How to Write an Effective Lay Abstract (Seminar)

Presented by:

• The MetNet Research Advocates

A lay abstract helps patients, their caregivers, and non-scientists understand your cancer research and learn how it can benefit them. Among other uses, a lay abstract is often a requirement when submitting grant applications. This workshop will provide insights on how to write a successful lay abstract, including: guidance on appropriate reader literacy level, concrete examples of how to adapt concepts and word choices from a scientific abstract to a lay abstract, and available online tools and additional resources.

NCI Genomic Data Commons (GDC) Tools Workshop: Feedback on Single Cell RNA-Seq Visualization

Presented by:

• Dave Sturgill | NCI GDC Project Officer
• Sharon Gaheen | FNL Technical Project Manager
• Bill Wysocki | University of Chicago Director of User Services
• Lauren Mogil | University of Chicago Lead Bioinformatician
• Xin Zhou | St. Jude Children’s Research Hospital, Director of Data Visualization

The NCI Genomic Data Commons (GDC) is a computational platform and repository for cancer researchers who need to understand cancer, its clinical progression, and response to therapy.

The GDC makes harmonized data and gene- and variant-level analysis tools available to the research community in the GDC Data Portal. This workshop will provide a brief overview of GDC analysis tools, and solicit feedback from junior investigators on the new Single Cell RNA-Seq Tool which supports the visualization of single-cell RNA-Seq data with cluster plots and gene expression overlays. This workshop will also provide information on GDC Support materials and feedback mechanisms.

Pre-requisites:

• Run analysis tool demos on the GDC Data Portal in the Analysis Center with focus on the Single Cell RNA-Seq Tool.
• Review the GDC Data Portal User’s Guide with focus on the Single Cell RNA-Seq tool User’s Guide.

GDC Office hours are available in advance of the workshop for workshop attendees to familiarize themselves with the prerequisites / knowledge /pre-work. 

Run analysis demos on the GDC Data Portal in the Analysis Center with a focus on the Single Cell RNA-seq Tool

Review the GDC Data Portal User's Guide with a focus on the Single Cell RNA-seq Tool User's Guide

There will be two GDC Office Hours Sessions: 

• Tuesday, August 5, 11: 00 - 12:00 PM PT / 2:00 – 3:00 PM ET - Join via WebEx 
• Friday, August 8, 8:00 - 9:00 AM PT / 11:00-12:00 PM ET - Join via WebEx

This workshop is limited to the 30 attendees on a first come first served sign up basis.

Automated Image Analysis of Large Highly-Multiplexed Tissue Images Using Nextflow and MCMICRO

Presented by: the developers of MCMICRO from the Laboratory of Systems Pharmacology at Harvard Medical School, in collaboration with the MC2 Center team at Sage Bionetworks.

Are you tasked with generating and analyzing highly-multiplexed tissue imaging data? Are you struggling to handle large (GB-to-TB sized) datasets? If so, you’ll find this workshop essential. But even if you don’t, you’ll still learn valuable skills related to Nextflow and its applications, expanding your bioinformatics toolkit. Join our virtual workshop on analyzing terabyte-sized highly-multiplexed tissue imaging data with Nextflow and MCMICRO. You’ll learn:

• Nextflow Fundamentals:

  Understand the basic principles and advantages of Nextflow, a cutting-edge bioinformatics workflow language and ecosystem.

• MCMICRO Pipeline:

  Get acquainted with MCMICRO, an open-source multiplexed tissue imaging pipeline written in Nextflow. You’ll learn how to deploy essential tasks for processing large high-plex image data, including image registration, illumination correction, cell segmentation, and quantification, through reproducible, containerized processes that scale to images hundreds of GB to TB in size.

• Hands-On Practice:

  Run MCMICRO on exemplar datasets and acquire the tools to explore the Nextflow community and ecosystem for your own research projects.

Learn with experts from Harvard Medical School’s Lab of Systems Pharmacology, Sage Bionetworks, and the MC2 Center. No prior experience with these tools needed, just comfort with command line and bioinformatics basics.

Pre-requisites:

• Comfort with Command Line: Participants should be comfortable using the command line.
• Bioinformatics Experience: Some experience with bioinformatics tools is required, but prior experience with Nextflow or MCMICRO is not necessary.
• Image analysis experience: Some experience with image analysis tools (ImageJ, Cellprofiler, QuPath) is helpful but not necessary.
• Computer access. Whether you’re using a laptop or desktop, please see Pre-workshop instructions (below). The workshop will be conducted using a reproducible cloud environment provided to all participants.

Pre-Workshop Instructions for MCMICRO workshop

Thank you for registering for our workshop on Automated Image Analysis of Large Highly-Multiplexed Tissue Images Using Nextflow and MCMICRO. As the workshop date approaches, we want to ensure you are fully prepared to make the most of this hands-on training session.

To facilitate the workshop, we will be using cloud development environments hosted on Gitpod. To get started, please complete the following steps before the workshop:

If you encounter any issues with registration or accessing Gitpod, please don’t hesitate to reach out to Adam Taylor at adam.taylor@sagebase.org.

Don’t forget to complete the pre-workshop instructions on your computer prior to the workshop! You’ll need it to participate in the hands-on activities and explore the tools we’ll be covering.

We look forward to seeing you on August 19 for what promises to be an insightful and productive session.

Resources

Here are some helpful resources to help you decide if this workshop is for you or to expand your knowledge of the tools and communities we will be using:

• mcmicro.org
• nextflow.io
• nf-core