The workshops at RMGH consist of two different tracks.  They run in parallel, so you will have to choose and register for one.  Please see the information below to help you determine which workshop you want to register for. 


Complex and Dynamic Analysis of Nascent Transcription

Instructor(s): Robin Dowell

Transcription is the critical first readout of the human genome.  Steady state expression (RNA-seq) has long been utilized as a method of assaying for changes in transcription. Consequently there are mature and powerful methods of analysis of RNA-seq data. However, steady state measures reflect both transcription and RNA stability. Recently, nascent transcription techniques such as GRO-seq and PRO-seq provide a direct readout on transcription.  Only recently have sophisticated methods for analysis of nascent transcription become available.  Using these techniques, eRNAs can be identified and transcription factor activity can be inferred.

In this workshop, students will utilize open source software and cluster compute resources to analyze matched RNA-seq and GRO-seq data, with an emphasis on the unique properties of each data.   Special emphasis will be placed on nascent transcription analysis.   Prior experience with Linux/Unix is expected.

Day 1:
Session 1:  Studying Transcription -- an Overview
Session 2:  Garbage In, Garbage Out: Quality control on sequence data
Session 3: Maximize read usage through mapping strategies

Day 2:
Session 4 (e.g. 8:30 am for 1 hour):  Learning to count: quantifying 
signal
Session 5: Assessing changes in data (part I: differential expression)
Session 6: Assessing changes in data (part II: resorting to statistics)
Session 7: Annotation agnostic analysis: finding new things in the data
Session 8: Getting the most from your data: Integration with relevant 
other data



Containerization and Workflows

Instructor(s): Exciting speakers from companies specializing in containerization and computational workflows

Learn to Build and Refine Pipelines In and Out of the Cloud!  Pipelining with Containerization and Workflows Workshop. 


The second concurrent workshop track at Rmgh ‘18 will focus on strategies for containerizing and automating bioinformatics pipelines.  Representatives from Docker, Singularity, CWL, NextFlow, SnakeMake, CyVerse, the NCI Cloud Resources, and Galaxy will be giving short hands-on sessions for deploying their tools in creating bioinformatics pipelines.  While hands-on sessions will be focused on deploying new applications with these tools, there will be time for networking, consultation and collaboration with tool organizers and authors.

Day 1: June 18th

Session 1: Galaxy Workflows

  • Plenary Session -- James Taylor -- 1:30 - 2:15 pm

  • Working and Networking session -- 2:15 - 2:45 pm

Coffee and Additional Networking 2:45 - 3:15 pm

Session 2: Cyverse/Atmosphere/Jetstream (and Galaxy)

  • Plenary Session -- Upendra Devisetty -- 3:15 - 4:00 pm

  • Working and Networking session -- 4:00 - 4:30 pm

Session 3:  Snakemake and Bioconda

  • Plenary Session -- Johannes Koster -- 4:30 - 5:15 pm

Open working and networking session until 6pm


Day 2: June 19th

Coffee and additional networking 9:30-10:00

Session 4: Docker (and Galaxy and Cyverse and Bioconda)

  • Plenary Session -- Docker -- 10:00 - 10:45 am

  • Working and Networking session -- 10:45 - 11:15 pm

Session 5: Singularity (and Bioconda and Docker and Galaxy and Cyverse)

  • Plenary Session -- Singularity -- 11:15 - 12:00 pm

  • Working and Networking session -- 12:00 - 12:30 pm

Break for Lunch 12:30 - 1:30 pm

Session 6: CWL (and Bioconda and Singularity and Docker and Galaxy and Cyverse)

  • Plenary Session -- Michael Crusoe -- 1:30 - 2:15 pm

  • Working and Networking session -- 2:15 - 2:45 pm

Coffee and Additional Networking 2:45 - 3:15 pm

Session 7: NextFlow (and Bioconda and CWL and Singularity and Docker and Galaxy and Cyverse)

  • Plenary Session -- Evan Floden -- 3:15 - 4:00 pm

  • Working and Networking session -- 4:00 - 4:30 pm

Open working and networking session until 6pm