SPARC FAIR Codeathon Showcase 2022

Join us for the SPARC FAIR Codeathon showcase!

Event Details

Updated at: 09/21/2022

The SPARC Data and Resource Center, with funding from the National Institutes of Health (NIH), hosted a three-day in-the-cloud codeathon August 6-8, 2022.The second annual public global SPARC FAIR Codeathon is now over but you can register for the showcase!

Join us for the SPARC FAIR Codeathon showcase on Sept. 29, 4-5pm, EDT! In this webinar, teams will present their projects and Dr. Susan Tappan will moderate the discussion which will touch on open science, the codeathon experience, FAIR principles, and of course, what was created! Register now to join the conversation live or be informed when the recording is available on the SPARC YouTube channel.

codeathon

Five Projects:

SPARC Metadata Editor (sparc-me)

Grand Prize, $20,000 USD

The SPARC Metadata Editor (sparc-me) is a python tool to explore, enhance, and expand SPARC datasets and their descriptions in accordance with FAIR principles. Examples and tutorials are provided to demonstrate the use of the tool to programatically access curated datasets and their protocols, create new datasests, enhance dataset descriptions via schema extensions, conversion of data from other formats to the SPARC dataset structure, and demonstrates how the tool can be used with existing SPARC infrastructure such as o²S²PARC and the SciCrunch knowledgebase. GitHub YouTube

Sparclet

2nd Prize, $10,000 USD

A python library to generate and interact with flatmaps in a jupyter notebook using the ipyleaflet library.A python library to generate and interact with flatmaps in a jupyter notebook using the ipyleaflet library. GitHub YouTube

Quilted Tutorials

3rd Prize, $7,000 USD

In this project, we have created an online tutorial hub to guide users within and outside the SPARC community on how to combine tools within the SPARC ecosystem to create unified workflows. We have populated our hub with tutorials on mapping 2D spatial data to a 3D scaffold and re-sampling data for computational simulations. Our hub will be continually updated with new tutorials developed by our team, as well as by others who wish to contribute, and become a key resource for the SPARC community. GitHub YouTube

Transcriptomic oSPARC

4th Prize, $3,000 USD

The project includes a chrome extension that provides a guide for downloading and analyzing transcriptomic data available on the SPARC portal and a link to access the oSPARC template. The oSPARC template to visualize genes expression data from processed csv files. Two options are provided: the first is for one dataset, it generates a volcano plot, tables and ontology graphs; and the second option is to compare two datasets of data, it provides Venn diagrams and tables. GitHub YouTube

SPARC Life Cycle

Expanding and enhancing metadata for SPARC to make it more interactive and user friendly for curious minds. GitHub YouTube


Closed: Applications for participation are due July 25, 2022 (5pm EDT)

Who can participate?

Please be aware: 1) There is no registration fee associated with attending either of this event and 2) you must have your own laptop/computer and access to the internet because 3) we do not offer financial support for participating in this event.

We encourage researchers and data scientists at any stage of their science journey to apply. Teams will greatly benefit from people who possess any of the following skills:

  • Data mining, image and text analysis
  • Working knowledge of scripting languages (e.g., Shell, Python, R)
  • Familiarity with methods for manipulating and/or analyzing large datasets (AI/ML, computational modeling, etc.)
  • Developing bioinformatics code, pipelines or tools
  • Data visualization
  • Knowledge graphs
  • Web development
  • Understanding of neuroscience and/or neurostimulation

The projects are:

  • Creating a dark theme for the SPARC Portal.
  • Leverage AWS Athena and Glue to index, query and find data from SPARC datasets and develop a dashboard with relevant information.
  • Develop a Slack integration to interact with the SPARC repository.
  • Explore display of dataset metadata.
  • Combining scaffold mapping tools with SODA
  • Using Leaflet to interact with flatmaps in a Jupyter notebook.
  • Explore new modes of interaction with organ scaffold maps.
  • Establish services on o²S²PARC to automatically analyze SPARC-relevant image data (e.g., from the SPARC Portal).
  • Establish model-order-reduction (MOR) functionality on o²S²PARC using o²S²PARC's parameterized modeling framework.
  • SimpleSCKAN Query UI - development of a simple SPARQL query UI that can use pre-made templates to run queries against the SCKAN SPARQL store.
  • Create tutorial/educational content on use of SPARC services using, for example, Jupyter Notebooks.
  • Simple Protocols.io widget that provides a quick overview of the protocol that could be integrated with the SPARC Portal.
  • Modules that can be run against SPARC dataset metadata to enhance and expand the metadata (via Python).

Team formation and communications

How to apply? To apply, please complete this application form. Applications are due July 25, 2022 by 5pm EDT. We will select participants based on their experience and their motivation to attend.

We will notify accepted applicants on August 3, 2022. Accepted applicants have until August 3 at noon EDT to confirm their participation. If you confirm, please make sure that you can participate, as confirming and not participating prevents other scientists from attending this event. Please provide a monitored email address, in case we have follow-up questions.

How are teams formed? Before the event, we will create up to thirty teams, comprised of five to six individuals each with various backgrounds and expertise. Each will be led by an experienced leader.

When and where is the codeathon? The in-the-cloud codeathon runs from Saturday, August 6 through to Monday, August 8, 2022 (US Eastern Daylight Time). Participants are expected to be available throughout the codeathon days (within reasonable hours for their local timezone).

Organization of the event

What will a typical day be like? We will meet regularly as a group throughout the codeathon, exact timing to be determined as teams are formed. SPARC Data & Resource Center teams will host regular office hours enabling teams to seek guidance.

What will we build? We will make all pipelines, other scripts, software, and programs generated in this codeathon available on a dedicated public GitHub organisation.

Teams may submit manuscripts describing the design and use of the software tools they created to an appropriate journal such as the F1000Research hackathons channel, GigaScience, or PLoS Computational Biology.

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.

Please contact fair-codeathon-support@sparc.science if you have questions or need more information.

Spread the word

Spread the word and post the flyer everywhere it can be seen! SPARC codeathon flyer

Legal
Participants retain ownership of all intellectual property rights (including moral rights) to the code submitted to as well as developed in the codeathon. Employees of the U.S. Government attending as part of their official duties retain no copyright to their work and their work is in the public domain in the U.S. The Government disclaims any rights to the code submitted or developed in the codeathon. Participants agree to publish the code and any related data on GitHub.


Closed: June 27, 2022 - 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.