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Openworm

On this episode, we are joined by Stephen Larson, the CEO of MetaCell and an affiliate of the OpenWorm foundation. Stephen discussed what the Openworm project is about. They hope to use a digital C. elegans nematode (C. elegans for short) to study the basics of life.

Stephen discussed why C. elegans is an ideal organism for studying life in the lab. He also discussed the steps involved in simulating a digital organism. He mentioned the constraints on the cellular scale that informed their development of a digital C. elegans.

Stephen discussed the validation process of the simulation. He discussed how they discovered the best parameters to capture the behavior of natural C. elegans. He also discussed how biologists embraced the project.

Stephen discussed the computational requirements for improving the simulation parameters of the model and the kind of data they require to scale up. Stephen discussed some findings that the machine-learning communities can take away from the project. He also mentioned how students can get involved in the Openworm project. Rounding up, he shared future plans for the project.

Resources

OpenWorm Website

OpenWorm GitHub Repository

Simulation Video

International C. elegans Conference 2024

Stephen Larson

Stephen Larson is a science entrepreneur and scientist who spends his time actively seeking new models of collaboration for scientific development at MetaCell, where he is CEO, co-founder, and senior consultant. He recently earned his Ph.D. in Neuroscience from the University of California, San Diego. His research focuses on the intersection between computer technology and biological systems and on how computer systems can help us understand fundamental principles of life. In addition to co-founding OpenWorm.org, an online community for the creation of an in silico virtual organism, his projects include online resources for neuroscience such as NeuroLex.org and WholeBrainCatalog.org. He has developed a patent, presented at more than two dozen forums, published in academic journals such as Frontiers in Neuroscience and Nature, and has had his work featured in the New York Times, Wired, Discover, and MSNBC.com. He has served as the Program Leader for the Startup Leadership Program in San Diego, building community amongst early career entrepreneurs. Prior to his graduate studies, he gained practical experience in software engineering and project management through the writing of software applications for the Equity Research division at Morgan Stanley in New York City. Stephen earned a Master and Bachelor of Computer Science from the Massachusetts Institute of Technology, where he wrote a Master’s thesis dealing with self-organizing knowledge representations in the field of artificial intelligence.