PyParis 2017 http://pyparis.org

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Using Python to fight Malaria
Pierre Poulain @pierrepo
Univ. Paris Diderot

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or why open science is
important in research
Using Python to fight Malaria

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Malaria?
a mosquito…

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carrying a parasite

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Symptoms
http://apps.who.int/iris/bitstream/10665/254991/1/WHO-HTM-GMP-2017.6-eng.pdf

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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

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Africa accounts for 90% of cases
http://gamapserver.who.int/gho/interactive_charts/malaria/cases/atlas.html

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Diagnosis by optical microscopy
Thick
blood smear
Thin blood
smear

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is the gold standard!

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Looking for parasites
thin blood smear

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harder...
thick blood smear

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Could technology help?
http://www.plantnet-project.org/page:MOBILE

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Could technology help?

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Could technology help?
Esteva et al., Nature, 2017, doi:10.1038/nature21056

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And for Malaria?
Das et al., Journal of Microscopy, 2015, doi: 10.1111/jmi.12270

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And for Malaria?
Das et al., Journal of Microscopy, 2015, doi: 10.1111/jmi.12270

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Data?
Source code?

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We need open data
& open source code

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MalariaSmearSearch

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MalariaSmearSearch
Upload blood smears
Annonate parasites

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MalariaSmearSearch
E-learning
Train technicians

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Athénaïs
Vaginay
Master student
Bioinformatics

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Back-end
Flask-Login
Flask-WTF
Flask-Uploads
Flask-JSGlue

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Front-end

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Add annotation

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Show annotations

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Edit annotation

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Data preparation, upload &
annotation

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Data archiving
Findable
Accessible
Interoperable
Reusable

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Image analysis

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Jake VanderPlas @jakevdp
PyCon 2017https://www.youtube.com/watch?v=ZyjCqQEUa8o

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Jake VanderPlas @jakevdp
PyCon 2017https://www.youtube.com/watch?v=ZyjCqQEUa8o

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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