2022 SPARC FAIR Codeathon

The SPARC Data and Resource Center, with funding from the National Institutes of Health (NIH), will host a three-day in-the-cloud codeathon August 6-8, 2022.
Updated at: 06/15/2022

SPARC FAIR Codeathon Learn more Submit a proposal

Submissions for project proposals are due June 27, 2022 (5pm EDT).

Sign up for the SPARC FAIR Codeathon listserv to make sure you keep informed about all things codeathon - announcements, important dates, open office hours, special events. See FAIR Codeathon FAQs.

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Project Proposal Submissions

In this codeathon, we are looking for exciting projects which use SPARC data and/or SPARC tools and resources in novel ways, particularly in enhancing, demonstrating, or measuring the findability, accessibility, interoperability, or reusability (FAIR) of the data. Total prize pool of US$50,000 -- including cash prizes and manuscript publication fees.

Projects must 1) demonstrate the value of SPARC’s public data and/or 2) directly integrate into or with any of the following SPARC tools and resources to improve their existing capabilities via the various APIs and services available:

There are several tools and resources available that may be leveraged when designing the projects. Codeathon projects should result in code, tools (see SODA for an example), datasets, or other outputs which are open and freely available. Projects from earlier SPARC codeathons are available here: https://github.com/SPARC-FAIR-Codeathon and see here for example project ideas. More information about the 2021 codeathon is available here.

SPARC investigators are generating lots of FAIR data from a range of species, and spanning all the major visceral organs and peripheral nerves, as they seek to better understand the autonomic nervous system. The data being collected includes microscopy, electrophysiological and mechanical time series, single-cell RNASeq, functional MRI, and more.

SPARC data is highly curated, ensuring the data is published in a FAIR manner and backed by a semantic knowledge base. SPARC data is further enriched by being mapped to 2D “flatmaps” that enable visual exploration of the topological anatomy of the peripheral nervous system. Where possible, data is also mapped to 3D organ scaffolds to provide a common coordinate system enabling comparison across subjects, species, and protocols as well as interactive environments to aid understanding and interpretation of SPARC data. The open-source tools for mapping data to scaffolds are available.

One special data resource, called “simulations”, consists of computational models and data analysis pipelines. These simulations can be run on o²S²PARC, which was designed to host, modularize, and ensure the reproducibility of simulations contributed by researchers. This is achieved by archiving contributed simulation code along with the code’s execution environment with versioning.

SPARC data, simulations, and maps are published on the SPARC Portal, an open-source platform for finding, exploring, visualizing, interacting with, and accessing SPARC data and associated computational models and analyses.

Each team will have access to training and computational resources in the cloud to turn your idea into a working prototype. Various SPARC experts will be available to help with technical advice as needed.

Here are examples of codeathon projects that may be of interest to potential applicants. Previous codeathon projects are available on GitHub: https://github.com/SPARC-FAIR-Codeathon and more information about the 2021 codeathon is available here.

Office hours

The SPARC FAIR Codeathon organizers will be holding open office hours during this proposal phase. Be sure to sign up to be informed on the scheduling of the open office hours or contact the organizers directly at: fair-codeathon-support@sparc.science

FAIR Codeathon FAQs:

What is FAIR? The volume of publicly available data continues to rise exponentially, but the capacity for fully employing this data is being hampered by a series of limitations. FAIR is a very powerful initiative that has taken root worldwide. The initiative has the potential to significantly increase the value of life science data sets. While the concept shares some commonality with the semantic web, FAIR data goes further to expand opportunities for knowledge-sharing and value. Here are four foundation papers on this exploding field:

Do I have to lead a team? You can choose to lead your project team, recommend someone, or we can try to find a suitable team lead. Providing a designated team lead dramatically increases the probability that we will select the project for the codeathon.

Do I need to assemble a team? No. We will create working groups of five to six individuals who have various backgrounds and relevant expertise to work on each project.

What are my responsibilities as a team lead? The team leader will coordinate a group of 5-6 people in defining the project and producing clear vision for developing a solution. To accomplish this goal, the team lead must define and delegate tasks, incorporate team members’ ideas to accomplish the goal, and ensure the team’s success.

What if I only want to participate? Applications for those who would like to participate in the codeathon will be available in July. Be sure to sign up to make sure you don’t miss the announcement.

Please feel free to contact the FAIR Codeathon team if you have questions or need more information: fair-codeathon-support@sparc.science.