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Using Python to fight Malaria, Pierre Poulain

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PyParis 2017
http://pyparis.org

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Using Python to fight Malaria, Pierre Poulain

  1. 1. 1 ~ PP Using Python to fight Malaria Pierre Poulain @pierrepo Univ. Paris Diderot
  2. 2. 2 ~ PP or why open science is important in research Using Python to fight Malaria
  3. 3. 3 ~ PP Malaria? a mosquito…
  4. 4. 4 ~ PP carrying a parasite
  5. 5. 5 ~ PP Symptoms http://apps.who.int/iris/bitstream/10665/254991/1/WHO-HTM-GMP-2017.6-eng.pdf
  6. 6. 6 ~ PP In 2015 214 millionmalaria estimated cases worldwide 429 000 deaths http://apps.who.int/iris/bitstream/10665/254991/1/WHO-HTM-GMP-2017.6-eng.pdf
  7. 7. 7 ~ PP Africa accounts for 90% of cases http://gamapserver.who.int/gho/interactive_charts/malaria/cases/atlas.html
  8. 8. 8 ~ PP Diagnosis by optical microscopy Thick blood smear Thin blood smear
  9. 9. 9 ~ PP is the gold standard!
  10. 10. 10 ~ PP Looking for parasites thin blood smear
  11. 11. 11 ~ PP harder... thick blood smear
  12. 12. 12 ~ PP Could technology help? http://www.plantnet-project.org/page:MOBILE
  13. 13. 13 ~ PP Could technology help?
  14. 14. 14 ~ PP Could technology help? Esteva et al., Nature, 2017, doi:10.1038/nature21056
  15. 15. 15 ~ PP And for Malaria? Das et al., Journal of Microscopy, 2015, doi: 10.1111/jmi.12270
  16. 16. 16 ~ PP And for Malaria? Das et al., Journal of Microscopy, 2015, doi: 10.1111/jmi.12270
  17. 17. 17 ~ PP Data? Source code?
  18. 18. 18 ~ PP We need open data & open source code
  19. 19. 19 ~ PP MalariaSmearSearch
  20. 20. 20 ~ PP MalariaSmearSearch Upload blood smears Annonate parasites
  21. 21. 21 ~ PP MalariaSmearSearch E-learning Train technicians
  22. 22. 22 ~ PPhttps://github.com/pierrepo/MalariaSmearSearch Athénaïs Vaginay Master student Bioinformatics
  23. 23. 23 ~ PP Back-end Flask-Login Flask-WTF Flask-Uploads Flask-JSGlue
  24. 24. 24 ~ PP Front-end
  25. 25. 25 ~ PP Add annotation
  26. 26. 26 ~ PP Show annotations
  27. 27. 27 ~ PP Edit annotation
  28. 28. 28 ~ PP
  29. 29. 29 ~ PP
  30. 30. 30 ~ PP Data preparation, upload & annotation
  31. 31. 31 ~ PP Data archiving Findable Accessible Interoperable Reusable
  32. 32. 32 ~ PP Image analysis
  33. 33. 33 ~ PP Jake VanderPlas @jakevdp PyCon 2017https://www.youtube.com/watch?v=ZyjCqQEUa8o
  34. 34. 34 ~ PP Jake VanderPlas @jakevdp PyCon 2017https://www.youtube.com/watch?v=ZyjCqQEUa8o
  35. 35. 35 ~ PP Credits Skeeze Pixabay CC0 Edward Boatman The Noun Project / CC-BY Ute Frevert & Margaret Shear Wikimedia / CC-BY Centes for Disease Control and Prevention Wikimedia / Public domain US Army Africa Flickr / CC-BY Gratisography CC0 markusspiske Pixabay / CC0

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