Computational Medicine Codeathon and AWS workshop at Chapel Hill in March

Computational Medicine Codeathon and AWS workshop at Chapel Hill in March

NIH is pleased to announce a computational medicine-focused codeathon. To apply, please complete the application form by February 25, 2020. We will also be offering a free workshop, AWS Technical Essentials, the day before the codeathon. Read on for more information about the event.

When and where are the codeathon and workshop?
The codeathon will be held at the University of North Carolina at Chapel Hill.  the codeathon runs from March 11-13, 2020. The optional workshop will be the day before the codeathon, March 10, 2020.

What will the pre-codeathon workshop cover?
AWS Technical Essentials introduces you to AWS products, services, and common solutions. It provides you with fundamentals to become more proficient in identifying AWS services so that you can make informed decisions and get started working on AWS.

Do I need to participate in both the workshop and the codeathon?
No. If you would like to only participate in the workshop, please email Allissa Dillman. If you would like to participate in the codeathon without attending the workshop you can indicate this in the application process.

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

  • Analyzing sequencing data types
  • Data mining and text analysis
  • Working knowledge of scripting (e.g., Shell, Python, R)
  • Familiarity with methods for manipulating and/or analyzing large datasets
  • Developing bioinformatics code, pipelines or tools
  • Data visualization

There is no registration fee associated with attending either of these events.

Note: You must bring your own laptop. We do not offer financial support for travel, lodging, or meals for this event.

What are some of the potential team projects?

  • Mining literature and datasets to find the interest in and applications of RNA sequencing technologies over time
  • Making a pipeline for fast conserved protein motif identification
  • Studying the impact of university reputation on election to a national academy
  • Integrating multi-omics data in yeast
  • Using deep learning to relearn RNA thermodynamic folding parameters
  • Diversifying the pipeline for identifying bulk RNA-seq derived-biomarkers of cancer risk within single-cell populations
  • Inferring intact transcript structure and discovering novel isoforms from long-read data
  • Automating tools to search and analyze large genome sequence repositories

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

What will a typical day be like?
We will meet from 9 am to 5 pm each day, with the potential to extend into the evening hours for continued work or optional social events.

Each day, teams will present short talks to introduce their project (day 1), discuss project progress (day 2), and present the results (day 3). We will also gather as a group for a few short presentations on a hot topic of interest to the bioinformatics and biomedical community (such as bioinformatics best practices, coding styles, related biomedical topics, etc.) and then break out to work on team project pipelines and tools for the analysis of large datasets within a cloud infrastructure.

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

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

How to apply?
To apply, please complete this application form.  Applications are due February 25, 2020 by 3 p.m. EST. We will select participants based on their experience and their motivation to attend.

We encourage prior participants and prior applicants to apply. We will notify the first round of accepted applicants on February 27, 2020. Accepted applicants have until March 3 at noon ET to confirm their participation. International applicants or those with particular skill sets may be accepted early. If you confirm, please make sure that you can attend, as confirming and not attending prevents other scientists from attending this event. Please provide a monitored email address, in case we have follow-up questions.

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.

Please contact Allissa Dillman if you have questions or need more information.


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