The workshop will mainly focus on teaching the fundamentals of bacterial genomics and basic bioinformatics analysis. As a sample data Vibrio cholerae genome will be used as the practice dataset, and workshop participants will try to reproduce the expected results. The workshop will start with detailed instructions on how to quality control the raw sequence […]
The workshop introduces Cytoscape (https://cytoscape.org/) – an open source platform for retrieval and visualization of complex biological interactions that are available from public interaction resources: The IMEx Consortium (https://www.imexconsortium.org/), STRING (https://string-db.org/) and BioGIRD (https://thebiogrid.org/). It covers querying for interactions data using built-in search interface, interaction data cleanup and visualization as well as overlying of the […]
Galaxy (https://usegalaxy.org/) is a web-based infrastructure for bioinformatics application. First, this workshop introduces participants to using Galaxy for analysis of Next-Generation Sequencing data. Next, this workshop covers the structure of Galaxy, data format and manipulation, obtaining and sharing data, and building and sharing workflows. We will use the tools installed on the UCLA galaxy to […]
This workshop will introduce the basic principles of DNA methylation and briefly describe available methods for DNA methylation assessment, focusing on bisulfite sequencing (BS-Seq). We will cover the principles of BSseq preprocessing, alignment and methylation calling, differential methylation analysis, annotation and visualization. Attendees will have the opportunity to work on real DNA methylation data provided […]
The workshop will cover experimental approaches to protein interaction determination; processing and presentation of interaction data available from online resources, and the role of interaction data in the interpretation of large scale datasets. Highly encourage: Students should working knowledge of python scripting.
This workshop provides an introduction to the microbiome analyses from the raw sequence data generated from the next-generation sequencing platforms. We will cover how to perform the 16S rRNA-based analysis using an open-source bioinformatics pipeline QIIME. We will also cover some downstream analyses of the microbiome data beyond QIIME, including statistical analyses and functional analyses.
This workshop uses materials developed by the Broad Institute to teach Variant Discovery with GATK. Attendees with no prior experience in variant calling are recommended to review all of the materials below before coming to the workshop. This early preparation will allow a focus on the specific issues of running GATK on the UCLA hoffman2 […]
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. […]
Mergeomics is a computational tool designed to elucidate the underlying pathways, networks, and key regulators of complex diseases by integrating multi-omics data (genomics, transcriptomics, epigenomics, proteomics, etc). With use of integrative omics concepts and network modeling methods, this tool can uncover disease-associated gene sets and biological pathways across omics layers and can identify key drivers […]
Join us for a tailored workshop designed to empower you with the skills and knowledge needed to excel in the competitive landscape of academia, industry, and beyond. Learn from experienced professionals, gain valuable insights, and expand your network. Guest Speakers: • Kathrin Burch, Associate Manager, Statistical Genetics, Regeneron • Max Shokhirev, Head of Bioinformatics at […]
