GUEST Seminars
December 10, 2025, 10:00 am to 12:30 pm
University of California San Francisco
Harnessing Computational Tools in Precision Medicine: Implementation and Future Directions
Thursday December 10, 2025, 10:00 am - 11:00 am
Achieving precision health will require AI advances spanning biomedical discovery to healthcare delivery. Yet the digital health ecosystem is siloed between discovery and delivery as well as between remote monitoring and in-person clinical care. This talk discusses how digital public utility -- as exemplified by JupyterHealth, an open-source platform that extends Jupyter tools to healthcare – enables real-world precision health solutions. Ida Sim, MD, PhD is Professor of Medicine (UCSF) and Computational Precision Health (UCSF and UC Berkeley) and Co-Director of the UCSF UC Berkeley Joint Program in Computational Precision Health. She obtained her B.Sc. in Biology, her MD, and her PhD in Medical Informatics from Stanford. A practicing primary care physician, Dr. Sim completed her Internal Medicine internship and residency at the Massachusetts General Hospital and a fellowship in General Medicine at the Palo Alto VA. Dr. Sim’s research is on cyberinfrastructure and policies for large-scale health data sharing and AI for managing multiple chronic conditions in primary care. She is Co-founder of Open mHealth, which defines the IEEE 1752 global open standard for patient-generated health data interoperability, and co-leads JupyterHealth, a new project bringing the Jupyter ecosystem to healthcare. She is also Co-founder of Vivli, the world's largest platform for clinical trial data sharing. In prior work, Dr. Sim was the founding Project Coordinator of the World Health Organization’s International Clinical Trials Registry Platform and led the establishment of the first global policy on clinical trial registration. Dr. Sim is a member of the National Academy of Medicine and the American Society for Clinical Investigation, a Fellow of the American College of Medical Informatics, and a recipient of the United States Presidential Early Career Award for Scientists and Engineers (PECASE).
SRI International
The BioCyc.org Genome and Metabolic Pathway Web Portal
Thursday December 10, 2025, 11:30 am - 12:30 pm
BioCyc.org is an extensive web portal containing 20,000 genomes and associated metabolic pathways for microbes, model eukaryotes, and humans. BioCyc provides extensive bioinformatics tools for search and analysis; those tools can also be applied to a company's proprietary genome data.
BioCyc databases combine curated information with data imported from multiple sources, and with computationally inferred data (metabolic pathways, operons, and orthologs). Curated databases receive intensive review and updating by Ph.D. biologists that includes entering new gene functions and metabolic pathways from the experimental literature, defining regulatory relationships, and creating protein complexes. 75 BioCyc databases have been curated from 153,000 publications.
BioCyc genome-related tools include a genome browser, sequence alignment, and extraction of sequence regions. Pathway-related tools include pathway diagrams, a tool for navigating zoomable organism-specific metabolic map diagrams, and a tool for searching for metabolic routes that transform a starting metabolite into a product metabolite. Regulation tools depict operons and regulatory sites, as well as showing full organism regulatory networks. Omics data analysis tools support enrichment analysis and painting of transcriptomics and metabolomics data onto individual pathway diagrams and onto zoomable metabolic map diagrams. The Omics Dashboard tool enables interactive exploration of omics datasets through a hierarchy of cellular systems.