Janet Matsen - Programming microbes using Python - PyCon 2018

Publié le: 13 mai 2018
sur la chaîne: PyCon 2018

4,261

Speaker: Janet Matsen

The genome of a typical microbe contains roughly 5 million base pairs of DNA including more than 4000 genes, which provide the instructions for cellular replication, energy metabolism, and other biological processes. At Zymergen, we edit DNA to design microbes with improved ability to produce valuable materials and molecules. Microbes with these edits are built and tested in high throughput by our fleet of robots. Genomes are far too large for exhaustive search, so identifying which edits to make requires machine learning on non-standard features. Our task to extract information from trees, networks, and graphs of independently representable knowledge bases (metabolism, genomics, regulation), in ways that respect the strongly causal relationships between systems. In this talk, I will describe how we use Python’s biological packages (e.g. BioPython, CobraPy, Escher, goatools) and other packages (NetworkX, TensorFlow, PyStan, AirFlow) to extract machine learning features and predict which genetic edits will produce high-performance microbes.

Slides can be found at: https://speakerdeck.com/pycon2018 and https://github.com/PyCon/2018-slides

Sur cette page du site, vous pouvez voir la vidéo en ligne Janet Matsen - Programming microbes using Python - PyCon 2018 durée heure minute seconde en bonne qualité , qui a été Téléchargé par l'utilisateur PyCon 2018 13 mai 2018, Partagez le lien avec vos amis et connaissances, sur youtube cette vidéo a déjà été regardée 4,261 fois et il a aimé 85 téléspectateurs. Bon visionnage!

10,571

300