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DTSTART;TZID=America/Los_Angeles:20261008T114000
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SUMMARY:BME 280B Seminar: Dr. Paulina Tolosa Tort\, Postdoctoral Scholar\, and Erich Weiler\, Senior Systems Architect and Engineer
DESCRIPTION:Welcome to the second week of our BME 280B seminar series\, a weekly seminar covering topics of current research in computational biology\, and bioinformatics. \nOpen to all\, food will be provided. Class enrollment is not required. \n  \nPlease join us this week to learn more about the works of Erich Weiler and Dr. Paulina Tolosa Tort: \nSpeaker 1 at 11:40 AM: Erich Weiler\, Senior Systems Architect and Engineer\, University of California\, Santa Cruz Genomics Institute \nTitle: Mastering HPC Workload Orchestration: A Strategic Guide to Slurm \nDescription: As high-performance computing (HPC) demands grow\, efficient workload orchestration and resource allocation become critical for maximizing cluster throughput and hardware return on investment. This presentation provides a comprehensive guide to understanding and leveraging the Simple Linux Utility for Resource Management (Slurm) within distributed HPC environments. Attendees will explore the core architecture of HPC clusters—including login nodes\, compute nodes\, and shared storage fabrics—alongside the central daemons (slurmctld\, slurmd\, and slurmdbd) that power execution\, control\, and accounting. \nThe talk breaks down the job execution lifecycle for both interactive and batch workloads\, detailing how Slurm evaluates job priorities using a multifactor system driven by job age\, size\, partition constraints\, and Fair Share algorithms (such as Fair Tree). Key operational focus areas include partition design\, backfill scheduling\, and the severe performance impacts of over-requesting CPU cores\, RAM\, GPUs\, and walltime. Practical best practices—such as I/O hygiene\, local scratch utilization\, and avoiding common resource bottlenecks—are highlighted to help researchers and engineers navigate queue mechanics\, optimize job scheduling\, and ensure equitable\, high-throughput cluster utilization. \nBio: Erich Weiler is a Senior Systems Architect and Engineer with over two decades of expertise in high-performance computing\, enterprise storage architectures\, and high-availability infrastructure. He currently serves as Genomics Systems Architect at the University of California\, Santa Cruz Genomics Institute\, where he manages multi-petabyte parallel file systems\, GPU-accelerated computing clusters\, and hybrid cloud environments supporting advanced comparative genomics and computational biology. Erich also provides specialized systems architecture consulting for prominent academic institutions and research facilities across the country\, including Johns Hopkins University\, Northeastern University\, and Claremont McKenna College. \nWith a deep background spanning Linux/UNIX systems administration\, cluster workload management via Slurm\, and complex high-speed networking\, Erich specializes in designing resilient\, scalable infrastructure for data-intensive research environments. His past work includes architecting a $5 million\, 5-petabyte high-performance storage installation for the NIH/NCI-funded Cancer Genomics Hub\, as well as engineering secure\, FISMA-compliant data deployment platforms. Erich holds a B.A. from Southwestern University. \n  \nSpeaker 2 at 12:25 PM: Dr. Paulina Tolosa Tort\, Postdoctoral Scholar\, University of California\, San Francisco \nTitle: Understanding Heterogeneity in Neurodegenerative Disease through Genomics: From Patients to Genomes \nDescription: Neurodegenerative diseases such as Alzheimer’s disease are becoming increasingly prevalent as populations age worldwide. These disorders show substantial heterogeneity across individuals in susceptibility\, clinical presentation\, and progression. Understanding the biological basis of this variation is important for clarifying disease mechanisms\, characterizing risk\, and identifying opportunities for prevention and treatment. This talk will examine how human genomics can be used to investigate heterogeneity in neurodegenerative disease\, from shared genetic architecture across disorders to variation in individual susceptibility. \nUsing Alzheimer’s disease and primary open-angle glaucoma as examples of neurodegenerative diseases\, the first part of the talk will focus on shared genetic architecture and pleiotropy between the two disorders\, integrating large-scale genomic and   data to identify shared genetic signals. The second part will examine how genetic susceptibility\, including polygenic risk\, operates in the context of clinical and potentially modifiable risk factors to shape cognitive outcomes and dementia risk. Together\, these approaches examine different sources of heterogeneity in neurodegenerative disease\, from shared biological processes across disorders to the interplay of genetic and non-genetic risk factors across individuals. \nFinally\, this talk will outline future directions exploring how long-read sequencing and pangenome-based representation may expand both the characterization and representation of human genomic diversity\, creating new opportunities to connect genomic variation with clinically meaningful differences in disease susceptibility and risk. \nBio: Paulina Tolosa-Tort\, MD\, PhD\, MPH\, is a postdoctoral scholar at the University of California\, San Francisco\, whose research focuses on the genetic and non-genetic determinants of heterogeneity in neurodegenerative disease. Her research perspective emerged from clinical training in medicine and ophthalmology at the National Autonomous University of Mexico (UNAM)\, where differences in disease onset\, presentation\, and progression motivated questions about the biological basis of individual susceptibility. She subsequently completed a Master of Public Health in Quantitative Methods at Harvard University and pursued doctoral training in Chronic Disease Epidemiology at Yale University\, where she used cross-disease genetic approaches to investigate biological processes shared between Alzheimer’s disease and primary open-angle glaucoma. At UCSF\, she investigates how genetic susceptibility interacts with clinical and environmental exposures to shape cognitive outcomes and dementia risk. \nHosted By: Professor of Biomolecular Engineering\, Dr. Benedict Paten
URL:https://events.ucsc.edu/event/bme-280b-seminar-100826/
LOCATION:Physical Sciences Building\, Physical Sciences Building\, Santa Cruz\, CA\, 95064
CATEGORIES:Lectures & Presentations,Seminars
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SUMMARY:BME 280B Seminar: Speaker Julian Lucas; and Speaker Theo Kell
DESCRIPTION:Title of Talk 1: Enabling Population-Scale Analysis of Human Centromere Diversity \nPresenter 1: Julian Lucas\, Graduate Student in Miga Lab\, University of California\, Santa Cruz \nDescription: Centromeres are essential for chromosome segregation\, yet their repetitive DNA has long been a blind spot in human genomics. Until recently\, they were largely missing from reference genomes\, and they are still omitted from many genomic analyses due to their rapid sequence divergence. Reference-quality assemblies from the Human Pangenome Reference Consortium (HPRC) now make it possible to compare centromeres across hundreds of human haplotypes. I will describe how we built these assemblies and developed methods to align their repetitive satellite arrays. Together\, these form a centromere pangenome that represents variation and supports analysis such as read mapping\, making centromeres accessible to genomics. Our analysis reveals large structural differences in and around centromeres\, as well as unexpected patterns in single-base changes that offer clues to how centromeric DNA evolves. \nBio: Julian is a graduate student in Karen Miga’s laboratory at the University of California\, Santa Cruz. His research uses pangenomes to characterize variation in human centromeres\, with the goal of bringing these historically difficult-to-analyze regions into mainstream human genetics. Recently\, he helped lead the assembly effort for Release 2 of the Human Pangenome Reference Consortium (HPRC)\, which produced reference-quality genome assemblies that better capture human genetic diversity. Before graduate school\, Julian worked at biotechnology startups\, most recently in non-invasive cancer detection. \nHosted by: Associate Professor of Biomolecular Engineering Karen Miga\, BME Department \n  \nTitle of Talk 2: Genomics Institute Computing Resources \nPresenter 2: Theo Kell\, Senior Systems Architect\, UC Santa Cruz Genomics Institute \nDescription: The backbone of the bioinformatics research at the Genomics Institute is its computing infrastructure. Members of the Genomics Institute have access to a wide array of resources\, including petabytes of storage capacity\, and a supercomputer cluster with over 7\,000 cores. There are also systems for hosting public websites\, sharing datasets with the world\, and collaborating on coding projects. The Genomics Institute IT team works with all stakeholders to make sure that the computing resources are accessible\, up-to-date\, and optimized for cutting-edge\, massively parallel bioinformatics research. \nThis presentation will give an overview of the computing assets that are available\, explain how they are used\, and elaborate on best practices. It is intended to be approachable for students who do not yet have experience with programming or using the command line\, while also providing a jumping-off point for students who are ready to dive in and begin running code. \nBio: Theo Kell is a Senior Systems Architect at the UC Santa Cruz Genomics Institute. After graduating from the Baskin School of Engineering’s Technology and Information Management program\, he worked as an IT System Administrator at Moss Landing Marine Laboratories and Cabrillo College before returning to UCSC to join the Genomics Institute IT team. He has a broad background in Linux/Unix systems\, virtualization\, cybersecurity\, networking\, and customer support.
URL:https://events.ucsc.edu/event/bme-280b-seminar-speaker-julian-lucas-speaker-theo-kell-genomics-institute-computing-resources/
LOCATION:Physical Sciences Building\, Physical Sciences Building\, Santa Cruz\, CA\, 95064
CATEGORIES:Lectures & Presentations,Seminars
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