Hackathon projects August 2024

2024 Schedule
2024 Hackathon projects
What is a hackathon? and other FAQs
Hackathon team roles
Code of conduct
Background reading

Participants work together in teams to develop research projects that undergraduate students will carry out in courses where they study biotechnology or related topics. Hackathon participants will learn about the uses of antibodies in diagnostics, research, and therapeutics, develop new skills in immunology-related bioinformatics programs and databases, learn about new laboratory techniques for working with antibodies, and become part of an exciting community. Faculty and students with varying levels of experience in working with antibodies are encouraged to apply.  Participants will be selected based on experience and motivation to attend. Applicants from community colleges will receive the highest priority.   

Only one project (Antibodies & AI) involves coding.

2024 Hackathon Projects:

  • Affordable Antibody Engineering:  (level = beginner - advanced, *wet lab option for participants located near LA Pierce College)  
    Team leader:  Aron Kamajaya, Los Angeles Pierce Community College, CA
    The goal for this project is to develop a low-tech method for screening antibody libraries. To reach that goal, the team has been investigating methods for purifying fluorescent proteins to use as targets and purifying single-chain antibodies to green fluorescent protein. This summer, the team will start working on an ELISA to measure binding.   
  • Antibodies and Algae:  (new, level = beginner - advanced) - *wet lab option for Houston participants
    Team leader:  Daniel Kainer, Lone Star College, Houston, TX 
    Several different kinds of cells are used in biotechnology for producing proteins.  Each commonly used system–insect cells, mammalian cells, E. coli, and yeast–has its own advantages and drawbacks. The outer membrane of E. coli for example, also called endotoxin, can induce shock and medical distress if therapeutic proteins are made in E. coli and endotoxin contaminates the final injectable drug. Since algae have long been consumed as health supplements, some companies have started antibodies in algae as a safer alternative.  This project will explore protein production in algae, with the goal of understanding how antibodies may be produced in algae as well.   
  • Antibodies & AI:  (level = medium - advanced, **This project involves coding.)
    Team leader:  Todd Smith, Digital World Biology, WA  
    The use of machine learning and artificial intelligence in predicting protein structure models has exploded in the past three years.  Smith’s team will be looking at ways to help instructors and novices understand machine learning and eventually use machine learning for predicting the best ways to modify antibodies. View Antibody Engineers Git Hub and NCBI Antibody Engineers Git Hub  to learn more.  
  • Antibodies vs Pathogens - Influenza H5N1:  (ongoing, level = medium - advanced)
    Team leader:  Erica Lannan, Prairie State Community College, IL
    Highly Pathogenic Avian Influenza (H5N1) has been detected at increasing concentrations in wild bird populations world-wide. Several other species, including humans, have also become infected directly from bird populations. There is concern from some that the virus may mutate and cause human to human (H2H) spread. This team will focus on identifying monoclonal antibodies in use for other forms of influenza that might have the ability to more broadly neutralize influenza strains, including strains such as the current seasonal influenza (H3N2) or avian influenza (H5N1).

    Participants will use the iCn3D molecular modeling visualization tool, the SabDab antibody database, and viral sequence database tools including nextstrain.org and influenza virus resources from NCBI to align new variants to the known structure(s) of current antibodies. Using the interactions tool within iCn3D, participants will make predictions on the strength of antibody binding to new variants through the gain or loss of various bonds.   
  • Epitopes and Immunity:  (ongoing, level = medium - advanced)  
    Team leader:  Sheela Vemu, Waubonsee Community College, IL
    Assistant team lead:  Feather Ives, Merritt Community College, CA
    This team has been investigating antibodies from the perspective of epitopes and has previously worked on projects related to the Immune Epitope Database (IEDB).  Recently, the IEDB team launched CEDAR, the Cancer Epitope Database and Analysis Resource. Vemu has had her microbiology students use CEDAR for research projects. This summer, her team will be using IEDB to investigate the immune response to mPox and the genetic features that control the ability to respond.    
  • Immune Defense:  (new, level = beginner - advanced) 
    Team leader:  Melanie Stegman, Maryland Institute College of Art, MD 
    Stegman is the creator of Immune Defense, a video game based on immunology. She has been updating and revamping the game. Participants in this project will work on game testing and exploring the utility of the game for teaching concepts in antibody structure and function.
  • NIST CHO cells & Monoclonal Antibodies:  (ongoing, level = medium - advanced) 
    Team leader:  Margaret Bryans, Montgomery County Community College, PA
    A few years ago, Dr. Bryans published a curriculum, widely used by community college biotech programs, for purifying antibodies from CHO cells. That cell line is no longer available; however, the National Institute for Standards and Technology (NIST) has been working to develop a CHO cell line that companies can use as a reference material for standardizing and comparing methods for antibody biomanufacturing. Last summer, Bryans’ NIST-CHO hackathon team identified multiple research projects that could be used to characterize this new resource.  

    This summer the team will continue to pursue ongoing questions around characterizing this cell line and the antibody it makes. The team is engaging in researching cell line stability, assays for titer determination, and developing the materials for an ELISA to quantify the antibody. Many of these projects will benefit NIST, industry, and the biotech workforce education community.   
  • Project Sea Star:  (ongoing, level = medium - advanced) 
    Team leader:  Thomas Onorato, LaGuardia Community College, NY 
    Researchers who study mice and humans can easily purchase antibodies to a variety of proteins.  But what about researchers who study non-model organisms?  Dr. Onorato joined last summer’s hackathon with an interest in determining if it would be possible to find antibodies that bind to proteins that are strongly homologous to those in the echinoderm, and from there, find a way to make, modify, and use those antibodies as research tools. His team will continue that work this summer. 

  • Other projects: Other projects may be added.  Want to try something with nanobodies?  Let us know!  If you have a project in mind that you would like to do, please consider volunteering as a team leader.  The team leaders we have, the more projects we can do.