Using Python to fight Malaria, Pierre Poulain
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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 ~ PP Using Python to fight Malaria Pierre Poulain @pierrepo Univ. Paris Diderot
- 2. 2 ~ PP or why open science is important in research Using Python to fight Malaria
- 3. 3 ~ PP Malaria? a mosquito…
- 4. 4 ~ PP carrying a parasite
- 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 ~ 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
- 11. 11 ~ PP harder... thick blood smear
- 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
- 20. 20 ~ PP MalariaSmearSearch Upload blood smears Annonate parasites
- 21. 21 ~ PP MalariaSmearSearch E-learning Train technicians
- 22. 22 ~ PPhttps://github.com/pierrepo/MalariaSmearSearch Athénaïs Vaginay Master student Bioinformatics
- 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 Jake VanderPlas @jakevdp PyCon 2017https://www.youtube.com/watch?v=ZyjCqQEUa8o
- 34. 34 ~ PP Jake VanderPlas @jakevdp PyCon 2017https://www.youtube.com/watch?v=ZyjCqQEUa8o
- 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