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 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 […]
High-throughput sequencing technologies have allowed researchers to extract DNA at the individual, population, and species levels. In this workshop, students will learn how to analyze and interpret population-level genetic information with PLINK and R. Students will also be exposed to the literature on the different topics, followed by hands-on exercises and paper discussion.
MATLAB is a powerful, high-level programing language for numerical computation, visualization, and application development. This workshop will start by introducing the MATLAB environment and then cover working with arrays and matrices, loops and conditional statements, writing your own functions, working with files and visualizing your data. The final day will briefly introduce utilizing MATLAB to […]
This workshop aims to provide skills needed to address principles of the assay, quality assessment, sequencing depth, data processing and functional downstream analyses of ChIP-seq datasets. Students will have opportunities to practice hands-on with state-of-the-art analytical tools.
Learn how to make your applications ready for production and distribution. This workshop will give you your introduction to setting up version control and containerization for your applications to ensure that changes are tracked and dependencies are documented and automatically installed. Git and Docker allow developers and users to quickly replicate code and computing environments […]
Through this seminar, attendees will walk away knowing when and how to run modern versions of traditional statistical analysis. These tests and the underlying bioinformatical lesson about resampling will be of use to most scientific disciplines. The course makes no assumptions about familiarity with traditional statistics – we will simply go through relatable experimental examples […]
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. […]
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.
