1. Ant genomics &
Bioinformatics for emerging
model organisms
@yannick__
http://yannick.poulet.org

2. © Alex Wild & others

3. Animal biomass (Brazilian rainforest)
Soil fauna excluding
earthworms,
ants & termites
Spiders
Earthworms
Mammals
Ants & termites
Other insects
Birds
Reptiles
Amphibians
from Fittkau & Klinge 1973

4. 454
Illumina
Solid...

5. 454
Illumina
Solid...

6. 454
Illumina
Solid...
This changes
everything.

7. Any lab can
sequence
anything!
454
Illumina
Solid...
This changes
everything.

8. Major questions

9. Major questions
Which genes are involved in social
behaviour?

10. Major questions
Which genes are involved in social
behaviour?
Which genes make it possible for
queens to live up to 30 years?

11. We need great tools.

12. Tools for genomics work on
emerging model organisms

13. Tools for genomics work on
emerging model organisms
Antgenomes.org

14. Tools for genomics work on
emerging model organisms
Antgenomes.org
SequenceServer.com
BLAST made easy

15. ACGACACGGCGCGTCGAGCGTGCACAGAGAAGTTGAATTATCGAGGGaGAAAAAGGGCGCGAGGGAGGGGCAGGACGGTCAAACACTGAGAAAGCAGGCAACATCCGCGAACCCGTAAATTAATTAGGGCCAACATAATAG
CTGGGAATGGCTGGTAGTGGTGGTTCGTCTTCGTGGTCCAGCTTGCGGTTCCCGAGTGCCCTCGCAGTTCGCGCGGTCATGCCTCGGAAACTACACGATACACCTTGCGTCATCCTTACACGAGGATACCTGTTTGCGATC
CCCTGAGGTATTAACGAGCGTATAAGCAGACTCAAAGTACGAACACACTGCTAGTTTCGCGTGCATGTTGCTCGTCGCCGTGCAGACGAGTTAGTACTGTCGACAAAGTAGTCGTAAAGTACGTAAGAGTCTTCCTCTAGT
AGCGAGGACTAATCTCCCGGTACATTAATCTATGTATATTTTATGATATACACACCTGTATTTATCGAAAGTTTATGTTTATCTCGAAAATTAACGTTAATTTTCGAGGACGCAAAAGCTGTCGCAAGTTTaTTTAATTTT
GTTTGtATTTTTTTTTCTTGCTCATTTTTATTTCGAAGTATGCAAATTGAATCTCTTGGTGGCATAACGAGAATTTTCGAAGCTTAAAGGGATCTGCGTTGGCGCGAAGAGAATGGGACTTGTTTTAAACTTTTCTTTCCA
ACGAACACCGTTTCCTTCATTGTAACGTAAAAATGGTGAGCTTCTGCGGCGCGATTGGTCTCATCTTTCCTCTCGTATCGTTCGTCATTTTGTCCGAGAGCGTGTAGATATTGTACCCGATAGAACGGAGACGGAATCACG
CTATACGGTTCCCTCCCAAATGTTCGTTCCTCACGGGCAAAAGTACAAGTAAAAGTAGGAGGGTCCGACTTTATGACCCTACGAGGCACAATAAAGGTTGATGACTACTAAACGTAGAAGAACACGTATACAGTCCGACGT
AAAGTTATTTTTCAATTCCGCGGTCCTCCGCCGCAGTCGTTTTGCCTTGACGTGGAAAAGGAAATTTCCCGGGTTCTAGTCGTCCGGTCTTCTTTtCGTTCTACTGACAATACCATAtTTTCGACATAGATCGATCTCCTT
TtCTCTTtCTCTCTCTCTCTCTCTCTCTCTCTTGAAAATGAAAGCGCGGAAGAGCCGGATCGTGCAACGCACAATGCGAGGCCGCTTTGTACGAGGTACGAGGAGTCCGTCATGCGCCGTAAAACGCCGGAATATGCAATA
CTACTTTCGCAGCGACGGGGCTTGCACGAAGTAATATCGTGAAACGTAGAACCGTTCTTTTCATACGGATATGCGGGAGAAGTTGCTCGTCCGCCCTCCGGCGCATACACGTCGCGCGAGAGTATCGTGCATCCGAAACTC
TGAGATGAAACTCTTCTGTAGTCGATATTCGTCGCGATAAATAGATAAGTCTCGGATAAGGTAGAGACATCGATAATTCCGTTACGAGAATACTCGAGAATAAGATCCAAGTGAAGTGATCACGCTCCATATGGTTTCAGA
TTAATCTCCAATCGGCTGACGAAGGAGGATCATCCTTTTACCGGTGGAAAATAGGGTGGATTGGCGGAGCAAGAAGGCTAAACAGAGAATAAACAGGAGCTATAGCCGAACGAGGGAGAAGGTAAGTAGATGCCTCGGAGA
ACGTGAGCGAAAAAAGGAAACGGGTACGAGAGAAAAAGAAACGGACGGAATAGCGGCTCGGGATTCGCATCCCAAGGAAAACCAAGGCTATACCGGGGTCTTGGATTATTCGAGGCACGACGACGATCTTCGAGTCAGCCG
ACTGTCTGTACCGTGAAAGTGGCACGTATCGATCGCACGGCTGGATTATCTTCCACTTCGATCTACGACGATTACTTCCGCCATCGTATATCCGGGCTTTGCACTAGCGAGGCTATTTAAAAATCTGCGCTCAGTAACTAC
TTATGATTTTTCCATCAGAAACGATTGTGGAGAGAAAAGAGGGAAAAAAAGAGATAGACAGCCTCTGGCTCGAAATGCTAATTTCGCAATCGAGAATTAAAATGCACTTCTTTGTATCTAAATTTTCGTAGAATTAAAATA
AAATTGAATAAAGCAATGAATAAATTGAATAAACTAAAATATAGCTAAATATTTTTTCCTCTATACAAGGTGAATATAATTATCAAATATTTAAGTATGTAGATTGAATTTAAACAGCCTCGGAAGAGAAAAGAATCGGAT
AAACGAAATGCTTTTGCCTCTATTTTCAAGCACGTGACGAATAAAATCTAGCAAAGCTTTTCGACACAATATGTCGACGCAAATGTGGTCTATTTTGGCTAATGATTATTACCGGGAGTCCCGGGCACGGTGTGTCCGCGG
CGCGATAAATTAGAGCGCGAATCGACTTCCACGGCCGTTGTAGAAGGTACTTTGGCAAACGTTATTTCTTCCTGTCTCGAAGGAAGCGCCACTCGAAAACTTGGAAAAGTTCGGCCAGCTGCACGCACCGCGATCTCGGGT
CCGTTCTGGCTCGGTGGCGTGCGCAGGACGGTTGTGAGACGAGAGAAAGAGAGAAAGGAGGATAGAGCGCGAGAGGGAAAGAAGAGGGAACATCCGCGTGCGTGGTTGTATATGGCGTTAATGGCGGCGAGCATAAAGCAT
CCCCGcGCCTGCACGCTCGACCACGGTCGTTTACAGTGCCACTATTTATGTTGATAACTTCGGAATGGAGTCAGATACACGGTACCGAGTGCCGGCGGTTCGGCGGTGGTCCGGCAGCGGTCTGGTAGCACTTGCAAAGTA
TGGGAGAAGAAGGGGGATGGTGGATTCGCGGATCTTTTTGGTCGTGCAAGGAAGGCGGGTCGGTTAGGGTAGGTAGAGAGGAGACGAGCCGAGTCGAGAACAAGATTCAAGCGGAAAGTTTTGCGAGTTAATGGTGCGGAG
GTAATGCCGCGGCCGCAACAGCAACAGCCATCCCCCTGCTTGTGTGTTCGCTCGCTCGCTCACTtCTTCCGTTCTCTCCTCTTCGCGCTAGTTCTCTCTCTCTCTCTCTCTCTCTCTCTGtCTTTCTTGGAATAGCCGTAG
AAAAAaGGAAAAGAAAGAGAGAGAAAGAACGAGACTCCTTTCTCCCCACGAATTCTCTCCTCTCTTTAAGCACACTCTCTCTTCCTGCaccCCCCCCCcTCcTCTCTCTCTCTTTCTCTCTCTATTTTCTTGTCTTCCTCA
CTTGCATCATCCCTCGTCCATTTCCcTCTGGAGAACGTGCCACGTTCTCACTTCCTCGTTCGTCGCTACTTTTTTTCTTCTTTAGTTGTCTCCTCTCACACCCTCGAGACGGCCCGATCTTTTCCTCGTACAGCTCCTATC
ACGAACAGTCGCTAACAAGTGCATCGAATGCAAGTTGCCGACAAACTTCTTCCACCGATTTGTGCTTGTTCTCTGTGCATGCGCGGGCATGTATATCTCTATTAGGCGACATCTGCTCTCAGCTTTTTCATAACGAGGTAG
CGCGGATTCGCGCTCCGAGAGACTTCACGAAGCACTTCCGATCTCGCTACAGTAGAATGCGTATTGTATTTTCTTGTCTCTCTCATTTACTCTTTTCTATCTTTCGTATCTAGCGTGAATACTCCCATGAGGAATGTAGAA
ACCAGATTTTGAAACGGCTTCTTCGTATCTAAATTTTCTTAACTATTTGTTCCTCAAAGTCCATTTTGACGTTATAAATTTTTATTTTTTAATGAGAATGTTTTTATGTGGAGAAGAAAAGTACAACTTTTTTCAAAATGC
AATTAAATTTATACAAGACTACTAAGATAAAAAAAGATGCAAATAATAATGTTCAACTTACTAACTGCTATATTATTAAGGCCAAGTTAAATTACAGATTTATGATGTTGCAGAATATAATAGAAAAGTTTCAAGAAAAAA
aCATTTTAAAGCTTAAAGAGTTTGTTTTCAAACCCATCAAATTTTTTtCTCTGGCAGTGCTGCTGCTCTGCGACGTCATTTTCAAGTCGATCAATGCAAAGTTAACAAAAGTATTTCAACTTTAAAATCATGCAGAAAGTT
GGGAAAAATTTGTTTTCAATTTTACTTAAATTTTAGTTACATTTTTTCTAAAAGCTTAAAATCTCCTCTTTAAAATATGTCTTTAAAAATTGAGCTATGATTTTTCTTCACCGAGTTATCGTAATTTGAAATGGCCAATCG
ACGTTTTCTTTTCATCACTAGGAATAATGCCGGCGGATTTAAGCTTTCAGAAGATTCCAAGCAAAGTTGAAAACAATTTGTTTGAATTCCGCATGATCTCAAAGTTGAAGCTAAAAAAATTTCACAAGACTTTAAAAGACA
AAAAGTCAATGTTGCACAATCGACTTGGAAATAACGCCACTTGGAGCAGAGAAGTATTGCCGAGAAAAAGCTTCGACCGGGTTTGAAAGCAGGATCTATAGGCTTCCAAACTTTTTTTTtGAAAAATGGAGCTTTAAGGTT
ACTTTTCACGAAATTGTATAAATTGTGTTTTGTTGtTTTTATCATCGATTCGAAATGATCCTTTCATTTTGTTCAAGAATGTATCATTAACTTAATGCAATGATATCTTTTAATAATTCAATACTTCTTACTAATTAGATT
TAGAAAAGTTTCATGAACAATTTTAGAACGGTTATTGCTAATTATTCGCCAAAAACAGACGCCTTTCTTCGAGGAGTAACAACTCAAGCTGCATTCGCGGTTGACGGCTTTCCGCGGCGCGTCGCGGTAATATGGCTCCTA
TTTAATTACCCGGTCCTTTGGGAGCTTAAACCAGCCAGAGCTGGAACGGCTGCGCCGTTATTCTATCTAGACTCCTTTGCTTTCTCAAGCAGGCGCGCGATCAAACCTTCTCGCATAAAAGACAATCGCAGCTGGCAGTCG
ACGACGCGcGGGACAGTCGAATCATGACCCGCTCCTCTCTAGTTACCGCCGTCAGTCTGCTCTACTTCCAGACGCCGCGCGTAATCTATTCGACATTAGTTGCTTGATTGCACCGTAAAATGCGACGGCGACGTGAACGAG
AACGACGACGACGACGACGACGACGACAACGACGACGACAATGACAACGACGACGACGACAAGAGTGGGTTCGTCGGTGCTCGATGGCGCCTCCGATTTCAACCGCAGCACGATGCAAGCCCATTACTATCGCCCGGAGCT
AAACGGCACCCGGAGCTCGTGCCATTAAGGGAATCTAGGGTCCGATCCACCTCATTGAATTCCGTTcAATTGCGATTATGATAATGCGTGAACGATCGCCGTGGACGTGAGCTACGGaCAACgAGGGTGTTCGTTCTCGGC
TCAGAGAAACGCAGCGATAAAATTATCAGTGACAGCTTCATTTTTGTTACATTTGACGTTGAAAAATTTGCGAAAGAAATGTGCATTATTCAACTACATTGACAATTGTAAATCTTACATGACCTTTTATTAATATACATA
TATGTAAGATATATGTTCCATCTCTAGTCTCGTTCGATAATGAAGAAATTATAGCTGCAACATAGACGCCGGATTATTCGCGGGGGAAACCGTTGATTATTTGGACTCCGTGGGCTCGGGGTCTGGTTTACTTCTTCCCTT
ATGTCCGGAGATAATGGACACTATTACCTTAACGAGGCCCCAGTCTCTTAGCCGGTAATTGCTTCGAGATATCCGAGAGAGCTCCGGCGTACGTTGCCGCCTGGTGTTGCAGGCAGAGAACCCaGACGGTATTATTGCCGC
CGAGGCTACTCGCCCGTTTCATGGTGGTTATTGTTATGGGCCTGCGGCATTAAGATGTACACCGCACTCTCATACGGGACCCACCACCCCATATACGAGCTGCATATATACTTATGCGGGGAGGATTTCATTACGCCGCTT
CATAACTGGCGGTCTTCAAAATCGCGATAAATCGGGATTGTCTTCCTTGTTAAATCAGCTCCCGTTCCCCTTCCTCATATCGCTGACGAAGCCAACGAGACGGATTAATCTGCGCGATTGAATGGCCTCTATGACGTAAGC
GCACCGTTTACTGGCACGGCTCCTCGTGTTCACGTGAAACGATTTGCGTCGTAAATATTTTATTTTAACATCGCAACATCAAGACAGACGAGGATCGGCTATTGCCTCGTGATCCTAAAAGGGAGATTCTCAAGGCGGAAT
CGGGGTAACGCGTTCGTTGATCTCGCCAAACTACGGCATCTTGAGGACTAGTCTTAGaGGAAAAAAAGACGACGAGGAGACACGGTGAGCATTAGATGAGAAAGAGACGGCGCGGCGCGGTGCGGCGGAGCGAGACGGAAA
GAGATCAAATCTGGATATCAGGATTAGGGTGGGTACGTAATCCGCAGGACGACGGGTGGTAGGAACGGTGGATCCGTCGGCAGATCTCATCGCGCGGAGGAACTCTGCGGGTACTTCGCCCGGCCAAATACGACAAGAGCA
GCAGCCTAACTCGAGTAGAGCCGCCGAGATGGTTTACGGCTCGTCGCAAGTTGGTGAAATTTAAGAGCGCATTTAAAACTGGTTTGGCGCGATGCCCTGCGCCTCCCTGCAGCAGGTACTGCCGGCGAGAGATACCGCTGG
GCTCCGACAGGAGTTTATCGCCCTAACATTCTTGGAAAGCTTCGGATGGATTTCCCTCCTCAACCCATTTCTTCCGGCAGCACCTCAAATCGTCGCTTCTTTCGAGCTCCCTGTGTCGTCCGTTCTTTCCCCTTGCCACGA
AAATTCTTCCAACAGACTCGACACCAAATCGTCACGACGATCATCGGTCAAGATACCCGGAGAAACGTCGCGGACGATGTTACCGTCAGATCGGACGCTTTTAGCTCCGCATTGGAGCTTTTTCCTCGACCGTCTCGGAGG
AGATTTAGCGGACCGACAACAAATGAAGGTCATCTTTCGCGCGAGAAAGCGTCTCACCTTGATTTCCGTCTCGTTTCTCCGGAAATTGGATATCAACCGGACGAACTGTAATGTGTACGTTAAATTGCCAATTATATATAT
AATGTAACAGCTGATTATCTCAAGTGTCCTAAAAACCATTATACTCTTAATTTCTGTGAAAAATGGCGAAAATAAAAAAGAAACCGATCTTAATAAAGATATTCTTCCTGATAGATGCCATGACCCACGTGGAAAACTTTT
TAGTTTTGTACAGTGGTATTATACGTTATCTTCCGCTGAACGTAAGACGTGCCTATCGCGCAATTTCATCGCGACGTCGTCGTATAGCGATTATGGCTACTCCATTAAAAATGAATTTTATAAAGGCAATCTTTCCAAGCG
ATCGTTGTAGGAGAAAAAGGCGAAAGCCGGAGCCAAAGGGGATGAGGCCACTACCTTTGGCTGATCCACTTCGAATGATAATCACCTCTAGGAGACTCAATTTCGCCCTGCTCCGCGTCCTTACCCGTTCCTATCTTCGGA
AGGTTCAACGCCGCAGCGGACTGCATCTTTCACTCCCTTCGTCACCACCGCCCTATTCCTATCGCCCTCCGCGCGCCTACCGCCCCTATATCCTTCCCTTCCTTCACtCCTAGACTATTCTGAACGACCTCTTCCCCCATT
CGCCAACGCTCACTCCTAACTGATTGGAGTACCAATCAATGCGGCATTCAGGCGGCCGTGCTGAAaCTTTAGGAAATTAACTATTCACTCTCTGGAAATGGTTATTTGGAAGGCCGGAAAGGCAGTCGGGACTACGTTACG
Sequencing a genome is
now cheap & easy.

16. ACGACACGGCGCGTCGAGCGTGCACAGAGAAGTTGAATTATCGAGGGaGAAAAAGGGCGCGAGGGAGGGGCAGGACGGTCAAACACTGAGAAAGCAGGCAACATCCGCGAACCCGTAAATTAATTAGGGCCAACATAATAG
CTGGGAATGGCTGGTAGTGGTGGTTCGTCTTCGTGGTCCAGCTTGCGGTTCCCGAGTGCCCTCGCAGTTCGCGCGGTCATGCCTCGGAAACTACACGATACACCTTGCGTCATCCTTACACGAGGATACCTGTTTGCGATC
CCCTGAGGTATTAACGAGCGTATAAGCAGACTCAAAGTACGAACACACTGCTAGTTTCGCGTGCATGTTGCTCGTCGCCGTGCAGACGAGTTAGTACTGTCGACAAAGTAGTCGTAAAGTACGTAAGAGTCTTCCTCTAGT
AGCGAGGACTAATCTCCCGGTACATTAATCTATGTATATTTTATGATATACACACCTGTATTTATCGAAAGTTTATGTTTATCTCGAAAATTAACGTTAATTTTCGAGGACGCAAAAGCTGTCGCAAGTTTaTTTAATTTT
GTTTGtATTTTTTTTTCTTGCTCATTTTTATTTCGAAGTATGCAAATTGAATCTCTTGGTGGCATAACGAGAATTTTCGAAGCTTAAAGGGATCTGCGTTGGCGCGAAGAGAATGGGACTTGTTTTAAACTTTTCTTTCCA
ACGAACACCGTTTCCTTCATTGTAACGTAAAAATGGTGAGCTTCTGCGGCGCGATTGGTCTCATCTTTCCTCTCGTATCGTTCGTCATTTTGTCCGAGAGCGTGTAGATATTGTACCCGATAGAACGGAGACGGAATCACG
CTATACGGTTCCCTCCCAAATGTTCGTTCCTCACGGGCAAAAGTACAAGTAAAAGTAGGAGGGTCCGACTTTATGACCCTACGAGGCACAATAAAGGTTGATGACTACTAAACGTAGAAGAACACGTATACAGTCCGACGT
AAAGTTATTTTTCAATTCCGCGGTCCTCCGCCGCAGTCGTTTTGCCTTGACGTGGAAAAGGAAATTTCCCGGGTTCTAGTCGTCCGGTCTTCTTTtCGTTCTACTGACAATACCATAtTTTCGACATAGATCGATCTCCTT
TtCTCTTtCTCTCTCTCTCTCTCTCTCTCTCTTGAAAATGAAAGCGCGGAAGAGCCGGATCGTGCAACGCACAATGCGAGGCCGCTTTGTACGAGGTACGAGGAGTCCGTCATGCGCCGTAAAACGCCGGAATATGCAATA
CTACTTTCGCAGCGACGGGGCTTGCACGAAGTAATATCGTGAAACGTAGAACCGTTCTTTTCATACGGATATGCGGGAGAAGTTGCTCGTCCGCCCTCCGGCGCATACACGTCGCGCGAGAGTATCGTGCATCCGAAACTC
TGAGATGAAACTCTTCTGTAGTCGATATTCGTCGCGATAAATAGATAAGTCTCGGATAAGGTAGAGACATCGATAATTCCGTTACGAGAATACTCGAGAATAAGATCCAAGTGAAGTGATCACGCTCCATATGGTTTCAGA
TTAATCTCCAATCGGCTGACGAAGGAGGATCATCCTTTTACCGGTGGAAAATAGGGTGGATTGGCGGAGCAAGAAGGCTAAACAGAGAATAAACAGGAGCTATAGCCGAACGAGGGAGAAGGTAAGTAGATGCCTCGGAGA
ACGTGAGCGAAAAAAGGAAACGGGTACGAGAGAAAAAGAAACGGACGGAATAGCGGCTCGGGATTCGCATCCCAAGGAAAACCAAGGCTATACCGGGGTCTTGGATTATTCGAGGCACGACGACGATCTTCGAGTCAGCCG
ACTGTCTGTACCGTGAAAGTGGCACGTATCGATCGCACGGCTGGATTATCTTCCACTTCGATCTACGACGATTACTTCCGCCATCGTATATCCGGGCTTTGCACTAGCGAGGCTATTTAAAAATCTGCGCTCAGTAACTAC
TTATGATTTTTCCATCAGAAACGATTGTGGAGAGAAAAGAGGGAAAAAAAGAGATAGACAGCCTCTGGCTCGAAATGCTAATTTCGCAATCGAGAATTAAAATGCACTTCTTTGTATCTAAATTTTCGTAGAATTAAAATA
AAATTGAATAAAGCAATGAATAAATTGAATAAACTAAAATATAGCTAAATATTTTTTCCTCTATACAAGGTGAATATAATTATCAAATATTTAAGTATGTAGATTGAATTTAAACAGCCTCGGAAGAGAAAAGAATCGGAT
AAACGAAATGCTTTTGCCTCTATTTTCAAGCACGTGACGAATAAAATCTAGCAAAGCTTTTCGACACAATATGTCGACGCAAATGTGGTCTATTTTGGCTAATGATTATTACCGGGAGTCCCGGGCACGGTGTGTCCGCGG
CGCGATAAATTAGAGCGCGAATCGACTTCCACGGCCGTTGTAGAAGGTACTTTGGCAAACGTTATTTCTTCCTGTCTCGAAGGAAGCGCCACTCGAAAACTTGGAAAAGTTCGGCCAGCTGCACGCACCGCGATCTCGGGT
CCGTTCTGGCTCGGTGGCGTGCGCAGGACGGTTGTGAGACGAGAGAAAGAGAGAAAGGAGGATAGAGCGCGAGAGGGAAAGAAGAGGGAACATCCGCGTGCGTGGTTGTATATGGCGTTAATGGCGGCGAGCATAAAGCAT
CCCCGcGCCTGCACGCTCGACCACGGTCGTTTACAGTGCCACTATTTATGTTGATAACTTCGGAATGGAGTCAGATACACGGTACCGAGTGCCGGCGGTTCGGCGGTGGTCCGGCAGCGGTCTGGTAGCACTTGCAAAGTA
TGGGAGAAGAAGGGGGATGGTGGATTCGCGGATCTTTTTGGTCGTGCAAGGAAGGCGGGTCGGTTAGGGTAGGTAGAGAGGAGACGAGCCGAGTCGAGAACAAGATTCAAGCGGAAAGTTTTGCGAGTTAATGGTGCGGAG
GTAATGCCGCGGCCGCAACAGCAACAGCCATCCCCCTGCTTGTGTGTTCGCTCGCTCGCTCACTtCTTCCGTTCTCTCCTCTTCGCGCTAGTTCTCTCTCTCTCTCTCTCTCTCTCTCTGtCTTTCTTGGAATAGCCGTAG
AAAAAaGGAAAAGAAAGAGAGAGAAAGAACGAGACTCCTTTCTCCCCACGAATTCTCTCCTCTCTTTAAGCACACTCTCTCTTCCTGCaccCCCCCCCcTCcTCTCTCTCTCTTTCTCTCTCTATTTTCTTGTCTTCCTCA
CTTGCATCATCCCTCGTCCATTTCCcTCTGGAGAACGTGCCACGTTCTCACTTCCTCGTTCGTCGCTACTTTTTTTCTTCTTTAGTTGTCTCCTCTCACACCCTCGAGACGGCCCGATCTTTTCCTCGTACAGCTCCTATC
ACGAACAGTCGCTAACAAGTGCATCGAATGCAAGTTGCCGACAAACTTCTTCCACCGATTTGTGCTTGTTCTCTGTGCATGCGCGGGCATGTATATCTCTATTAGGCGACATCTGCTCTCAGCTTTTTCATAACGAGGTAG
CGCGGATTCGCGCTCCGAGAGACTTCACGAAGCACTTCCGATCTCGCTACAGTAGAATGCGTATTGTATTTTCTTGTCTCTCTCATTTACTCTTTTCTATCTTTCGTATCTAGCGTGAATACTCCCATGAGGAATGTAGAA
ACCAGATTTTGAAACGGCTTCTTCGTATCTAAATTTTCTTAACTATTTGTTCCTCAAAGTCCATTTTGACGTTATAAATTTTTATTTTTTAATGAGAATGTTTTTATGTGGAGAAGAAAAGTACAACTTTTTTCAAAATGC
AATTAAATTTATACAAGACTACTAAGATAAAAAAAGATGCAAATAATAATGTTCAACTTACTAACTGCTATATTATTAAGGCCAAGTTAAATTACAGATTTATGATGTTGCAGAATATAATAGAAAAGTTTCAAGAAAAAA
aCATTTTAAAGCTTAAAGAGTTTGTTTTCAAACCCATCAAATTTTTTtCTCTGGCAGTGCTGCTGCTCTGCGACGTCATTTTCAAGTCGATCAATGCAAAGTTAACAAAAGTATTTCAACTTTAAAATCATGCAGAAAGTT
GGGAAAAATTTGTTTTCAATTTTACTTAAATTTTAGTTACATTTTTTCTAAAAGCTTAAAATCTCCTCTTTAAAATATGTCTTTAAAAATTGAGCTATGATTTTTCTTCACCGAGTTATCGTAATTTGAAATGGCCAATCG
ACGTTTTCTTTTCATCACTAGGAATAATGCCGGCGGATTTAAGCTTTCAGAAGATTCCAAGCAAAGTTGAAAACAATTTGTTTGAATTCCGCATGATCTCAAAGTTGAAGCTAAAAAAATTTCACAAGACTTTAAAAGACA
AAAAGTCAATGTTGCACAATCGACTTGGAAATAACGCCACTTGGAGCAGAGAAGTATTGCCGAGAAAAAGCTTCGACCGGGTTTGAAAGCAGGATCTATAGGCTTCCAAACTTTTTTTTtGAAAAATGGAGCTTTAAGGTT
ACTTTTCACGAAATTGTATAAATTGTGTTTTGTTGtTTTTATCATCGATTCGAAATGATCCTTTCATTTTGTTCAAGAATGTATCATTAACTTAATGCAATGATATCTTTTAATAATTCAATACTTCTTACTAATTAGATT
TAGAAAAGTTTCATGAACAATTTTAGAACGGTTATTGCTAATTATTCGCCAAAAACAGACGCCTTTCTTCGAGGAGTAACAACTCAAGCTGCATTCGCGGTTGACGGCTTTCCGCGGCGCGTCGCGGTAATATGGCTCCTA
TTTAATTACCCGGTCCTTTGGGAGCTTAAACCAGCCAGAGCTGGAACGGCTGCGCCGTTATTCTATCTAGACTCCTTTGCTTTCTCAAGCAGGCGCGCGATCAAACCTTCTCGCATAAAAGACAATCGCAGCTGGCAGTCG
ACGACGCGcGGGACAGTCGAATCATGACCCGCTCCTCTCTAGTTACCGCCGTCAGTCTGCTCTACTTCCAGACGCCGCGCGTAATCTATTCGACATTAGTTGCTTGATTGCACCGTAAAATGCGACGGCGACGTGAACGAG
AACGACGACGACGACGACGACGACGACAACGACGACGACAATGACAACGACGACGACGACAAGAGTGGGTTCGTCGGTGCTCGATGGCGCCTCCGATTTCAACCGCAGCACGATGCAAGCCCATTACTATCGCCCGGAGCT
AAACGGCACCCGGAGCTCGTGCCATTAAGGGAATCTAGGGTCCGATCCACCTCATTGAATTCCGTTcAATTGCGATTATGATAATGCGTGAACGATCGCCGTGGACGTGAGCTACGGaCAACgAGGGTGTTCGTTCTCGGC
TCAGAGAAACGCAGCGATAAAATTATCAGTGACAGCTTCATTTTTGTTACATTTGACGTTGAAAAATTTGCGAAAGAAATGTGCATTATTCAACTACATTGACAATTGTAAATCTTACATGACCTTTTATTAATATACATA
TATGTAAGATATATGTTCCATCTCTAGTCTCGTTCGATAATGAAGAAATTATAGCTGCAACATAGACGCCGGATTATTCGCGGGGGAAACCGTTGATTATTTGGACTCCGTGGGCTCGGGGTCTGGTTTACTTCTTCCCTT
ATGTCCGGAGATAATGGACACTATTACCTTAACGAGGCCCCAGTCTCTTAGCCGGTAATTGCTTCGAGATATCCGAGAGAGCTCCGGCGTACGTTGCCGCCTGGTGTTGCAGGCAGAGAACCCaGACGGTATTATTGCCGC
CGAGGCTACTCGCCCGTTTCATGGTGGTTATTGTTATGGGCCTGCGGCATTAAGATGTACACCGCACTCTCATACGGGACCCACCACCCCATATACGAGCTGCATATATACTTATGCGGGGAGGATTTCATTACGCCGCTT
CATAACTGGCGGTCTTCAAAATCGCGATAAATCGGGATTGTCTTCCTTGTTAAATCAGCTCCCGTTCCCCTTCCTCATATCGCTGACGAAGCCAACGAGACGGATTAATCTGCGCGATTGAATGGCCTCTATGACGTAAGC
GCACCGTTTACTGGCACGGCTCCTCGTGTTCACGTGAAACGATTTGCGTCGTAAATATTTTATTTTAACATCGCAACATCAAGACAGACGAGGATCGGCTATTGCCTCGTGATCCTAAAAGGGAGATTCTCAAGGCGGAAT
CGGGGTAACGCGTTCGTTGATCTCGCCAAACTACGGCATCTTGAGGACTAGTCTTAGaGGAAAAAAAGACGACGAGGAGACACGGTGAGCATTAGATGAGAAAGAGACGGCGCGGCGCGGTGCGGCGGAGCGAGACGGAAA
GAGATCAAATCTGGATATCAGGATTAGGGTGGGTACGTAATCCGCAGGACGACGGGTGGTAGGAACGGTGGATCCGTCGGCAGATCTCATCGCGCGGAGGAACTCTGCGGGTACTTCGCCCGGCCAAATACGACAAGAGCA
GCAGCCTAACTCGAGTAGAGCCGCCGAGATGGTTTACGGCTCGTCGCAAGTTGGTGAAATTTAAGAGCGCATTTAAAACTGGTTTGGCGCGATGCCCTGCGCCTCCCTGCAGCAGGTACTGCCGGCGAGAGATACCGCTGG
GCTCCGACAGGAGTTTATCGCCCTAACATTCTTGGAAAGCTTCGGATGGATTTCCCTCCTCAACCCATTTCTTCCGGCAGCACCTCAAATCGTCGCTTCTTTCGAGCTCCCTGTGTCGTCCGTTCTTTCCCCTTGCCACGA
AAATTCTTCCAACAGACTCGACACCAAATCGTCACGACGATCATCGGTCAAGATACCCGGAGAAACGTCGCGGACGATGTTACCGTCAGATCGGACGCTTTTAGCTCCGCATTGGAGCTTTTTCCTCGACCGTCTCGGAGG
AGATTTAGCGGACCGACAACAAATGAAGGTCATCTTTCGCGCGAGAAAGCGTCTCACCTTGATTTCCGTCTCGTTTCTCCGGAAATTGGATATCAACCGGACGAACTGTAATGTGTACGTTAAATTGCCAATTATATATAT
AATGTAACAGCTGATTATCTCAAGTGTCCTAAAAACCATTATACTCTTAATTTCTGTGAAAAATGGCGAAAATAAAAAAGAAACCGATCTTAATAAAGATATTCTTCCTGATAGATGCCATGACCCACGTGGAAAACTTTT
TAGTTTTGTACAGTGGTATTATACGTTATCTTCCGCTGAACGTAAGACGTGCCTATCGCGCAATTTCATCGCGACGTCGTCGTATAGCGATTATGGCTACTCCATTAAAAATGAATTTTATAAAGGCAATCTTTCCAAGCG
ATCGTTGTAGGAGAAAAAGGCGAAAGCCGGAGCCAAAGGGGATGAGGCCACTACCTTTGGCTGATCCACTTCGAATGATAATCACCTCTAGGAGACTCAATTTCGCCCTGCTCCGCGTCCTTACCCGTTCCTATCTTCGGA
AGGTTCAACGCCGCAGCGGACTGCATCTTTCACTCCCTTCGTCACCACCGCCCTATTCCTATCGCCCTCCGCGCGCCTACCGCCCCTATATCCTTCCCTTCCTTCACtCCTAGACTATTCTGAACGACCTCTTCCCCCATT
CGCCAACGCTCACTCCTAACTGATTGGAGTACCAATCAATGCGGCATTCAGGCGGCCGTGCTGAAaCTTTAGGAAATTAACTATTCACTCTCTGGAAATGGTTATTTGGAAGGCCGGAAAGGCAGTCGGGACTACGTTACG
Sequencing a genome is
now cheap & easy.
But making it
useable is hard.

17. Gene prediction
Dozens of software algorithms: dozens of predictions
Yandell & Ence 2013 NRG
TTTTtACCTGTTTTtGAAAAGGTAATTTTCTTTAGATATATACAGTTTGTAATaTTAGGTATTTTATAAACAGTGTGTATATTTCTTACAATATAAAAGACACAATTGCAAACTAGCATGATTGTAAACAATTGCTAAACGGATCAATATAAATTAAAATTGTAATATTAAGTATCAAACCGATAATTTTT

18. Gene prediction
Dozens of software algorithms: dozens of predictions
TTTTtACCTGTTTTtGAAAAGGTAATTTTCTTTAGATATATACAGTTTGTAATaTTAGGTATTTTATAAACAGTGTGTATATTTCTTACAATATAAAAGACACAATTGCAAACTAGCATGATTGTAAACAATTGCTAAACGGATCAATATAAATTAAAATTGTAATATTAAGTATCAAACCGATAATTTTT
Yandell & Ence 2013 NRG
Evidence

19. Gene prediction
Dozens of software algorithms: dozens of predictions
TTTTtACCTGTTTTtGAAAAGGTAATTTTCTTTAGATATATACAGTTTGTAATaTTAGGTATTTTATAAACAGTGTGTATATTTCTTACAATATAAAAGACACAATTGCAAACTAGCATGATTGTAAACAATTGCTAAACGGATCAATATAAATTAAAATTGTAATATTAAGTATCAAACCGATAATTTTT
Evidence
Yandell & Ence 2013 NRG
Consensus:

20. Gene prediction
Dozens of software algorithms: dozens of predictions
TTTTtACCTGTTTTtGAAAAGGTAATTTTCTTTAGATATATACAGTTTGTAATaTTAGGTATTTTATAAACAGTGTGTATATTTCTTACAATATAAAAGACACAATTGCAAACTAGCATGATTGTAAACAATTGCTAAACGGATCAATATAAATTAAAATTGTAATATTAAGTATCAAACCGATAATTTTT
Evidence
20% failure rate:
Yandell & Ence 2013 NRG
Consensus:

21. Gene prediction
Dozens of software algorithms: dozens of predictions
TTTTtACCTGTTTTtGAAAAGGTAATTTTCTTTAGATATATACAGTTTGTAATaTTAGGTATTTTATAAACAGTGTGTATATTTCTTACAATATAAAAGACACAATTGCAAACTAGCATGATTGTAAACAATTGCTAAACGGATCAATATAAATTAAAATTGTAATATTAAGTATCAAACCGATAATTTTT
Evidence
20% failure rate:
•missing pieces
Yandell & Ence 2013 NRG
Consensus:

22. Gene prediction
Dozens of software algorithms: dozens of predictions
TTTTtACCTGTTTTtGAAAAGGTAATTTTCTTTAGATATATACAGTTTGTAATaTTAGGTATTTTATAAACAGTGTGTATATTTCTTACAATATAAAAGACACAATTGCAAACTAGCATGATTGTAAACAATTGCTAAACGGATCAATATAAATTAAAATTGTAATATTAAGTATCAAACCGATAATTTTT
Evidence
20% failure rate:
•missing pieces
•extra pieces
Yandell & Ence 2013 NRG
Consensus:

23. Gene prediction
Dozens of software algorithms: dozens of predictions
TTTTtACCTGTTTTtGAAAAGGTAATTTTCTTTAGATATATACAGTTTGTAATaTTAGGTATTTTATAAACAGTGTGTATATTTCTTACAATATAAAAGACACAATTGCAAACTAGCATGATTGTAAACAATTGCTAAACGGATCAATATAAATTAAAATTGTAATATTAAGTATCAAACCGATAATTTTT
Evidence
20% failure rate:
•missing pieces
•extra pieces
•incorrect merging
Yandell & Ence 2013 NRG
Consensus:

24. Gene prediction
Dozens of software algorithms: dozens of predictions
TTTTtACCTGTTTTtGAAAAGGTAATTTTCTTTAGATATATACAGTTTGTAATaTTAGGTATTTTATAAACAGTGTGTATATTTCTTACAATATAAAAGACACAATTGCAAACTAGCATGATTGTAAACAATTGCTAAACGGATCAATATAAATTAAAATTGTAATATTAAGTATCAAACCGATAATTTTT
Evidence
20% failure rate:
•missing pieces
•extra pieces
•incorrect merging
•incorrect splitting
Yandell & Ence 2013 NRG
Consensus:

25. Gene prediction
Dozens of software algorithms: dozens of predictions
TTTTtACCTGTTTTtGAAAAGGTAATTTTCTTTAGATATATACAGTTTGTAATaTTAGGTATTTTATAAACAGTGTGTATATTTCTTACAATATAAAAGACACAATTGCAAACTAGCATGATTGTAAACAATTGCTAAACGGATCAATATAAATTAAAATTGTAATATTAAGTATCAAACCGATAATTTTT
Evidence
20% failure rate:
•missing pieces
•extra pieces
•incorrect merging
•incorrect splitting
Visual inspection... and
manual fixing required.
Yandell & Ence 2013 NRG
Consensus:

26. Gene prediction
Dozens of software algorithms: dozens of predictions
TTTTtACCTGTTTTtGAAAAGGTAATTTTCTTTAGATATATACAGTTTGTAATaTTAGGTATTTTATAAACAGTGTGTATATTTCTTACAATATAAAAGACACAATTGCAAACTAGCATGATTGTAAACAATTGCTAAACGGATCAATATAAATTAAAATTGTAATATTAAGTATCAAACCGATAATTTTT
Evidence
20% failure rate:
•missing pieces
•extra pieces
•incorrect merging
•incorrect splitting
Visual inspection... and
manual fixing required.
1 gene = 20 minutes to 3 days
Yandell & Ence 2013 NRG
Consensus:

27. Gene prediction
Dozens of software algorithms: dozens of predictions
TTTTtACCTGTTTTtGAAAAGGTAATTTTCTTTAGATATATACAGTTTGTAATaTTAGGTATTTTATAAACAGTGTGTATATTTCTTACAATATAAAAGACACAATTGCAAACTAGCATGATTGTAAACAATTGCTAAACGGATCAATATAAATTAAAATTGTAATATTAAGTATCAAACCGATAATTTTT
Evidence
20% failure rate:
•missing pieces
•extra pieces
•incorrect merging
•incorrect splitting
Visual inspection... and
manual fixing required.
1 gene = 20 minutes to 3 days
15,000 genes * 20 species =
impossible.
Yandell & Ence 2013 NRG
Consensus:

28. Monica Dragan
https://github.com/monicadragan/GeneValidator

29. Monica Dragan
https://github.com/monicadragan/GeneValidator

30. Monica Dragan
https://github.com/monicadragan/GeneValidator

31. Gene prediction
Dozens of software algorithms: dozens of predictions
TTTTtACCTGTTTTtGAAAAGGTAATTTTCTTTAGATATATACAGTTTGTAATaTTAGGTATTTTATAAACAGTGTGTATATTTCTTACAATATAAAAGACACAATTGCAAACTAGCATGATTGTAAACAATTGCTAAACGGATCAATATAAATTAAAATTGTAATATTAAGTATCAAACCGATAATTTTT
Evidence
20% failure rate:
•missing pieces
•extra pieces
•incorrect merging
•incorrect splitting
Visual inspection... and
manual fixing required.
1 gene = 20 minutes to 3 days
15,000 genes * 20 species =
impossible.
Yandell & Ence 2013 NRG
Consensus:

32. Crowd-sourcing the visual inspection + correction.
Anurag Priyam http://afra.sbcs.qmul.ac.uk

33. Crowd-sourcing the visual inspection + correction.
Begin
Curate
Being curated
Submit
Curate
Curate
Being curated
Submit
Being curated
Submit
“
create nex
Anurag Priyam http://afra.sbcs.qmul.ac.uk

34. Crowd-sourcing the visual inspection + correction.
Scientific software + Facebook +
Points + Badges + Redundancy
Begin
Curate
Being curated
Submit
Curate
Curate
Being curated
Submit
Being curated
Submit
“
create nex
Anurag Priyam http://afra.sbcs.qmul.ac.uk

36. My aim is to make
bioinformatics software:

37. My aim is to make
bioinformatics software:
Shared

38. My aim is to make
bioinformatics software:
Shared
Robust

39. My aim is to make
bioinformatics software:
Shared
Robust
User-friendly

40. With the fellowship I will:

41. With the fellowship I will:
• Organize
a local Software-Carpentry-type event.

42. With the fellowship I will:
• Organize
• Include
a local Software-Carpentry-type event.
software & reproducibility best practices on two new
MSc & existing BSc.

43. With the fellowship I will:
• Organize
a local Software-Carpentry-type event.
• Include
software & reproducibility best practices on two new
MSc & existing BSc.
• Promote/lobby
in line with SSI’s mission (internally/talks/conf//
networking/publications/web).

44. With the fellowship I will:
• Organize
a local Software-Carpentry-type event.
• Include
software & reproducibility best practices on two new
MSc & existing BSc.
• Promote/lobby
in line with SSI’s mission (internally/talks/conf//
networking/publications/web).
• Seek
funds to create great sustainable bioinformatics software.

45. Thanks!
@yannick__
y.wurm@qmul.ac.uk
http://yannick.poulet.org