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EuroPythonCode of ConductLive 📹

On the benefits of using workflows: insights from two software tools in the context of computational neuroscience

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45 minutes


The Blue Brain Project strives to simulate the whole mouse brain. The amount of data and code this implies is astoundingly high, and it requires the development of software tools that have both a strict and clear structure and that are resilient to errors that will manifest when developing complex code. Workflows are a straightforward way to maintain structure in toolchains that grow increasingly complex. Workflow management packages such as Luigi bring functionality to run different tasks in parallel, keep track of completed tasks and improve the reproducibility. This poster will present two Blue Brain Project software tools, the e-model-packages software and BluePyEModel, focusing on the creation and distribution of in-silico neuron cells. The e-model-packages software collects cells from an in-silico brain circuit and arranges them in individual ‘neuron packages’ to be distributed to the public through the Blue Brain online portals. The cells packages it creates are designed to be easily run with the open source EModelRunner package. The BluePyEModel software creates and optimizes in-silico neurons and is able to reproduce features from real neuronal experiment recordings. Under the hood, it uses the open source BluePyEfe and eFel packages to extract the electrophysiological features from experimental cells, and the open source BluePyOpt simulator to optimize and validate the parameters of the in-silico neurons.


The speaker

Aurélien Jaquier

Hi, my name is Aurélien Jaquier, from Switzerland, I am 27 and I currently work for the Blue Brain Project as a Scientific Software Developer. I have a Master of Science MSc in Physics from the EPFL (Ecole Polytechnique Fédérale de Lausanne), with a master thesis centered on dwarf galaxy simulation. I love sciences and coding, and have been blessed with a job where I can help fundamental brain research with my coding skills. I develop and maintain different software in the context of neuron cell simulation and electrophysiological parameter optimization, such as EModelRunner, BluePyOpt or eFel. Feel free to talk to me in english, french or japanese.

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