Antibody Engineering Hackathon August 2022

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AUGUST 8-11

The second Virtual Hackathon for Developing CURES in Antibody Engineering will be held August 8-11th, 2022.

The application period has ended.  If you are interested in future hackathons, please sign up for our mailing list.

 

All acceptances have been mailed.  If you have not received an emailed request to confirm your participation, please check your spam folder and / or email sandra at digitalworldbiology.com

This work is funded by a grant from the National Science Foundation's Advanced Technological Education program (DUE 2055036).

    This event is free.  Participants work together in teams to develop research projects for undergraduate students studying 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 (yeast display) for undergraduate classrooms. This method will enable academic institutions with low budgets to offer antibody engineering experience to their students without expensive equipment. 
       
    • ImmunoZoo & iCn3D for education:  (level = beginner - advanced) This project includes multiple activities: 
      • aligning molecular modeling activities with NGSS and Vision and Change.
      • creating a data set of antibody structures from multiple creatures.
      • developing and testing an essential feature set for an educational version of iCn3D.  
         
    • Anti-SARS Antibodies vs Variants:  (ongoing, level = medium - advanced) This project focuses on identifying the interactions between commercial antibodies and the SARS-CoV-2 spike protein and making and testing predictions about the ability of commercial antibodies to neutralize the delta variant. 
       
    • Virtual reality & iCn3D: (new, level = advanced) contribute to developing a version of iCn3D with a virtual reality component.
       
    • 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.
       
    • Machine Learning / Artificial Intelligence & Antibodies: (new, level = medium - advanced) contribute to developing an antibody data set and classroom examples to help students better understand machine learning and AI.
       
    • The Antibody Company Game: (new, level = beginner - advanced) contribute to developing and play testing a game that simulates the process of drug development.
       
    • 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 8 - Kick off, intro talks, teams meet & start working
      Tuesday, Aug 9 - group meeting, short talks, teams work
      Wednesday, Aug 10 - morning check in meeting, teams work
      Thursday, Aug 11 - 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 will get the chance to learn new skills and work with other faculty, scientists, and students on developing research projects and classroom materials. Each day, we will have experts give demonstrations of different types of software and databases (for example: NextStrain.org, IEDB, NCBI, iCn3D, SAbDab, QUBES).

      Student participants will get 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 6-9 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, may have access to limited amounts of funding to cover the costs of lab supplies.  An eventual goal 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, IEDBNCBI databases, and others.  Any software modifications developed through the hackathon will be open source and freely available.
       

      Other info:

      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.