Galaxy for NGS Data Analysis – Day Two

The Collaboratory 610 Charles E Young Drive East - BOYER HALL ROOM 529, Los Angeles, CA, United States

Learn how to analyze NGS data using Galaxy!

Free

W10: Mathematical Modeling of Cell Signaling

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

Molecular biology has taught us a great deal about what is happening inside a cell, that is that pathways can get very complicated and life is not just independent pathways but networks. Fortunately, we can use computational tools to understand dynamics of complex networks. This workshop introduces the basic concepts of modeling cell signaling pathways. […]

W28: Introduction to Phylogenetics

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

Phylogenetics – the reconstruction of the evolutionary history of a the variety of species known to us, is among the most fundamental and traditional tasks in Biology. With the dramatic developments in molecuar biology and the exponential growth in annotated genetic sequences, novel directions and goals have been developed in this seemingly stagnant field. Phylogenetic […]

W15: Bacterial Genomics

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

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 […]

W22: Intro to Cytoscape

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

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 […]

W4: Galaxy for NGS Data Analysis

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

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 […]

W6: BS-DNA Methylation Analysis with Hoffman2 and R

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

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 […]

W23: Advanced Cytoscape

ZOOM CA, United States

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.