Monday, September 23rd    

11:00 am–12:00 pm Help Desk NCBI Codeathon Team
This will be an optional session for individuals who are having trouble accessing Slack, GitHub, and GCP. Please only attend if you need support with codeathon platforms.

12:30–1:30 pm Whole group meeting: Welcome and introduction 

• Logistical information (including GitHub, Slack, Zoom, Cloud Access, Support)
• Discussion of team roles
• Overview on accessing NDARO and Pathogen Resource Data
• Event photo: Codeathon zoom mosaic 

1:30–5:00 pm Team breakout meetings: Initial planning and work time 

• Introduce team members 
• Assign team roles
• Decide on initial approach; Outline readme introduction; Create workflow diagram 

4:30–5:00 Team Lead meeting | Push work to GitHub 

Tuesday, September 24th 

11:00 am–12:00 pm Exploring NCBI Resources: Pathogen project & NDARO

12:30–1:30  Whole group meeting: Teams present proposed workflows (3 minutes per team) 

1:30–5:00 Team meetings and work time 

4:30–5:00 Writers’ meeting | Push work to GitHub 

Wednesday, September 25th    

11:00 am–12:00 pm NCBI Codeathon Alumni Discussion & Networking

12:30–1:30 Whole group meeting: Lightning stand ups

1:00–5:00 Team meetings and work time 

4:30–5:00 Push work to GitHub 

Thursday, September 26th  

11:00 am–12:00 pm Meet NIAID Staff
Participants will have the opportunity to meet and interact with NIH Training and Program Officers, Scientific Review Officers, and staff from the Bioinformatics and Computational Bioscience Branch. In breakout sessions, participants can ask questions about NIAID Programs and activities, funding opportunities and grant submissions, and learn about bioinformatics resources available at NIAID.

Speaker Information:

• Jyothi Arikkath, PhD – Program Officer, Office of Training and Special Programs
• Mariam Quinones, PhD – Head of Science Support Services, Bioinformatics and Computational Bioscience Branch
• Annie Walker-Abbey, PhD – Scientific Review Officer, Scientific Review Program
• Barry Margulies, PhD – Scientific Review Officer, Scientific Review Program
• Nancy Ernst, PhD – Program Officer, Division of Microbiology and Infectious Diseases
• Glen McGugan, PhD – Program Officer, Division of Microbiology and Infectious Diseases

12:30–1:30 pm Whole group meeting: Lightning stand ups

1:30–4:00 Team meetings and work time 

4:00–5:00 Prepare final presentations | Push work to GitHub 

Friday, September 27th  

12:30–3:30 Final team presentations (7 minutes per team with slides), breaks included 

Schedule Details 

• Team Lead conveys scientific objectives to team, coordinates work. 
• Tech Lead coordinates software installation and data acquisition, manages version control and the team’s GitHub repository, troubleshoots technical issues with tech support. 
• Writer ensures that all work is documented, manages GitHub README and Team Report 
• Flex fills various roles and assumes responsibilities for tasks as needed. 

Proposed workflow presentations (3 min per team) 

Each team will share their plans and get feedback from other teams. Ideally, the team will present 1 slide or an outline of the proposed work in their readme.
Suggested topics to cover briefly: 

• What software (if any) exists to help your project? 
• What metrics will you use to measure performance?
• What data will you use?
• What is your planned workflow for the codeathon? 

Lightning stand-ups (3 min per team) 

Each team will report on the previous day’s progress and any roadblocks they’ve encountered. This is an opportunity to troubleshoot and share expertise across teams. 

Final team presentations (7 min per team, plus short discussion) 

Each team will present their codeathon product and suggest opportunities for follow-up work. Time permitting, the codeathon team will accept 1-2 questions from the audience, and the rest of the discussion is encouraged in the chat or on Slack.  

Team Lead meeting 

All Team Leads and the event organizers meet to discuss team management issues, opportunities for inter-team collaboration, and questions about the codeathon. 

Writers’ meeting 

All Writers and the event organizers meet to discuss documentation, including the GitHub READMEs and Team Reports. 

Push work to GitHub 

We encourage you to continuously commit your progress to git and push to the team GitHub repository often. To ensure that every participant’s work is committed and shared at least once a day, we will reserve the last half hour of the end of each working day for committing, merging, and pushing any unfinished work.