Eligibility: Competitors from the United States and abroad are eligible.
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. Several prizes of up to US$10,000 each will be awarded.
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:
- SPARC Portal
- o²S²PARC simulation and analysis platform
- ApiNATOMY anatomical connectivity models
- Biolucida image server
- SPARC collection of experimental protocols
- Pennsieve data management platform
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. See here for example project ideas.
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.
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.
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:
- The FAIR Guiding Principles for Scientific Data Management and Stewardship
- The Healthcare and Life Sciences Community Profile for Dataset Descriptions
- Publishing FAIR Data: An Exemplar Methodology Utilizing PHI-Base
- 5 Principles for FAIR Software
FAIR Codeathon FAQs:
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 early June
Please feel free to contact the FAIR Codeathon team if you have questions or need more information: email@example.com.