G-OnRamp

Create Genome Browsers for Genome Annotation

G-OnRamp Workshop June 2018

Genome Browser created by G-OnRamp

  • 15 participants from 15 institutions
  • 7 genome assemblies
  • Assembly sizes: 34MB – 2.1GB
  • Number of scaffolds: 64 – 5,065
  • 5 genomes with RNA-Seq data
  • 4 UCSC Genome Browser, 3 JBrowse

 

 

 

June 2018 Workshop Materials

TopicDescriptionTypeLast updateLevel
G-OnRamp workshop 2018 agendaG-OnRamp Beta Testers Workshop AgendaAgenda06/2018Beginner
Introduction to the GEP, Galaxy and G-OnRampOverview: Brief Introduction to the GEP, Galaxy and G-OnRamp; Goals for the Workshop
Lecture06/2018Beginner
Overview of GalaxyOverview of Galaxy: Quick review of Galaxy 101/102
Lecture06/2018Beginner
Using Galaxy to analyze RNA-Seq dataUsing Galaxy for handling RNA-seq data
Walkthrough06/2018Beginner
Introduction to G-OnRampIntroduction to G-OnRamp
Lecture06/2018Beginner
Introduction to G-OnRamp WalkthroughUse G-OnRamp to create a genome browser for the D. biarmipes F elementWalkthrough06/2018Beginner
Customize the Genome Browsers produced by G-OnRampCustomize the Genome Browsers produced by G-OnRamp
Walkthrough06/2018Advanced
Explore the Genome Browsers created by G-OnRampExplore the Genome Browsers created by G-OnRampWalkthrough06/2018Advanced
Explore the Genome Browsers created by G-OnRamp (answers)Explore the Genome Browsers created by G-OnRamp answersWalkthrough06/2018Advanced
Transfer large genomic datasets to G-OnRampTransfer large genomic datasets to G-OnRampWalkthrough06/2018Advanced
Use G-OnRamp to set up a collaborative annotation environment on ApolloUse G-OnRamp to set up a collaborative annotation environment on ApolloLecture06/2018Advanced
Use Apollo to do collaborative genome annotationUse Apollo to do collaborative genome annotationWalkthrough06/2018Advanced
Comparative Gene Annotation with Galaxy / G-OnRampComparative Gene Annotation with Galaxy / G-OnRampWalkthrough06/2018Advanced
Deployment options for G-OnRampDeployment 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)Lecture06/2018Advanced
Virtual Machine Installation WalkthroughInstall G-OnRamp virtual machine image on your computerWalkthrough06/2018Advanced
CloudLaunch Deployment WalkthroughLaunch the G-OnRamp instance on the cloudWalkthrough06/2018Advanced
Storing and Accessing G-OnRamp’s Assembly Hubs outside of GalaxyStoring and Accessing G-OnRamp’s Assembly Hubs outside of GalaxyLecture06/2018Advanced
Differential expression analysis with RNA-Seq Differential expression analysis with RNA-SeqLecture06/2018Advanced
G-OnRamp GlossaryG-OnRamp glossary: explanation on commonly used terms, datatypes, and toolsSupplement 06/2018Beginner