Congrats to our winners!
BroadHacks 2024 Feature Challenge: Team 14 - BroadHive
BroadHacks 2024 Judge's Choice Award: Team 3 - Targeted Correction of Missense Mutations through Non-Genetic Protein Scaffolding
BroadHacks 2024 Broadie's Choice Award: Team 13 - Broad Atlas
See all BroadHacks 2024 Project Submissions here!
See photos here!
Workshops
Jean Chang
Amelia Hall
Annie Moriondo
Leyla Tarhan
Aseel Awdeh
Esteban Miglietta
Olivia Kotsopoulos
Christina Roberts
Derek Caetano-Anolles
Anton Kovalsky
Sophie Webster
Samantha Miller
Abby Hopper
Michelle Wartak
BroadHacks Ideathon
Noam Shoresh
Jonathon Livny
Alan González
Hackathon Judges
Ray Jones
Kiran Garimella
Dawn Chen
Claudia Ctortecka
Barbara De Kegel
Sean Misek
Logistics and Marketing
C Williams
Shata Dasgupta
Jacob Huang
John Doench
Mary Kuczkowski
Facilities
BITS
Valerie Park
Mark Holton
June 11, 4-6p
Pitch an idea or problem, network, and find like-minded Broadies!
Sign up to pitch an idea here: https://forms.gle/9Zg7q1CHvBCACEFs7Â
See you at future BroadHacks events!
*Participation in the hackathon or pitching an idea is NOT required to attend
June 17 - June 24
Register for workshops here:Â
https://forms.gle/N1jN8MBVHqcGDUDH9Â
*Participation in the hackathon is NOT required to attend a workshop
June 24, 11a-1p [UPDATED]
Brainstorm hackathon ideas to tackle the unique challenges and opportunities in integrating datasets, featuring leaders across Broad’s platforms and programs!
RSVP here:
https://forms.gle/b3ECpDkHnmcgfeKR9Â
*Participation in the hackathon is NOT required to attend
Thur June 27 - Fri June 28, 2024
Registration is now closed.
The BroadHacks project expo is open to all Broadies on Friday, June 28th, from 2-3pm! Come vote on your favorite project!!
Thursday June 27
2p: Opening remarks and Hacking official starts
5-6p: Dinner (Pizza and Cup Ramen Bar!)
9p: Midnight snacks (Ice Cream! and additional fruits, crackers, and dip)
Firday June 28
9-10a: Breakfast (Bagels, cream cheese, lunch meats and lox, yogurt, fruits)
12-1p: Lunch (Wraps, Cobb Salad, cheese and meat trays)
2-3p: Hacking ends, expo and judging starts
3-3:30p: Closing remarks and awards
See more details below about judging and awards!
Broadies are eager innovators, learners, and collaborators. We have many original and potentially transformative ideas in bioinformatics, computational biology, and software engineering. However, our schedules are busy, and we find ourselves constrained by time and resources. BroadHacks aims to provide Broadies a unique opportunity to dive into our untapped ideas, explore new skills, and foster institute-wide collaborations with a 24-hour hackathon event.Â
BroadHacks also features events and resources prior to the hackathon open to ALL Broadies to build computational skills and facilitate institute-wide discussions on opportunities and solutions in computational research at the Broad:
Workshop Series (1.5-4 hour workshops over June 17 - June 24): 5 workshops spanning intro to UNIX to analyzing imaging data!Â
BroadHacks Ideathon (June 11, 4-6pm): We want to hear about your pet project or idea! Come share and listen to speed talks and "pitches" about ideas and problems across the Broad and initiate action!
Opportunities include, but are not limited to:
Meet and collaborate with Broadies from different labs and programs
Explore different fields of research, available resources, and datasets at the Broad
Learn and develop skills in computation and software
Create unique computational solutions to investigate biological questionsÂ
Thursday June 27 - Friday June 28, 2024.
75 Ames/415 Main 2nd floor connector.
Participants and mentors
Anyone with a Broad affiliation and badge access.
Anyone with expertise or want to learn computational biology, bioinformatics, and software engineering or expertise are welcome!
Projects
Anything in the realm of computational biology, bioinformatics, and software engineering! Consider this as an opportunity to level up your computational skills, learn about a different domain, work on something you have not had the time to yet, and connect with different Broadies. We will provide events to facilitate team building and honing in on particular goal or project.
Awards
We want to recognize the ideas and ingenuity that the hackers bring to the event and the computational research ecosystem at the Broad. We will have the following awards:
BroadHacks 2024 Feature Challenge: Broad platforms and groups have produced unique and valuable datasets that will catalyze scientific discovery. We challenge hackers to innovate ways to integrate multiple datasets together in unique and creative ways to drive biological discoveries or enhance infrastructure and standards to perform cross-modality research. See Data Integration Brainstorming Event section below for information!
BroadHacks 2024 Best Overall Project: We want to see what problems or ideas matter to you, and the innovative ways you tackle them!
People's Choice award: All Broadies are invited to the expo to see what Broadhacks teams have worked on and vote on their favorite project!
Additional eligibility for awards include:Â
Teams must have between 2-4 hackers (inclusive). All participating team members must be a Broad affiliate.
The team must submit their Expo Presentation (guide-template available here) to our website (submission form here)
At least one team member must be present in person to present the project at the expo.
Note that teams may include remote Broadies, and that work on the submitted project may begin anytime prior to the official "24 hour" hackathon event. So if you already have a team or already made progress on an idea before June 27, your project is still eligible for awards!
Judging Criteria
The BroadHacks 2024 Feature Challenge and Best Overall Project will be judged based on three equally weighted criteria:
Motivation and Objective: Can the team explain with clarity the relevance or potential impact of their idea, and what they aimed to achieve during the hackathon?
Technical Execution: How did the team work towards their objective? What technologies or tools did they use? Were they resourceful and/or creative?
Results and outcomes: What was the outcome of their work? Does the project provide value (i.e. a working product, proof of concept, insight that informs future research directions, etc.) towards the research ecosystem at the Broad?
See the Judging Criteria Matrix for more details.
Looking for inspiration or help with your project ideas? Â We have organized workshops, talks, and ideation events to help you learn new skills, get familiar with available data sets and resources, find a team, and explore exciting ideas.
These workshops are designed for all levels of computational experience, but with a specific focus towards complete beginners and non-computationalists for participation in the hackathon event. ALL Broadies are welcome to participate in any of these workshops, whether attending the hackathon event or not.
Please sign up for workshops here: https://forms.gle/N1jN8MBVHqcGDUDH9Â
Uncollapse this section to see more details on all the offered workshops!
Intro to TerraÂ
DSP user education team: Derek Caetano-Anolles and Anton Kovalsky
Monday, June 17, 2024, 1p-4p, 75A-4-Yosemite (4001)
Experience level: Beginner. Learners are expected to have some familiarity with biological concepts and basic statistics. **Participants must register prior to the event to set up their Terra accounts.
Workshop website: 2023-Oct-Introduction-to-TerraÂ
Imaging Data Analysis with Morpheus:
Cimini Lab: Esteban Miglietta
Tuesday, June 18, 2024, 1:30p-3p, UPDATE: 75A-M1-Joshua Tree (M1201)
Experience level: Beginner to Intermediate. Learners are expected to have some familiarity with biological concepts and basic statistics. Participants should bring their laptops and plan to participate actively.
Workshop website: BBBC021_Morpheus_Exercise
Keywords: Morphological profiling, Image-based profiles, Cell Painting, MorpheusÂ
Want to learn how to explore the hidden biology of your microscopy images? This workshop will help you understand how to turn microscopy images into image-based/morphological profiles (just like proteomic/transcriptomic profiles) using an open-source web-based software called Morpheus. These profiles will help in identifying the similarities and differences between your “treated” cells and the controls. Interestingly, this can also help one to find unexpected biological relationships between the treated groups and the features that drive these relationships.
Workshop Highlights:
Explore the hidden biology within your microscopy screens.
Learn to convert microscopy images into powerful image-based/morphological profiles, and identify similarities and differences in your several conditions.
Discover unexpected biological relationships between treated groups; and the defining features of these relationships.
Unix 101
Amelia Hall, Jean Chang, Sophie Webster
Friday, June 21, 2024, 11:30a-1:30p, 415M-2-Monadnock
Experience level: Beginner. This lesson assumes no prior experience with the tools covered in the workshop. However, learners are expected to have some familiarity with biological concepts. Participants should bring their laptops and plan to participate actively.
Workshop website: 01-introduction.htmlÂ
Command line interface (CLI) is a powerful tool to interact with data and a computer’s operating system. For most bioinformatics tools, you’re going to need to use the CLI/ shell. The command line allows you to work more efficiently by automating and simplifying repetitive and tedious tasks. To use remote computers or cloud computing, you often need to use the shell.
Intro to Python
Jean Chang and Annie Moriondo
Monday, June 24, 2024, 1p-5p, 415M-2-Monadnock
Experience level: Beginner.
Workshop website: https://broadinstitute.github.io/2024-06-24-python-novice-lesson/Â
Intro to WDL on TerraÂ
DSP user education team: Derek Caetano-Anolles and Anton Kovalsky
Monday, June 24, 2024, 1p-4p, 75A-11-Cascades (11032)Â
Experience level: Intermediate and Advanced. Learners are expected to have prior experience in programming. No prior WLD programming required. **Participants must register prior to the event to set up their Terra accounts.
Workshop website: 2023-May-June-WDL-Bootcamp-WorkshopÂ
Time: Tuesday June 11, 4-6pm
Location: Serengeti (6th Floor between 415M and 75A)
This is an event open to all Broadies to share ideas and problems relating to or could benefit from computational biology, bioinformatics, and software engineering. The event features speed-talks or "pitches" and an open mic session for anyone to step up and pitch, followed by time to mingle and discuss ideas and problems.
Part 1: Pre-scheduled speakers (5 minutes, 2-3 slides optional)
Part 2: Open mic; anyone can come up to the podium and talk about a problem! (max 2 minutes)
Part 3: Mingle with speakers and other audience members and hackathon participants
Why participate or attend?
If you are participating in the Hackathon event, this is a great opportunity to find your team, pitch an idea you already have, and brainstorm a hackathon project!
If you have ideas you would like Broadies participating in the hackathon to work on, this is also a great time to share, inspire, and collaborate!
Sign up to speak!
If you are interested in pitching an idea or problem worth solving, please sign up here! https://forms.gle/9Zg7q1CHvBCACEFs7.  Thank you to all attendees for a wonderful Ideathon! We heard some great ideas about LLM based tools, new visualizations, and extracting features from diverse datasets!
This form will also be open during the open-mic session during the event itself. All speakers who sign-up will be entered for a raffle prize!
RSVP here so we can order food! https://forms.gle/b3ECpDkHnmcgfeKR9Â
Brainstorm hackathon ideas to tackle the unique challenges and opportunities in integrating datasets, featuring leaders across Broad’s platforms and programs!
Noam Shoresh: Associate director of the Epigenomics Program
Jonathan Livny: Co-director of the Microbial Omics Core in the Infectious Disease and Microbiome Program and Head of the Technology Core of the Broad’s Genome Center for Infectious Diseases
Alán Fernando Muñoz González: Post-doc in the Carpenter-Singh Lab and Imaging Platform
The Big Idea: We could gain potential biological insights from querying across datasets with shared axes, such as compound screening, perturbations and gene knockouts, epigenomic characterization, shared cell or tissue of orgin, etc. Performing such multi-dataset analyses is challenging due to the need for deep expertise in the data source and metadata. We encourage hackers to think about exciting ways to combine multiple datasets to discover (1) novel relationships between datasets and datatypes that inform our understanding of biology, and (2) tackle challenges in performing these integrations.
Some example axes:
Identify compounds that similarly impact host and pathogen with compound screening data across cell lines, TB, and imaging data
Some big ideas on how to stream line data integration:
Using LLMs to query across datasets with standard structure
Accessibility and standardized infrastructure/systemic organization
Attend this event to help learn more about the datasets at the Broad and brainstorm the first steps to take during the hackathon to approach these ideas!
Please reach out to the CodeRATS chairs if you have questions about participating or supporting the event!
Claudia Chu (cchu@broadinstitute.org)
Jordan Safer (jsafer@broadinstitute.org)
Hackathons are opportunities for participants to learn,and/or collaborate on projects/ideas they want to explore that are eitherÂ
 completely out of their domain, orÂ
 solve a particular problem/idea they have already been thinking about but haven't had the time set aside to address it.Â
We do not specify exactly what participants will work on besides being loosely in the realm of bioinformatics, computational biology, and software engineering. However, we are organizing talks, workshops, and team building events prior to the event to help participants identify ideas or problems that are interesting to them and form teams (2-4 people). We are also reaching out to different platforms across the Broad to propose or incentivize participants to work on projects using their datasets or products. More details will be available in April, and any suggestions or if you have suggestions on projects to work on, please let us know in the registration form or by contacting one of the team members via email or slack!
A: Not at all! The hackathon is for the Broad community, and is open to all with a Broad badge.
There's no doubt that many hackathon projects will have a heavy coding component, however, every team will benefit from a collaboration between biologists and computationalists! During team matching, we will work to bring computational-minded and biology-minded folk together :)Â
There are many ways to get involved with BroadHacks
Attend workshops and talks
Pitch ideas and recruit CAs/software engineers to help
Learn new computational skills!
This event is free for Broadies to participate in! Food will be provided.
Ideally participants will be able to attend the full hackathon. If you plan to attend, we highly advise that you notify your supervisor or team as soon as possible to make appropriate arrangements. That said, we are working with Broad leadership so everyone will be allowed and encouraged to fully participate.
If you are interested in participating in this event, please fill out the registration form so we can take this information to Broad leadership!
As an official Broad event, participating in this hackathon should NOT require you to take any vacation or PTO time. This is a great opportunity for you to level-up your skills, make connections, and explore new ideas in research. We highly encourage you to let your team know in advance that you plan to fully participate so you can plan accordingly. If you have concerns, please reach out or let us know when you register so we can coordinate.