Women-Led Codeathon. . .A First for NLM

Participants of the first all women-led NLM codeathon rejoice on the last day. 

It was an idea whose time had come. NLM is well known and respected for hosting and sponsoring codeathons that bring together researchers and coders from diverse technical backgrounds together to create tools that solve relevant problems for the biomedical community in a collaborative—not competitive—way. But now NLM can also be known for bringing gender diversity to codeathon leadership.

NLM had never hosted an all women-led codeathon. That changed earlier this year when, after five years and more than 40 codeathons, NLM hosted its first codeathon with  all female leadership.

It won’t be the last.

“Though codeathons have a wealth of subject matter experts, codeathon culture, as in many technical fields, has a large gender gap, with only 20%-25% female participants,” said Biomedical Data Science Outreach Coordinator and coordinator of NLM codeathons Allissa Dillman, PhD.  “We wanted to do something about this, so we created a codeathon with an all-female organization and leadership and team projects proposed, led, developed, and presented by women.”

Miranda Darby and Amanda Bell (left to right) collaborate during the codeathon.

Forty-six women from 11 NIH institutes, 10 universities, two consulting firms, two industrial companies, and a software company met at the Cloisters on the NIH campus to work together as teams on eight projects. Over three days, teams tackled scientific problems with an emphasis on sharing expertise and insights throughout the event.

The three days of intense coding sessions were interspersed with informative speakers, the opportunity to engage with female leadership at NLM, and an optional group dinner for further networking. The codeathon ended with final presentations and exciting live demonstrations.

One participant said, “I absolutely loved that all the projects were led by women, and that the chosen participants were women. I’ve never participated in a codeathon before, and one of the primary reasons is that it’s hard to feel comfortable being in an extreme minority.” Another participant commented on the unique sense of community, noting that “the fact that it turned out being only-women was for me unexpected and had strong positive points. I’m a strong, opinionated woman that always worked comfortably among powerful male bosses, but this women codeathon experience was incredibly empowering.”

And all this energy and interest didn’t end with the codeathon.

Several teams continued to collaborate on their codeathon projects after the event was over, conducting analyses, writing manuscripts, and preparing posters for upcoming conferences. The work continues—and so will the codeathons.

Want to learn more about upcoming events?  Check out https://ncbi-codeathons.github.io/

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Summer Rankin and Kymberleigh Pagel (left to right) relax and work at the codeathon. (All photos by Bart Trawick, PhD, of NLM)

Projects from the First Women-Led Biodata Codeathon

  • OVARIE: An open-source genetic variant and gene annotation package.
  • HIPS: A pipeline for finding structural variants in public aggregated human data.
  • Viral-VDAP: A virus-variant discovery and annotation pipeline.
  • FANI-PACK: An R-based ICD medical code converter for use in tracking pipelines tracking and evaluating disease and diagnosis.
  • PubImproved: A machine learning and natural language processing tool to assist researchers and nonscientists in finding relevant PubMed citations.
  • PIPS: A pipeline for the design of patient-specific disease progression phenotypes.
  • TraIN: An R tool for discovering cell-to-cell communication molecules from RNAseq data.
  • FAIR: An automated pipeline for extracting, structuring, and merging data from clinical case report forms and PDF files.

Box 1. Projects created by the teams in the Women-Led Biodata Codeathon. Source code for all National Center for Biotechnology (NCBI) codeathon projects is available on the NCBI GitHub repository.

Bringing Diversity into Codeathons

To learn more about why it’s crucial to build diversity into codeathons, NLM in Focusspoke with Allissa Dillman, PhD, biomedical data science outreach coordinator and coordinator of NLM codeathons.

What’s your background?

I grew up in a rural farming community in northern Minnesota that was so small, my graduating high school class was 16 people. I was the first member of my family to graduate from college.  Thanks to the undergraduate scholarship program (UGSP) here at NIH I had my first plane ride, at 19, to our nation’s capital. Having the opportunity to study and work at NIH changed the entire trajectory of my life. I chose NIH’s graduate partnership program (GPP) as a way to fulfill my dreams of studying abroad in Sweden at the Karolinska Institutet, where I received my PhD in computational neuroscience.  It’s been a unique and wild ride and I owe a lot to the amazing training programs here at NIH that support students from diverse backgrounds.

Why did you choose to study science?

After I almost blew up our family bathroom mixing various household chemicals, my father suggested perhaps I would grow up to be a scientist.  I pursued this interest throughout elementary and high school exploring subjects such as how the brain works and how to make a hovercraft out of a shop vacuum through science fair projects.  The hovercraft idea was inspired by my dad’s large collection of Popular Mechanics magazines and his own excitement for building things.  I participated in science “magic shows,” and took every science elective.  All of this freedom and exploration was due in large part to my high school science teacher.  He always found ways to get access to materials, resources and support so I could reach my potential. To me, the beauty of science is the never-ending puzzle and lifelong learning required to attempt to solve it.

Why are you so passionate about bringing more women and underrepresented minorities into the scientific community?

I have worked in very male-dominated fields of study, from chemistry to computer science. From these experiences, I have a keen understanding of the importance of diverse mentorship and supportive community spaces. Coming from a rural area, I understand how important access is. My mother still goes to the public library to use the internet, and it impacts her ability to interact with the world and the types of information she consumes. The amazing thing about technology is that it has the potential to level the playing field. At NLM, we focus on workshops and training around coding, data science, and bioinformatics skills that create a solid foundation and use codeathons as an opportunity to apply those skills creatively and collaboratively to come up with solutions that impact the entire community. As the codeathon team lead, I always strive to work with diverse communities to build events that offer equitable access for all.

What differences have you noticed when a diverse group of people is involved?

Having a diverse group of solvers offers more unique solutions. I have also noticed more team cohesion and collaboration. One of the more surprising things was that more teams were sharing information and discussing project ideas on Slack well before the most recent women-led codeathon. The community also has a more persistent feel, with participants reaching out to each other and me long after the event is over to offer support, be supported, and share their successes. I think diversity and inclusion bring more success! 


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