APOLLO: developers call

Nathan Dunn, Monica Munoz-Torres, Colin Diesh§, Deepak Unni§, Ian Holmes, Christine G. Elsik§, and Suzanna Lewis. Berkeley Bioinformatics Open-Source Projects (BBOP), Genomics Division, Lawrence Berkeley National Laboratory. § Divisions of Animal and Plant Sciences, University of MissouriApollo Developers Open Call – February 5th, 2015

OUTLINE

PROGRESS  UPDATE    •  MILESTONE  2.0    

•  ARCHITECTURE  simpler,  extensible  

•  LAYOUT  what’s  new?  

 •  MILESTONE  1.0.4  

pending  issues,  Lmeline  for  tesLng  and  release  

 •  FROM  THE  COMMUNITY  

quesLons,  comments,  updates  

Web  Apollo  CollaboraLve  CuraLon  and    InteracLve  Analysis  of  Genomes  

2

APOLLO MILESTONE 2.0 3

MILESTONE 2.0

APOLLO ARCHITECTURE 4

ARCHITECTURE

APOLLO ARCHITECTURE 5

ARCHITECTURE(continued)

APOLLO LAYOUT 6

LAYOUT

APOLLO LAYOUT 7

Multiple Organisms

APOLLO LAYOUT 8

Reference Sequence Search & Selection

APOLLO LAYOUT 9

Track Details & Selection

APOLLO LAYOUT 10

Details per feature

APOLLO LAYOUT 11

Checks & Warnings

Details per exon

APOLLO MIL,ESTONE 1.0.4 12

MILESTONE 1.0.4

APOLLO WORDS FROM THE COMMUNITY 13

FROM THE COMMUNITY

ALL ARE WELCOMEcall or email to join the Apollo community

Open  Call  for  Developers  on  the  Second  Thursday  of  each  month  at  9:00AM  (Pacific  Time).  

Next  call:  March  12,  2015.      Message  @monimunozto  for  details.  

BBOP Projects 14

Join  the  conversaLon  by  submi\ng  your  email  at    h]ps://lists.lbl.gov/sympa/subscribe/apollo  

h]p://GenomeArchitect.org      On  GitHub  at  h]ps://github.com/GMOD/Apollo    

•  Web  Apollo  is  supported  by    • NaLonal  InsLtutes  of  Health  (NIH)  grants  5R01GM080203  from  NIGMS,  and  5R01HG004483  from  NHGRI,    

• Contract  No.  60-­‐8260-­‐4-­‐005  from  the  NaLonal  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  United  States  Department  of  Energy  under  Contract  No.  DE-­‐AC02-­‐05CH11231.  

•  Insect  images  used  with  permission:  h]p://AlexanderWild.com  

•  For  your  a;en=on,  thank  you!  

Thank you. 15

GenSAS  

Stephen  Ficklin  

 

Gene  Ontology  

Chris  Mungall  

Seth  Carbon  

Heiko  Dietze  

 

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  

NAL  team  

HGSC  at  BCM  

fringy  Richards  

Dan  Hughes  

Kim  Worley  

 

AraPort  

Vivek  Krishnakumar    

 Phytozome  /  JGI  

Richard  D.  Hayes