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Microbiome Hackathon

How-To Guide

A hackathon is a great way to expose students to microbial genomics. It is a low-pressure, supportive, fun, collaborative and creative environment. We have held two hackathons (our third was canceled due to COVID-19 closures) and have learned a lot! Check out our past events: 2019 Hackathon and 2018 Hackathon. Here is a document to share what we have put together to share best practices.


1. Theme

Students are most motivated by topics they connect with or relate to current events. Our first hackathon was focused on antibiotic resistance (diagnosing, treating, prevention, predicting) and our second was focused on microbiomes). Whereas some hackathons provide topics for all of the teams to solve, ours allowed students were able to come up with their own ideas. In their post-hackathon responses, students appreciated this open-ended type of hackathon where they could choose the topics. Students will sometimes change topics during the hackathon if they come to a dead end on their initial path. This is okay, but it can slow teams down and has the potential to be demoralizing. In order to best help students and avoid this, we asked students during registration (2+ weeks before) about their interests and had mentors check in early and often with teams at the start of the hackathon. Once students had coalesced around a shared interest, we encouraged them to develop a high-level question and then ask a more refined/narrower question that they could tackle in the context of a 2-day event and given the available data sources. There have been cases where students recapitulated findings in a paper, and, though this was discouraged, that team got a lot out of learning to code and also comparing their results with those in the paper.

2. Access to Data

This can be a big time sink. We tried to identify datasets that students would want to use prior to the hackathon based on their interests and had mentors working with them to download data from MGNify, SRA, MG-RAST, PATRIC and other sources. Even though it is often tricky to combine datasets correctly, we encouraged teams to do so if they could answer a specific question they had, with the caveat that there are likely biases linked to the datasets being collected and processed differently.

3. Location

We used a student lounge used for student entrepreneurship (Cornell’s eHub). The space had a large room for parts of the event requiring full participation, a large kitchenette, and smaller lounge areas/nooks and small rooms where groups set up for the entire weekend. The smaller rooms had projectors, which helped students share screens. This can also be accomplished with screen-sharing software like Zoom or Skype. Each group would choose a name early on in the event and they post their name on a sign near their location, which serves as a meeting point for the mentors during regular check-ins. Regarding space needs, you may need to think about audio-visual capabilities for group talks, capacity, access, and custodial needs.

4. Schedule

Friday night: We recommend a kickoff event that includes dinner, an energetic introduction to the event by the organizers, a dynamic speaker related to the topic (preferably someone who has developed their career using genomics), and a team-formation exercise. For the latter, we have had students who want to pitch an idea give 1-minute pitches to the group and then locate themselves throughout the space. Other students will then move to those groups and the groups start to form. Rarely is intervention needed, although in some cases it can be helpful. Fostering a welcoming and inclusive community is crucial to all aspects of the hackathon. Teams have as much time after dinner to start putting together their ideas. Efforts to diversify teams in terms of skillsets and exposure to a topic are also encouraged. Teams should be 4-6 members (5 works best).

Saturday: Breakfast is offered at the start of the day. Teams are encouraged to hone in on their questions and identify useful datasets. Before lunch, there is a mentoring check-in where a subset of mentors will discuss progress with each of the teams and help them with whatever they need help doing. Lunch is offered. Either during or after lunch, we recommend having a second speaker that could introduce the audience to a new skillset (previous suggestions include: D3 plotting, There is a second check-in towards late afternoon/dinner. Dinner is offered and teams can stay as late as they want. Mentors mingle throughout the day in case there are questions.

Sunday: Breakfast is offered. A final check in with teams at the start of the day. Early afternoon (3pm), judges go around to teams and hear a 5-minute (strict timing) presentation with 2 minutes for questions from the judges. Depending on the number of teams, all or a subset of teams will present in front of the audience. Judges and audience members can ask questions. Prizes are awarded.

Milestones are set throughout the entire day: pick a team name, come up with large question, more detailed question, identify dataset(s), identify genomics/statistical strategy, present results, conclude and extrapolate, form presentation. Teams upload team information (name, description, members) to the hackathon website at specified times during the event.

5. Mentors

This is a crucial part of the hackathon! The mentors really make the experience for the student teams. They help them through tough spots, help identify data, offer suggestions for analysis, help conceptualize problems, offer suggests on visualizing data. Having a large mentoring team (1:8 ratio is appropriate) is key. This can consist of faculty, postdocs, experienced students from the labs that are hosting the events, community members that are involved in related projects. Mentors should sign up for time slots and be offered food and schwag. Mentors should be recognized on the website prior to the event and coached about what the expectations are for mentors. Having diverse skillsets within the mentoring team helps with handling diverse questions. Mentors should be available during the various check-ins, at the least.

6. Advertising

We used a combination of advertising on various listservs, posting flyers around campus, making announcements in large, relevant undergraduate classes and posting on social media and various websites.

7. Support leading to the hackathon

Students may be apprehensive about a data-heavy hackathon. Many students will have limited experience with coding and only a cursory understanding of a topic. In order to get students more adapted, we have offered a 1-credit weekly course leading up to the hackathon where students are exposed to the type of data available for microbial genetics and also how to access data within python. This has further reduced the bar to join the hackathon and has improved turn-out and satisfaction during the event. The course consisted of hands-on accessing data and also brainstorming events around the topic.

8. Website resources

Links to data repositories, python tutorials, graphing assistance, and bioinformatics tools are available on the hackathon website.

9. Evaluation and Prizes

A set of judging criteria is made clear to teams at the start of the event. Judges should be relatively removed from team mentoring. Judges should be people who are versed in a topic and the microbial genomics techniques used. We used the following judging categories: Most Creative Scientific Question, Best Data Visualization, Best Analysis, Most Creative Use of Methods and Best Presentation. We gave monetary prizes. Judging is based on the final presentations and answers given to the judges and audience.

10. Schwag

We made a custom t-shirt each year. We have also offered books with custom monograms and other goodies. Students love these and the t-shirts (especially if they are well-designed and comfortable) serve as a good reminder of the event and repeat advertisement.

11. Evaluation of the event

We gave students a survey before and after the event to identify what worked well and areas for improvement and also to determine what impacts the hackathon had on students. Our surveys can be found here.

12. Career development

We recommend having 1-2 career-minded talks throughout the event where people working in the topic area can come and discuss the ins and outs of their work. Judges can also be chosen from various organizations or companies that may be interested in recruiting students to work at the event. If students are interested in being recruited, they can provide their CV and talk with people from various organizations and companies invited to the event.

13. Sponsorship

Our event was sponsored exclusively by the National Sciences Foundation. Depending on the topic area, it may be possible to offer recruitment opportunities to companies in exchange for defining the topic area (or a specific sub-topic or track) and judging. Your budget will depend on the number of people, prize money, costs associated with rental space, custodial needs, and schwag, but it will likely cost between $5,000-$10,000 for roughly 50-100 people.

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