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Details on Each Session

Welcome and Introductions: 5/9

  • Opening Remarks (Titus)
  • Portal Session Overview (Jessica)
  • HMP Session Intro (Titus)
  • Kids First Session Intro (Deanne and Jonathan)
  • RNAseq with GTEx data Session Intro (Rayna)
  • SPARC Session Intro (Jeff)
  • Logistics and Closing Remarks (Jessica)

CFDE Portal Demonstration: Demonstration, 5/9

The (Common Fund Data Ecosystem Coordinating Center) CFDE-CC supports efforts to make Common Fund data sets more findable, accessible, interoperable, and reusable (FAIR) for the scientific community through collaboration, end-user training, and data set sustainability. The CFDE-CC manages and organizes CFDE activities, engage with participating Common Fund programs, connect with user communities, support training, develop tools and standards, and provide technical expertise to Common Fund programs.

The Common Fund Data Ecosystem (CFDE) Portal Demonstration on Monday, May 9 will be a demonstration session. Participants will learn about how to use the CFDE portal and can ask questions about it.

Working with Human Microbiome Project Data: Lesson, 5/10

This session will involve getting Human Microbiome Project (HMP) data off of the CFDE Portal and working in the cloud using Amazon Web Services. Participants will be provided with an Amazon Web Services account and do basic bioinformatics analysis with sequencing data.

Gabriella Miller Kids First Pediatric Research Program (Kids First): Lesson, 5/10

The goal of the Gabriella Miller Kids First Pediatric Research Program (Kids First) is to help researchers uncover new insights into the biology of childhood cancer and structural birth defects, including the discovery of shared genetic pathways between these disorders. Children with birth defects have an increased risk of developing childhood cancer. This suggests there are shared genetic pathways underlying some types of childhood cancer and structural birth defects. Analyzing genetic sequence data from children with childhood cancer and structural birth defects together may lead to the discovery of new genetic pathways.

This session will teach participants how to access and use federated CFDE graph data though the Human BioMolecular Atlas Program-Kids First collaboration.

Introduction to R for RNA Sequencing Analysis: Lesson, 5/11

RNA-Sequencing (RNA-Seq) is a popular method for determining the presence and quantity of RNA in biological samples. In this 3 hour workshop, we will use R to explore publicly-available RNA-Seq data from the Gene Expression Tissue Project (GTEx). Attendees will be introduced to the R syntax, variables, functions, packages, and data structures common to RNA-Seq projects. We will use RStudio to import, tidy, transform, and visualize RNA-Seq count data. Attendees will learn tips and tricks for making the processes of data wrangling and data harmonization more manageable. This workshop will not cover cloud-based workflows for processing RNA-seq reads or statistics and modeling because these topics are covered in our RNA-Seq Concepts and RNA-Seq in the Cloud workshops. Rather, this workshop will focus on general R concepts applied to RNA-Seq data. Familiarity with R is not required but would be useful.

Stimulating Peripheral Activity to Relieve Conditions (SPARC): Demonstration, 5/11

The Common Fund’s Stimulating Peripheral Activity to Relieve Conditions (SPARC) program accelerates development of therapeutic devices that modulate electrical activity in nerves to improve organ function. This therapeutic strategy, also known as “bioelectronic medicine,” could offer new treatment options for diverse diseases and conditions such as hypertension, heart failure, gastrointestinal disorders, and more.

SPARC will host a session on providing information on access to SPARC resources via the SPARC portal and associated APIs.

Social Co-working

If you attended a hackathon session and would like to work through related exercises, connect with organizers and instructors via Zoom during this time to discuss.