Computational techniques and resources to characterize translational relevance of model organisms in Alzheimer’s Disease

The Jackson Laboratory for Genomic Medicine

June 15, 2023

9:00 am - 5:00 pm

Instructors: Amelia Kallaher, Ravi Pandey, Greg Cary

Helpers: Asli Uyar, Sue McClatchy

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General Information

This workshop aims to accelerate targeted use of Alzheimer’s Disease (AD) mouse models in preclinical studies by providing participants with hands-on training on computational approaches for concurrent analysis of omics data from both human and mouse studies. In this workshop, we will use resources from the AD Knowledge Portal (adknowledgeportal.org), a public data repository that shares data generated by multiple collaborative research programs focused on aging, dementia, and AD.

After attending this workshop, the participants should be able to:

Locate data in the AD Knowledge Portal.
Annotate data with the associated metadata.
Utilize state-of-the-art bioinformatics tools for rigorous QC, pre-processing and comparative analysis of transcriptomic data in R-Studio.
Perform interspecies analysis for mouse-to-human mapping of transcriptomics signatures.
Optimize study designs with insights from existing data and by incorporating robust computational workflows in their ADRD research.

The course is aimed at researchers who want to incorporate existing omics data resources in their AD and related dementias (ADRD) or aging research.

Where: Leo Holt Conference Room, 10 Discovery Drive, Farmington, CT. Get directions with OpenStreetMap or Google Maps.

When: June 15, 2023. Add to your Google Calendar.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below).

Accessibility: We are committed to making this workshop accessible to everybody. For workshops at a physical location, the workshop organizers have checked that:

The room is wheelchair / scooter accessible.
Accessible restrooms are available.

Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.

Contact: Please email asli.uyar@jax.org or susan.mcclatchy@jax.org for more information.

Roles: To learn more about the roles at the workshop (who will be doing what), refer to our Workshop FAQ.

Who can attend?: This workshop is open to those at JAX and neighboring institutions. Prerequisite: This course requires basic R programming experience.

Code of Conduct

Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.

Surveys

Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey

Schedule

Thursday, June 15

Before	Pre-workshop survey
9:00	Introduction to the AD Knowledge Portal and MODEL-AD
9:45	Working with portal data using RStudio
10:30	Morning break
11:00	RNA-Seq analysis workflow
12:00	Lunch break
13:00	Mouse-human alignment of transcriptomic signatures
14:30	Afternoon break
15:00	Functional Alignment using AD Biological Domains
16:45	Wrap-up
17:00	END

Setup

To participate in this workshop, you will need access to software as described in the setup instructions.