G-OnRamp Workshop July 2018

Genome Browsers created by G-OnRamp

• 16 participants from 15 institutions
• 6 genome assemblies
• Assembly sizes: 200MB – 1.8GB
• Number of scaffolds: 2,027 – 32,218
• 5 genomes with RNA-Seq data
• 1 UCSC Genome Browser, 5 JBrowse

 

 

 

July 2018 Workshop Materials

Topic	Description	Type	Last update	Level
G-OnRamp workshop 2018 agenda	G-OnRamp Beta Testers Workshop Agenda	Agenda	07/2018	Beginner
Introduction to the GEP, Galaxy and G-OnRamp	Overview: Brief Introduction to the GEP, Galaxy and G-OnRamp; Goals for the Workshop	Lecture	07/2018	Beginner
Overview of Galaxy	Overview of Galaxy: Quick review of Galaxy 101/102	Lecture	07/2018	Beginner
Using Galaxy to analyze RNA-Seq data	Using Galaxy for handling RNA-seq data	Walkthrough	07/2018	Beginner
Introduction to G-OnRamp	Introduction to G-OnRamp	Lecture	07/2018	Beginner
Introduction to G-OnRamp Walkthrough	Use G-OnRamp to create a genome browser for the D. biarmipes F element	Walkthrough	07/2018	Beginner
Customize the Genome Browsers produced by G-OnRamp	Customize the Genome Browsers produced by G-OnRamp	Walkthrough	07/2018	Advanced
Explore the Genome Browsers created by G-OnRamp	Explore the Genome Browsers created by G-OnRamp	Walkthrough	07/2018	Advanced
Explore the Genome Browsers created by G-OnRamp (answers)	Explore the Genome Browsers created by G-OnRamp (answer key)	Walkthrough	07/2018	Advanced
Transfer large genomic datasets to G-OnRamp	Transfer large genomic datasets to G-OnRamp	Walkthrough	07/2018	Advanced
Bringing Genomics Research into the Undergraduate Curriculum	Bringing Genomics Research into the Undergraduate Curriculum	Lecture	07/2018	Beginner
Use G-OnRamp to set up a collaborative annotation environment on Apollo	Use G-OnRamp to set up a collaborative annotation environment on Apollo	Lecture	07/2018	Advanced
Set up a collaborative annotation environment on Apollo for Drosophila	Set up a collaborative annotation environment on Apollo for Drosophila biarmipes	Walkthrough	07/2018	Advanced
Use Apollo to do collaborative genome annotation	Use Apollo to do collaborative genome annotation	Walkthrough	07/2018	Advanced
Comparative Gene Annotation with Galaxy / G-OnRamp	Comparative Gene Annotation with Galaxy / G-OnRamp	Walkthrough	07/2018	Advanced
Comparative Gene Annotation with Galaxy / G-OnRamp (answer key)	Comparative Gene Annotation with Galaxy / G-OnRamp (answer key)
Deployment options for G-OnRamp	Deployment options for G-OnRamp (e.g., centralized server, Docker, Virtual Machines) on local servers or on a public cloud (e.g., Amazon EC2, Microsoft Azure, Jetstream)	Lecture	07/2018	Advanced
Virtual Machine Installation Walkthrough	Install G-OnRamp virtual machine image on your computer	Walkthrough	07/2018	Advanced
CloudLaunch Deployment Walkthrough	Launch the G-OnRamp instance on the cloud	Walkthrough	07/2018	Advanced
Storing and Accessing G-OnRamp’s Assembly Hubs outside of Galaxy	Storing and Accessing G-OnRamp’s Assembly Hubs outside of Galaxy	Lecture	07/2018	Advanced
Differential expression analysis with RNA-Seq	Differential expression analysis with RNA-Seq	Lecture	07/2018	Advanced
G-OnRamp Glossary	G-OnRamp glossary: explanation on commonly used terms, datatypes, and tools	Supplement	07/2018	Beginner