Events


CFDE May Hackathon: Welcome + Intro to Data

Date: 05/09/2022
Time: 9:00 am PDT - 11:00 am 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/

This session will provide an overview of data sets in this event.



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-GlyGen Bi-Weekly Meeting

Date: 05/09/2022
Time: 9:30 am EDT - 10:00 am EDT

CFDE-GlyGen Bi-Weekly Meetings: 6:30 – 7:00am PST / 9:30 – 10:00am EST

Zoom link: https://us06web.zoom.us/j/85394892643?pwd=YU16TitweDM3Zzh2eUZaMkpuQjhQZz09

Agenda: https://docs.google.com/document/d/1WaVunCQ97yRYxW7TCQlHo6dm5OHl14O_pBw6gPEhzPM/edit#



CFDE May Hackathon: CFDE Portal Demo

Date: 05/09/2022
Time: 1:00 pm PDT - 2:00 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 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.



Variant Working Group

Date: 05/09/2022
Time: 1:00 pm PDT - 2:00 pm PDT

File location: https://drive.google.com/drive/folders/1UcF8OS9OSkqwg1BXN-HxNu3MKN0IzJm3?usp=sharing

Who: Please contact support@cfde.atlassian.net if you do not have a calendar invite, or have any additional questions.

What: The goal of the Variant Working Group (VWG) is to make CFDE variant data FAIR and to make variant data and knowledge accessible across CFDE projects and the wider scientific community.

When: Every month on the second Monday 1pm PST / 4pm EST

Where: https://us06web.zoom.us/j/87047199698?pwd=MVBHakpoQ2t0L1FDU2xEZVZ0T0N4QT09

Charter: https://docs.google.com/document/d/1L84L20Z3v4wPYjdqjQz0JpGFud0JPNUK/edit?



Gene Expression Working Group

Date: 05/09/2022
Time: 2:00 pm EDT - 3:00 pm EDT

Gene Expression Working Group – Agenda & Notes
Agenda : https://docs.google.com/document/d/1XVe7qPOOvADdxXI3m4pIwhKYf0qUxcYUMUz2vTdDL8I/edit
Who: Please contact ROCarter@som.umaryland.edu or support@cfde.atlassian.net if you do not have a calendar invite.
What: This group will survey and evaluate existing resources and then recommend standards for metadata, file formats, and an API for the CFDE to facilitate storing, retrieving, and querying gene expression data.
When: Every other Monday at 11am PT / 2pm ET
Where: https://umaryland.zoom.us/j/99610147492?pwd=clRiSk8vcjZxWUVXOVU0U3FDUlVSdz09

Important Docs/Links:

WG Charter