Bioinformatics Classes

This session describes the application of the web-based interactive OmicCircos in R Shiny to construct circular plots with desired biological features. Example data from human and mouse genomes will be used to demonstrate over thirty plot functions along with the color selection, annotation, labeling, and zoom capabilities. User-guide, take-home video and sample plots from publications will be provided. No R Programming experience is required.

Clinical variant analysis is a three-stage process that entails quality control and processing of data, creating a draft report for cell variant evaluations using different genomic databases and annotation sources, assessing the draft report, and signing-off on the final report. VSClinical is software that uses a single testing paradigm to consolidate and automate the workflow of this three-part analysis.

VSClinical is designed for researchers to efficiently process the clinical interpretation of cell variants based on Association for Molecular Pathology (AMP) and American College of Medical Genetics and Genomics (ACMG) guidelines. This class will demonstrate how VSClinical enables labs to test for both germline and somatic cell variants according to the American College of Medical Genetics (ACMG) and AMP guidelines in an automated fashion.

Evaluating variants according to the American College of Medical Genetics and Genomics (ACMG) guidelines can be an extensive process that requires an in-depth understanding of all available criteria for any cell variant. VSClinical is software that uses a single testing paradigm to automate the complex ACMG guidelines process. Copy Number Variation (CNV) is a type of structural variation in which sections of the genome are duplicated or deleted.

The Human Gene Mutation Database (HGMD) database provides quick access to known published gene lesions responsible for human inherited disease. This session will explore how to query genes and mutations in HGMD and how to view the curated content.

Single nucleotide polymorphism (SNP) & Variation Suite (SVS) is an analytic tool created to empower researchers to perform complex analyses and visualizations on genomic and phenotypic data. Genome-Wide Association Studies (GWAS) continues to be an effective method for identifying disease susceptible genes in humans and other organisms.

VSClinical is designed for researchers to efficiently process the clinical interpretation of variants based on Association for Molecular Pathology (AMP) and American College of Medical Genetics and Genomics (ACMG) guidelines. This class will review the importance and value of automating the search for available clinical trials for the improvement of cancer treatment and prevention. Attendees will explore content and examples leveraged by VSClinical for site, inclusion criteria, relevant drugs, and matching biomarkers.

Key Pathway Advisor (KPA) is a web application for biological pathway analysis of OMICs data. This session will demonstrate using KPA to: explore the biological meaning of data; predict key protein activity changes that could be the root cause of gene expression alterations; understand how biological pathways are impacted by data; create hypotheses about new targets, mechanisms of action, biomarkers and disease associations; and align results with current knowledge of biomarkers and drug targets. Bioinformatics experience is not required to use this tool.

Galaxy is a scientific workflow, data integration, data analysis, and publishing platform that makes computational biology accessible to research scientists that do not have computer programming experience. This workshop will introduce RNA-seq data analysis followed by tutorials showing the use of popular RNA-seq analysis packages and preparing participants to independently run basic RNA-Seq analysis for expression profiling. The hands-on exercises will run on the Galaxy platform using Illumina paired-end RNA-seq data.

The training will overview the current status of pathway tools, with focus on software available to NIH community.  It will discuss the biological interoperation of mutation and expression data in the context of pathways, pathway databases, and popular web-based pathway tools. The pathway software GSEA, g: Profiler, and PATHVIEW will be used to demonstrate how to run the pathway analysis of expression data against GO (Gene Ontology), KEGG (Kyoto Encyclopedia of Genes and Genomes), and MSigDB (Molecular Signatures Database).

For the Introductory Training we will cover basic topics such as: MetaCore overview; how to use MetaCore as a knowledge mining tool; how to upload data; running functional enrichments and exploring pathway maps; and running workflows.

For the Advanced Training, topics covered depend upon survey results: find key hubs using over-connectivity analysis; using Microarray repository for gene comparisons against public data; building networks with MetaCore; constructing your own pathway maps; performing toxicogenomic analysis in MetaCore; analyzing and building networks with miRNA and mRNA data; analyzing multi-omics data (RNA-seq, proteomics, metabolomics, etc).

Galaxy is a scientific workflow, data integration, data analysis, and publishing platform that makes computational biology accessible to research scientists that do not have computer programming experience. This workshop will cover exome sequencing data analysis, followed by tutorials showing the use of exome analysis workflow. The hands-on exercise will run on a Galaxy platform using Illumina paired-end exome sequencing data. This workshop will be taught by NCI staff and is open to NIH and HHS staff. 

Galaxy is a scientific workflow, data integration, data analysis, and publishing platform that makes computational biology accessible to research scientists that do not have computer programming experience. This training will introduce ChIP sequencing data analysis followed by a tutorial showing ChIP-seq analysis workflow.  This workshop will be taught by NCI staff and is open to NIH and HHS staff.