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W2: Using NGS Analysis Tools

529 Boyer Hall 611 Charles E Young Dr E,, Los Angeles, CA, United States

High-throughput sequencing technology involves a number of concepts and techniques that shape a project before application-specific processes are utilized. First, this workshop introduces the more “universal” aspects of high-throughput sequence analysis—from experimental design to sequencing and alignment methods. Next, this workshop covers common file formats for sequence data and limitations of sequencing technologies. We will […]

W18: Advanced Python

529 Boyer Hall 611 Charles E Young Dr E,, Los Angeles, CA, United States

This workshop will cover some more advanced topics in python including an overview of object-oriented python (this will not be an in-depth course on object-oriented programming), use of the numpy and pandas libraries (python libraries for efficient handling of large numeric and heterogenous datasets, and matplotlib for plotting results. At the end of this workshop, […]

W1b: Intro to Unix command line II

529 Boyer Hall 611 Charles E Young Dr E,, Los Angeles, CA, United States

This workshop (UNIX Command Line II) continues Workshop W1: UNIX Command Line I and uses the Hoffman2 campus computing cluster. The focus is on features that make dealing with large files or large numbers of files or repetitive tasks easier. These include shell variables, substitutions, redirections, pipes, loops, conditionals, subshells, shell functions, and shell scripts. […]

W3: Intro to R and Data Visualization

529 Boyer Hall 611 Charles E Young Dr E,, Los Angeles, CA, United States

R (www.r-project.org) is a free software environment for statistical computing and graphics. First, this workshop introduces basic concepts, syntax, and usage in R programming, statistical analysis, and visualization techniques. We will conduct hands-on tutorials throughout the session, giving attendees a chance to see R in action. This course is a pre-requisite for several other Collaboratory […]

W37: Applications of Large Language Models

529 Boyer Hall 611 Charles E Young Dr E,, Los Angeles, CA, United States

This 3-day interactive workshop introduces the overarching principles guiding generative modeling and specifically Large-Scale Language Models (LLM), their application in Python for inference, and specific use-cases in Genomics. Experience with Python is necessary, and basic knowledge about ML workflows is preferred. At the end of this workshop, you WILL be comfortable with loading, inferencing and […]

Research-in-Progress (RIP) Seminar: Alex Bermudez (Lin), Graduate Student in Bioengineering

Boyer Hall 130

TITLE: "Metabolic Reprogramming during Epithelial Crowding Underlies Jamming Transition" ABSTRACT: Jamming, crucial for maintaining tissue integrity during morphogenesis and wound healing, becomes dysregulated in carcinoma metastasis and asthma. Despite its pathological significance, the molecular mechanisms governing jamming remain poorly understood. In this study, we utilized time-course transcriptome analysis and isotopologue metabolomics to elucidate the metabolic […]

Research-in-Progress (RIP) Seminar: Selina Wu (Boutros), Graduate Student in Medical Informatics

Boyer Hall 130

TITLE: "Evolutionary Consequences of Tumor Initiation in Hereditary Leiomyomatosis and Renal Cell Cancer" ABSTRACT: Hereditary leiomyomatosis and renal cell cancer (HLRCC ) is a rare hereditary condition with individuals at risk of developing renal cell carcinoma (RCC) associated with poor prognosis. Although RCC risk and cancer penetrance of this condition has been studied, whole genome […]