
ARCHITECTURE 9
REST / JSON
Websockets
Annotation Engine (Server)
Shiro
LDAP
OAuth
JBrowse Data
Organism 2
Annotations
Security
Preferences
Organisms
Tracks
BAM
BED
VCF
GFF3
BigWig
Annotators
Google Web Toolkit (GWT) /
Bootstrap
JBrowse DOJO / jQuery JBrowse Data
Organism 1
Single Data Store
PostgreSQL, MySQL,
MongoDB, ElasticSearch
Apollo v2.0
Load genomic
evidence for
selected organism
Single Data Store
PostgreSQL, MySQL,
MongoDB, ElasticSearch
A single, queryable datastore houses annotations
NEW!
Apollo v2.0
HIGHLIGHTED IMPROVEMENTS

scalability
SCALABILITY 10
•  Improvements	
  to	
  architecture:	
  easier	
  deployment,	
  be]er	
  documentaJon	
  
•  Supports	
  mulJple	
  organisms	
  per	
  server,	
  improved	
  comparaJve	
  tools	
  
•  Easier	
  to	
  query	
  the	
  data	
  and	
  build	
  extensions	
  
	
  
•  More	
  flexible	
  user	
  interface	
  via	
  removable	
  side-­‐dock	
  with	
  customizable	
  tabs;	
  
be]er	
  search	
  funcJonality,	
  validaJon	
  checks,	
  and	
  ediJng	
  capability	
  
	
  
•  Allows	
  larger	
  set	
  of	
  sequence	
  annotaJons	
  based	
  on	
  the	
  Sequence	
  Ontology	
  
	
  
•  Offers	
  fine-­‐grained	
  user	
  and	
  group	
  level	
  permissions	
  
HIGHLIGHTED IMPROVEMENTS

removable side dock with customizable tabs
HIGHLIGHTED IMPROVEMENTS 11
Tracks Organism Users Groups PreferencesAnnotations
Reference
Sequence
HIGHLIGHTED IMPROVEMENTS

annotation details, exon boundaries, data export
HIGHLIGHTED IMPROVEMENTS 12
Annotations Reference
Sequences
1 2 3
1
2
3
HIGHLIGHTED IMPROVEMENTS

visible in the Apollo window
HIGHLIGHTED IMPROVEMENTS 13
AutomaJcally	
  calculates	
  upstream	
  and	
  
downstream	
  acceptor	
  and	
  donor	
  sites.	
  
OTHER IMPROVEMENTS

behind the scenes
OTHER IMPROVEMENTS 14
h]ps://github.com/GMOD/Apollo	
  
APOLLO

demonstration
DEMO 15
See	
  Apollo	
  DemonstraJon	
  Video	
  at:	
  
h]ps://youtu.be/VgPtAP_fvxY	
  	
  	
  
COLLABORATIONS

Apollo is open-source and extensible
HIGHLIGHTED IMPROVEMENTS 16
The Genome Sequence Annotation Server (GenSAS)
Annotate
Examples:	
  	
  
•  GenSAS	
  	
  
whole-­‐genome	
  structural	
  
annotaJon	
  pipeline.	
  
•  i5K	
  Workspace@NAL	
  
space	
  to	
  display	
  and	
  share	
  
genome	
  assemblies	
  &	
  
gene	
  models,	
  and	
  conduct	
  
manual	
  annotaJon	
  
efforts.	
  
Apollo	
  users	
  can	
  add	
  so.ware	
  to	
  support	
  their	
  own	
  workflow.	
  
FUTURE PLANS

currently working on
Footer 17
JOIN US

Footer 18
h]p://GenomeArchitect.org/	
  
Nathan	
  Dunn	
  	
  
Apollo	
  Technical	
  Lead	
  
Please	
  bring	
  your	
  suggesJons,	
  requests,	
  
and	
  contribuJons	
  to:	
  
Special	
  Thanks	
  to:	
  
Stephen	
  Ficklin	
  
GenSAS,	
  Washington	
  
State	
  University	
  	
  
Deepak	
  Unni	
  
Colin	
  Diesh	
  
Apollo	
  Developers,	
  	
  
University	
  of	
  Missouri	
  
Suzi	
  Lewis	
  
Principal	
  InvesJgator	
  
BBOP	
  
Eric	
  Yao	
  
JBrowse,	
  UC	
  Berkeley	
  
•  Berkeley	
  Bioinforma9cs	
  Open-­‐source	
  Projects	
  (BBOP),	
  
Berkeley	
  Lab:	
  Web	
  Apollo	
  and	
  Gene	
  Ontology	
  teams.	
  
Suzanna	
  E.	
  Lewis	
  (PI).	
  
•  §	
  Chris5ne	
  G.	
  Elsik	
  (PI).	
  University	
  of	
  Missouri.	
  	
  
•  *	
  Ian	
  Holmes	
  (PI).	
  University	
  of	
  California	
  Berkeley.	
  
•  Arthropod	
  genomics	
  community:	
  i5K	
  Steering	
  
Commi]ee	
  (esp.	
  Sue	
  Brown	
  (Kansas	
  State)),	
  Alexie	
  
Papanicolaou	
  (UWS),	
  BGI,	
  Oliver	
  Niehuis	
  (1KITE	
  
h]p://www.1kite.org/),	
  and	
  the	
  Honey	
  Bee	
  Genome	
  
Sequencing	
  ConsorJum.	
  
•  Apollo	
  is	
  supported	
  by	
  NIH	
  grants	
  5R01GM080203	
  from	
  
NIGMS,	
  and	
  5R01HG004483	
  from	
  NHGRI;	
  by	
  Contract	
  
No.	
  60-­‐8260-­‐4-­‐005	
  from	
  the	
  NaJonal	
  Agricultural	
  Library	
  
(NAL)	
  at	
  the	
  United	
  States	
  Department	
  of	
  Agriculture	
  
(USDA);	
  and	
  by	
  the	
  Director,	
  Office	
  of	
  Science,	
  Office	
  of	
  
Basic	
  Energy	
  Sciences,	
  of	
  the	
  U.S.	
  Department	
  of	
  Energy	
  
under	
  Contract	
  No.	
  DE-­‐AC02-­‐05CH11231.	
  
•  Insect	
  images	
  used	
  with	
  permission:	
  
h]p://AlexanderWild.com	
  
•  For	
  your	
  aAen9on,	
  thank	
  you!	
  
Thank you. 19
Web	
  Apollo	
  
Nathan	
  Dunn	
  
Colin	
  Diesh	
  §	
  
Deepak	
  Unni	
  §	
  	
  
	
  
Gene	
  Ontology	
  
Chris	
  Mungall	
  
Seth	
  Carbon	
  
Heiko	
  Dietze	
  
	
  
BBOP	
  
Web	
  Apollo:	
  h]p://GenomeArchitect.org	
  	
  
i5K:	
  h]p://arthropodgenomes.org/wiki/i5K	
  
GO:	
  h]p://GeneOntology.org	
  
Thanks!	
  
NAL	
  at	
  USDA	
  
Monica	
  Poelchau	
  
Christopher	
  Childers	
  
Gary	
  Moore	
  
HGSC	
  at	
  BCM	
  
fringy	
  Richards	
  
Dan	
  Hughes	
  
Kim	
  Worley	
  
	
  
JBrowse	
   	
   	
   	
  	
  Eric	
  Yao	
  *	
  

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Apollo: Scalable & collaborative curation of genomes - Biocuration 2015

  • 1. APOLLO: Scalable and collaborative genome curation Monica Munoz-Torres, PhD | @monimunozto
 
 Nathan Dunn, Colin Diesh*, Deepak Unni*, Seth Carbon, Heiko Dietze, Christopher Mungall, Nicole Washington, Ian Holmes*, Christine Elsik*, and Suzanna E. Lewis
 
 Berkeley Bioinformatics Open-Source Projects
 Genomics Division, Lawrence Berkeley National Laboratory
 
 8th International Biocuration Conference. Beijing, China. 24 April, 2015
  • 2. OUTLINE
 •  LAST  TIME   where  we  le.  off  last  year     •  IMPROVEMENTS   architecture,  scalability,  features     •  COLLABORATIONS   JBrowse  &  GenSAS     •  FUTURE  PLANS   what  lies  on  the  horizon   Apollo  Scalable  and  CollaboraJve     Genome  CuraJon   2OUTLINE
  • 3. APOLLO
 genome annotation editing tool 3 v  Web  based,  integrated  with  JBrowse.   v  Supports  real  Jme  collaboraJon!   v  AutomaJc  generaJon  of  ready-­‐made  computable  data.     v  Supports  annotaJon  of  genes,    pseudogenes,  tRNAs,  snRNAs,   snoRNAs,  ncRNAs,  miRNAs,  TEs,  and  repeats.   v  IntuiJve  annotaJon,  gestures,  and  pull-­‐down  menus  to  create  and   edit  transcripts  and  exons  structures,  insert  comments  (CV,  freeform   text),  GO  terms,  etc.   INTRODUCTION
  • 4. DETAILS FROM OUR LAST UPDATE
 •  ~  100  insJtuJons  worldwide     •  >  60  genomes  across  the  tree  of  life:     •  from  plants  to  arthropods,  to  fungi,     to  fish  and  other  vertebrates  including   human,  bovine  ca]le,  and  dog   PREVIOUSLY WE LEARNED 4 ©BroadInsJtute.org     Nature Rev Gen 2009 ©alexanderwild.com ©alexanderwild.com ©outdooralabama.com National Agricultural Library
  • 5. LESSONS WE HAVE LEARNED
 What  we  have  learned:     •  CollaboraJve  work  disJlls  invaluable  knowledge   •  We  must  enforce  strict  rules  and  formats   •  We  must  evolve  with  the  data   •  A  li]le  training  goes  a  long  way   •  NGS  poses  addiJonal  challenges   PREVIOUSLY WE LEARNED 5
  • 6. HIGHLIGHTED IMPROVEMENTS
 scalability SCALABILITY 6 •  Easier  deployment,  more  detailed  documentaJon   •  Supports  mulJple  organisms  per  server,  improved  comparaJve  tools   •  Easier  to  query  the  data  and  build  extensions     •  More  flexible  user  interface  via  removable  side-­‐dock  with  customizable  tabs;   be]er  search  funcJonality,  validaJon  checks,  and  ediJng  capability     •  Allows  larger  set  of  sequence  annotaJons  based  on  the  Sequence  Ontology   •  Offers  fine-­‐grained  user  and  group  level  permissions  
  • 7. NEW APOLLO ARCHITECTURE
 simpler, more flexible ARCHITECTURE 7 Web-­‐based  client  +  annotaJon-­‐ediJng  engine  +  server-­‐side  data  service   REST / JSON Websockets Annotation Engine (Server) Shiro LDAP OAuth JBrowse Data Organism 2 Annotations Security Preferences Organisms Tracks BAM BED VCF GFF3 BigWig Annotators Google Web Toolkit (GWT) / Bootstrap JBrowse DOJO / jQuery JBrowse Data Organism 1 Load genomic evidence for selected organism Single Data Store PostgreSQL, MySQL, MongoDB, ElasticSearch Apollo v2.0
  • 8. NEW APOLLO ARCHITECTURE
 simpler, more flexible ARCHITECTURE 8 REST / JSON Websockets Annotation Engine (Server) Shiro LDAP OAuth JBrowse Data Organism 2 Annotations Security Preferences Organisms Tracks BAM BED VCF GFF3 BigWig Annotators Google Web Toolkit (GWT) / Bootstrap JBrowse DOJO / jQuery JBrowse Data Organism 1 Single Data Store PostgreSQL, MySQL, MongoDB, ElasticSearch Apollo v2.0 Single Data Store PostgreSQL, MySQL, MongoDB, ElasticSearch     Grails controllers (J2EE servlet) route requests to the appropriate JBrowse data directory for a given organismNEW! Load genomic evidence for selected organism
  • 9. NEW APOLLO ARCHITECTURE
 simpler, more flexible ARCHITECTURE 9 REST / JSON Websockets Annotation Engine (Server) Shiro LDAP OAuth JBrowse Data Organism 2 Annotations Security Preferences Organisms Tracks BAM BED VCF GFF3 BigWig Annotators Google Web Toolkit (GWT) / Bootstrap JBrowse DOJO / jQuery JBrowse Data Organism 1 Single Data Store PostgreSQL, MySQL, MongoDB, ElasticSearch Apollo v2.0 Load genomic evidence for selected organism Single Data Store PostgreSQL, MySQL, MongoDB, ElasticSearch A single, queryable datastore houses annotations NEW! Apollo v2.0
  • 10. HIGHLIGHTED IMPROVEMENTS
 scalability SCALABILITY 10 •  Improvements  to  architecture:  easier  deployment,  be]er  documentaJon   •  Supports  mulJple  organisms  per  server,  improved  comparaJve  tools   •  Easier  to  query  the  data  and  build  extensions     •  More  flexible  user  interface  via  removable  side-­‐dock  with  customizable  tabs;   be]er  search  funcJonality,  validaJon  checks,  and  ediJng  capability     •  Allows  larger  set  of  sequence  annotaJons  based  on  the  Sequence  Ontology     •  Offers  fine-­‐grained  user  and  group  level  permissions  
  • 11. HIGHLIGHTED IMPROVEMENTS
 removable side dock with customizable tabs HIGHLIGHTED IMPROVEMENTS 11 Tracks Organism Users Groups PreferencesAnnotations Reference Sequence
  • 12. HIGHLIGHTED IMPROVEMENTS
 annotation details, exon boundaries, data export HIGHLIGHTED IMPROVEMENTS 12 Annotations Reference Sequences 1 2 3 1 2 3
  • 13. HIGHLIGHTED IMPROVEMENTS
 visible in the Apollo window HIGHLIGHTED IMPROVEMENTS 13 AutomaJcally  calculates  upstream  and   downstream  acceptor  and  donor  sites.  
  • 14. OTHER IMPROVEMENTS
 behind the scenes OTHER IMPROVEMENTS 14 h]ps://github.com/GMOD/Apollo  
  • 15. APOLLO
 demonstration DEMO 15 See  Apollo  DemonstraJon  Video  at:   h]ps://youtu.be/VgPtAP_fvxY      
  • 16. COLLABORATIONS
 Apollo is open-source and extensible HIGHLIGHTED IMPROVEMENTS 16 The Genome Sequence Annotation Server (GenSAS) Annotate Examples:     •  GenSAS     whole-­‐genome  structural   annotaJon  pipeline.   •  i5K  Workspace@NAL   space  to  display  and  share   genome  assemblies  &   gene  models,  and  conduct   manual  annotaJon   efforts.   Apollo  users  can  add  so.ware  to  support  their  own  workflow.  
  • 18. JOIN US
 Footer 18 h]p://GenomeArchitect.org/   Nathan  Dunn     Apollo  Technical  Lead   Please  bring  your  suggesJons,  requests,   and  contribuJons  to:   Special  Thanks  to:   Stephen  Ficklin   GenSAS,  Washington   State  University     Deepak  Unni   Colin  Diesh   Apollo  Developers,     University  of  Missouri   Suzi  Lewis   Principal  InvesJgator   BBOP   Eric  Yao   JBrowse,  UC  Berkeley  
  • 19. •  Berkeley  Bioinforma9cs  Open-­‐source  Projects  (BBOP),   Berkeley  Lab:  Web  Apollo  and  Gene  Ontology  teams.   Suzanna  E.  Lewis  (PI).   •  §  Chris5ne  G.  Elsik  (PI).  University  of  Missouri.     •  *  Ian  Holmes  (PI).  University  of  California  Berkeley.   •  Arthropod  genomics  community:  i5K  Steering   Commi]ee  (esp.  Sue  Brown  (Kansas  State)),  Alexie   Papanicolaou  (UWS),  BGI,  Oliver  Niehuis  (1KITE   h]p://www.1kite.org/),  and  the  Honey  Bee  Genome   Sequencing  ConsorJum.   •  Apollo  is  supported  by  NIH  grants  5R01GM080203  from   NIGMS,  and  5R01HG004483  from  NHGRI;  by  Contract   No.  60-­‐8260-­‐4-­‐005  from  the  NaJonal  Agricultural  Library   (NAL)  at  the  United  States  Department  of  Agriculture   (USDA);  and  by  the  Director,  Office  of  Science,  Office  of   Basic  Energy  Sciences,  of  the  U.S.  Department  of  Energy   under  Contract  No.  DE-­‐AC02-­‐05CH11231.   •  Insect  images  used  with  permission:   h]p://AlexanderWild.com   •  For  your  aAen9on,  thank  you!   Thank you. 19 Web  Apollo   Nathan  Dunn   Colin  Diesh  §   Deepak  Unni  §       Gene  Ontology   Chris  Mungall   Seth  Carbon   Heiko  Dietze     BBOP   Web  Apollo:  h]p://GenomeArchitect.org     i5K:  h]p://arthropodgenomes.org/wiki/i5K   GO:  h]p://GeneOntology.org   Thanks!   NAL  at  USDA   Monica  Poelchau   Christopher  Childers   Gary  Moore   HGSC  at  BCM   fringy  Richards   Dan  Hughes   Kim  Worley     JBrowse          Eric  Yao  *