Events


May 2022 Hackathon

Date: 05/09/2022 - 05/13/2022
Time: 9:00 am PDT - 3:00 pm PDT

We are pleased to announce that the NIH Common Fund Data Ecosystem will be hosting a hackathon on NIH Common Fund data sets. This hackathon has both synchronous and asynchronous work, with concentrated hackathon sessions on specific data sets. Participants can attend whichever hackathon sessions they are interested in, and also form working groups and tackle issues throughout the week organized in a GitHub repository. There is no minimum work requirement, all are welcome to participate as much or as little as schedules and interest allows!

View the Event Website here: https://nih-cfde.github.io/2022-may-hackathon/

Hackathon Benefits:

– Gain experience with Common Fund data sets and have access to data set curators!

– See an immediate product from a short burst of concentrated effort!

– Meet researchers with common interests and potentially spur collaborations or funding efforts!

Participant Skill Level:

The hackathon is open to the public, and anyone can attend. Despite the name “hackathon”, participants don’t need to be experts in computer science! The most important criteria is interest in the data sets, and some familiarity with the command line and GitHub is helpful but not required.

Common Fund Session Details:

Gabriella Miller Kids First Pediatric Research Program

The goal of the Gabriella Miller Kids First Pediatric Research Program 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.

Kids First will host a session on accessing and using federated Common Fund Data Ecosystem graph data through the Kids First-Human BioMolecular Atlas Program graph database with an API.

Stimulating Peripheral Activity to Relieve Conditions

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.

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

Human Microbiome Project

The Human Microbiome project has DNA sequencing data to characterize the microbiome in healthy adults and people with specific microbiome-associated diseases. It also contains integrated datasets with multiple biological projects from the microbiome and host over time for specific microbiome associated diseases.

A session on Human Microbiome Project data will involve obtaining this data from the Common Fund Data Ecosystem search portal and working with it using Amazon Web Services.

Common Fund Data Ecosystem Search Portal 

The Common Fund Data Ecosystem Coordinating Center supports efforts to make Common Fund data sets more findable, accessible, interoperable, and reusable for the scientific community through collaboration, end-user training, and data set sustainability.

The Common Fund Data Ecosystem Portal Demonstration will be a demonstration session on how to access data in the Portal.

Data Harmonization and Visualization in R with Genotype-Tissue Expression Data

The Genotype-Tissue Expression Program established a data resource and tissue bank to study the relationship between genetic variants (inherited changes in DNA sequence) and gene expression (how genes are turned on and off) in multiple human tissues and across individuals.

This session will showcase how R can be used for a variety of data visualizations with Gene Tissue Expression data.

Schedule

Day Date Time Topic
Monday 5/9/22 9 – 11 am PT Welcome + Introduction to Data Sets
Monday 5/9/22 1 – 2 pm PT CFDE Portal Demo
Tuesday 5/10/22 9 – 11 am PT iHMP Data Exploration
Tuesday 5/10/22 1 – 3 pm PT Using APIs to Access KidsFirst Data
Wednesday 5/11/22 9 am – 12 pm PT Introduction to R for RNA Sequencing Analysis with GTEx Data
Wednesday 5/11/22 1 – 3 pm PT Exploring SPARC data on organ – nervous system connectivity
Thursday 5/12/22 9 – 11 am PT Social Co-working
Thursday 5/12/22 1 – 3 pm PT Social Co-working
Friday 5/13/22 9 – 11 am PT Closing Session

 



CFDE May Hackathon: Intro to RNAseq with GTEx Data

Date: 05/11/2022
Time: 9:00 am PDT - 12:00 pm PDT

This event is part of the Common Fund May Hackathon.

A full schedule for this event is available on our website at https://nih-cfde.github.io/2022-may-hackathon/

The event overview is available at https://www.nih-cfde.org/events/may-2022-hackathon/

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.



CFDE-IDG Bi-Weekly Meeting

Date: 05/11/2022
Time: 12:00 pm EDT - 12:30 pm EDT

CFDE-IDG Bi-Weekly Meeting – 9:00 – 9:30 AM PST / 12:00 – 12:30 EST

Zoom Link: https://us06web.zoom.us/j/84751789699?pwd=SDhLeFdhLzFzS1QyRGQ3d09ZU1o2dz09

Running Agenda Link: https://docs.google.com/document/d/1K5-wqCnI9pBviCQ9P0advSAKugnpnyEohuH7SIi6yjo/edit#heading=h.3ia46913z0oa

 

Discuss project management for IDG CFDE award



CFDE May Hackathon: Exploring SPARC Data

Date: 05/11/2022
Time: 1:00 pm PDT - 3:00 pm PDT

This event is part of the Common Fund May Hackathon.

A full schedule for this event is available on our website at https://nih-cfde.github.io/2022-may-hackathon/

The event overview is available at https://www.nih-cfde.org/events/may-2022-hackathon/

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.