The third Virtual Hackathon for Developing CURES in Antibody Engineering will be held August 7-10th, 2023.
We have sent out acceptances and requests to confirm attendance. We have also sent invitations to join our Slack group.
If you haven't heard from us or gotten an invitation to join Slack, please check your spam folder and / or email sandra@digitalworldbiology.com
If you're confused about Slack, please email sandra@digitalworldbiology.com.
We will be using Slack quite a bit next week and you will need to use it to coordinate with your team.
Our pre-hackathon orientation was July 17th, at 10 am PST on Zoom.
This work is funded by a grant from the National Science Foundation's Advanced Technological Education program (DUE 2055036).
This event is free and mostly virtual.
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.
Potential Projects:
- Affordable Antibody Engineering: (level = beginner - advanced) This project focuses on developing a low-tech antibody screening method for undergraduate classrooms. This method will enable academic institutions with low budgets to offer antibody engineering experience to their students without expensive equipment.
- Immune-profiling: (level = beginner - advanced) This project involves using datasets from sequencing the Immunome. In immune-profiling, large numbers of genes for B cell and T cell receptors are sequenced. The results can provide insights into the immune response. For example, we can learn about the kinds of T cells that attack tumors and discover new targets for therapies. Learn more and view the resources.
- Pathogens vs Antibodies: (ongoing, level = medium - advanced) This project focuses on identifying the interactions between commercial antibodies and pathogens and determining if sequence changes will allow pathogens to escape the immune system. This project builds on earlier work with SARS-CoV-2, commercial antibodies, and NextStrain.org.
- Engineering Therapeutic Antibodies: (new, level = beginner - advanced) Participants will locate and characterize therapeutic antibodies, identify problems with developability and work out plans for improving antibody characteristics.
- IEDB research projects: (ongoing, level = medium - advanced) The IEDB (Immune Epitope Data Base) is an important tool for identifying and exploring the sequences and substances that are recognized by antibodies and T cell receptors. This project will address developing course-based research projects related to IEDB.
- NIST CHO cells & Monoclonal Antibodies: (new, level = medium - advanced) Work on research projects related to NIST CHO cells and producing monoclonal antibodies. This project is perfect for faculty who are interested in teaching cell and gene therapy and biomanufacturing.
- Other projects: Other projects may be added. Want to try making antibodies in algae? Or 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.
Frequently Asked Questions
Do we have to stay up all night? What will the schedule be like?
No, but we do ask you to commit to approximately 8 hours a day. Our goal is to build community and work together to develop interesting undergraduate research projects related to antibody engineering. The tentative schedule will look something like this:
Monday, Aug 7 - Kick off, intro talks, teams meet & start working
Tuesday, Aug 8 - group meeting, short talks, teams work
Wednesday, Aug 9 - morning check in meeting, teams work
Thursday, Aug 10 - presentations
What is a CURE?
A CURE is a Course-based Undergraduate Research project. These projects can vary in length. Some projects might be completed in 1-2 weeks, some might require an entire quarter or semester, and some might continue through multiple semesters.
How would participating benefit me as a faculty member or as a student?
Faculty participants get the chance to learn new skills and collaborate with other faculty, scientists, and students on developing research projects and classroom materials.
Each day, we will have a talk related to antibody or immune engineering. We will also have experts give demonstrations of different types of software and databases (for example: NextStrain.org, IEDB, NCBI, iCn3D, SAbDab, QUBES).
Student participants will get to experience working as part of a multi-disciplinary team to plan and carry out a scientific project. These can be great experiences to include on a resume. Read about one student's experience in the January 2022 Hackathon.
Do I need to assemble a team?
No. We will assemble working groups of 4-9 individuals for each project. Each team will also have mentors with technical expertise.
What will we create?
The teams will create (or locate and assemble) instructions, background information, data sets, lists of materials, and the assessments so that faculty can implement the projects with their students. After the Hackathon, teams may continue working together and depending on the project, and may have access to limited amounts of funding to cover the costs of lab supplies.
One of our goals is to publish the research projects in QUBESHub and make the projects available to a wider audience.
Check out our first publication: Porter, S., Hilgert, U., Lannan, E., Stieber, M. (2022). Evaluating the potential for immune escape: how likely is an antibody to protect against a specific SARS-CoV-2 variant?. Antibody Engineering, QUBES Educational Resources. doi:10.25334/82D0-AT65
Will we be able to use the research projects and materials we create in our courses?
Yes! We want faculty participants to work on projects with their students. We may also be able to provide you with a small amount of funding for lab supplies.
Can we suggest projects?
Sure! But, we may have to tackle your project next year.
Who owns what we make?
Our computational work will focus on programs and databases that are publicly available and open-source wherever possible. These will include iCn3D, IEDB, NCBI databases, SabDab, TheraDab, and others. Any software modifications developed through the hackathon will be open source and freely available.
Other info:
- Code of Conduct
- 2023 Hackathon schedule - Updated! This goes to the 2023 schedule.
- Helpful information and background reading
- Team roles
Participants agree to make the projects available on QUBESHub.
If you have questions or need additional information, please email sandra@digitalworldbiology.com
The first Virtual Hackathon for Developing CURES in Antibody Engineering took place January 13-16th, 2022 and was carried out in collaboration with the NIH Office of Data Science Strategy.