Science in the Open at the Allen Institute for Neural Dynamics



Time: 10:30-12:00 on Thur.,Oct.12, 2023

Venue:E109,Biomedicine Hall

Speaker: Dr.Saskia de Vries

Host: Dr.Zengcai Guo

Title: Science in the Open at the Allen Institute for Neural Dynamics




The Allen Institute for Neural Dynamics is a new Allen Institute, started in 2021, with the goal of deciphering how our brains understand the world around us in order to guide fundamental human behaviors. We leverage cutting edge neuroscience technologies to study the behavior and physiology of the brain. This spans brain wide high-density electrophysiology, optical physiology at both the population and the compartment level to record both neural activity as well as neuromodulators, diverse behavioral assays centered on a dynamic foraging behavior, and detailed anatomy and morphology through full brain reconstructions of molecularly defined neurons. A key part of our goal is to pursue these scientific goals openly, employing a model of open science that we call “Science in the Open.” In this talk I will present the strategy that our Scientific Computing team is using to build cloud-based infrastructure to manage, store, and share these large amounts of diverse neural data. Data and tools are shared as we acquire them, and our own analysis of data occurs in a shared platform, in order to facilitate collaboration and data re-use within the scientific community.



Saskia de Vries joined the Allen Institute for Brain Science in 2012 as a Scientist in the neural coding team. With a background in systems neuroscience, she has studied visual processing in both vertebrate and invertebrate systems using a combination of physiological, computational, behavioral, and molecular tools to parse how neural circuits process visual information and use that information to select appropriate behavior. At the Allen Institute, she led the team that created the Allen Brain Observatory Visual Coding dataset, a systematic survey of physiological activity in the mouse visual cortex collected using 2-photon calcium imaging, and has published several papers using these data to examine the functional organization of the mouse visual cortex. Recognizing the importance of open science, Saskia has been instrumental in facilitating the accessibility and utilization of the Allen Brain Observatory Visual Coding dataset by scientists beyond the Institute's walls. She has championed this mission by conducting numerous workshops and tutorials since the dataset's initial release. In 2022, Saskia joined the Allen Institute for Neural Dynamics as the Principal Product Manager. She is working within the Scientific Computing team to build infrastructure and tools that promotes “Science in the Open,” organizing and sharing our data to promote collaboration and data re-use. De Vries received a B.S. from Yale University in Molecular Biophysics and Biochemistry and a Ph.D. in Neurobiology from Harvard University and was a Postdoctoral Scholar in the Department of Neurobiology at Stanford University.