We are pleased to announce that the NIH Common Fund Data Ecosystem will be hosting a hackathon on NIH Common Fund data sets from May 9 - 13! This follows on our first hackathon (see recap blog post).
This hackathon has both synchronous and asynchronous work, with concentrated hackathon sessions on specific data sets and co-working sessions on Thursday. Participants can attend whichever hackathon sessions they are interested in. There is no minimum work requirement, all are welcome to participate as much or as little as schedules and interest allow!
See our schedule and find more information about this event here: https://nih-cfde.github.io/2022-may-hackathon/
Register for the hackathon here: https://www.nih-cfde.org/events/may-2022-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!
Common Fund Session Details
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.
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.
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.
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.
Introduction to R for RNA-Seq Analysis Workshop
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.
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.
See our schedule and find more information about this event here: https://nih-cfde.github.io/2022-may-hackathon/
Register for the hackathon here: https://www.nih-cfde.org/events/may-2022-hackathon/
Please don’t hesitate to contact training@cfde.atlassian.net with any questions!
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