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

TopicDescriptionTypeLast updateLevel
G-OnRamp workshop 2018 agendaG-OnRamp Beta Testers Workshop AgendaAgenda07/2018Beginner
Introduction to the GEP, Galaxy and G-OnRampOverview: Brief Introduction to the GEP, Galaxy and G-OnRamp; Goals for the Workshop
Lecture07/2018Beginner
Overview of GalaxyOverview of Galaxy: Quick review of Galaxy 101/102
Lecture07/2018Beginner
Using Galaxy to analyze RNA-Seq dataUsing Galaxy for handling RNA-seq data
Walkthrough07/2018Beginner
Introduction to G-OnRampIntroduction to G-OnRamp
Lecture07/2018Beginner
Introduction to G-OnRamp WalkthroughUse G-OnRamp to create a genome browser for the D. biarmipes F elementWalkthrough07/2018Beginner
Customize the Genome Browsers produced by G-OnRampCustomize the Genome Browsers produced by G-OnRamp
Walkthrough07/2018Advanced
Explore the Genome Browsers created by G-OnRampExplore the Genome Browsers created by G-OnRampWalkthrough07/2018Advanced
Explore the Genome Browsers created by G-OnRamp (answers)Explore the Genome Browsers created by G-OnRamp (answer key)Walkthrough07/2018Advanced
Transfer large genomic datasets to G-OnRampTransfer large genomic datasets to G-OnRampWalkthrough07/2018Advanced
Bringing Genomics Research into the Undergraduate CurriculumBringing Genomics Research into the Undergraduate CurriculumLecture07/2018Beginner
Use G-OnRamp to set up a collaborative annotation environment on ApolloUse G-OnRamp to set up a collaborative annotation environment on ApolloLecture07/2018Advanced
Set up a collaborative annotation environment on Apollo for DrosophilaSet up a collaborative annotation environment on Apollo for Drosophila biarmipesWalkthrough07/2018Advanced
Use Apollo to do collaborative genome annotationUse Apollo to do collaborative genome annotationWalkthrough07/2018Advanced
Comparative Gene Annotation with Galaxy / G-OnRampComparative Gene Annotation with Galaxy / G-OnRampWalkthrough07/2018Advanced
Comparative Gene Annotation with Galaxy / G-OnRamp (answer key)Comparative Gene Annotation with Galaxy / G-OnRamp (answer key)
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)Lecture07/2018Advanced
Virtual Machine Installation WalkthroughInstall G-OnRamp virtual machine image on your computerWalkthrough07/2018Advanced
CloudLaunch Deployment WalkthroughLaunch the G-OnRamp instance on the cloudWalkthrough07/2018Advanced
Storing and Accessing G-OnRamp’s Assembly Hubs outside of GalaxyStoring and Accessing G-OnRamp’s Assembly Hubs outside of GalaxyLecture07/2018Advanced
Differential expression analysis with RNA-Seq Differential expression analysis with RNA-SeqLecture07/2018Advanced
G-OnRamp GlossaryG-OnRamp glossary: explanation on commonly used terms, datatypes, and toolsSupplement 07/2018Beginner