Using Python to fight Malaria

PyParis 2017.
Univ Paris Diderot, CNRS & FCRM
License: Creative Commons Attribution (CC-BY)

Transcript

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