David Haussler, Scientific Director, UC Santa Cruz Genomics Institute, University of California, Santa Cruz.
Matt Elliot, PhD Student, UC Santa Cruz Genomics Institute
David Parks, PhD Student, UC Santa Cruz Department of Computer Science
Lon Blauvelt, Software Engineer, UC Santa Cruz Genomics Institute
Cordero Core, Senior Research Software Engineer
Don Setiawan, Senior Research Software Engineer
Cerebral organoids are derived from induced or natural stem cells, including from mouse or human cells, within a laboratory setting. Once they are differentiated, these structures offer an avenue for researchers and students to probe and stimulate neural networks using AI programs. While their potential is astounding, they are currently only accessible to a select number of prestigious labs equipped with the necessary Biosafety Level 2 facilities, specimens, and tools.
WetAI is an innovative online platform designed to democratize neuroscience education and neuroscience experiments involving cerebral organoids by providing remote access and AI interactivity. This digital system empowers researchers and students to not only observe and manipulate neural network activity, but also to fine-tune remote devices during experiments and collaborate seamlessly across various institutions.
The initial prototype of the WetAI system has already been embraced by a consortium of institutions, including the University of California (UC) Santa Cruz Genomics Institute, UC San Francisco, UC Santa Barbara, and Washington University St. Louis, with many others anticipated to join within the coming year. However, the current iteration of WetAI is constrained in its practicality and user-friendliness. To achieve the envisioned growth and widespread adoption and thereby dismantle research and educational barriers, an enhancement in DevOps capability is essential. Addressing this challenge, the Scientific Software Engineering Center (SSEC) is constructing an automated cloud-based framework on GitHub Codespaces to deploy WetAI. This endeavor will culminate in a unified code base encompassing Docker containers, Jupyter Notebooks, and Python packages. By employing an adaptable, maintainable, and enduring infrastructure, SSEC aims to establish a solid underpinning for researchers, educators, and students to seamlessly utilize the WetAI platform.
Notably, over 1,000 students internationally will be conducting experiments on the platform, while scientists from multiple establishments will successfully collaborate on research involving cerebral organoids even when separated by considerable distances.
SSEC’s software engineering efforts aim to bridge the knowledge gap in neurobiology by deploying an environment that students can access from any internet-connected browser or cell phone. Additionally, SSEC intends to democratize access to AI and experimental neurobiology equipment by creating a robust and easily accessible platform. Through these software engineering endeavors, SSEC hopes to promote education, collaboration, and a vibrant, AI-enhanced community within the realm of neuroscience research, thereby accelerating advancements in the field as a whole.