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             <div>Public Engagement</div>
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             <div>Collaborations</div>
 
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           <div class="sectionTitle" id="Section 1">Mick and Mates Podcast</div>
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           <div class="sectionTitle" id="Section 1">Modelling Collaboration with UChicago</div>
 
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                 In an effort to broaden the horizons of the general public in regards to Synthetic Biology, team member Eddie Micklovic began a podcast, meant to elaborate on the work being done in the synthetic biology field, the opposing viewpoints that arise from that work, and how we all can stay informed. In the inaugural episode of the podcast, Eddie interviews Hank Greely, professor of law and director of  the Stanford Center for Law and the Biosciences, breaking down some of the legal and political ramifications that Synthetic Biology has posed. In his second episode, Eddie talks to UVA student Jacob Anish to discuss and explain Synthetic Biology from a surface-level perspective. These episodes are informative and enjoyable, and helped us to develop how we speak about the field itself. We hope you enjoy them as well. <br/>
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                 Our modeling team orchestrated a collaboration with the University of Chicago modeling team focused on enzyme concentration optimization. Their team created an R-based software which utilizes reaction parameters from a multi-enzyme pathway to find the most efficient enzyme stoichiometry. Through many zoom meetings to share reaction parameters and debug syntax, their software demonstrated the estimated increase in yield of our system with optimized enzyme concentrations (seen below). According to their model, concentrations in our optimized system are 2.05e-07, 4.74e-05, 6.43e-05, and 7.07e-05 M which correspond to ACS, ACC, 4CL, and STS enzymes respectively. Our project allows for direct control of these enzyme ratios due to the zinc-finger domain patterns apparent in our DNA scaffolds. Therefore, we will use these findings in our future DNA scaffold assemblies to further test the efficiency of the MANIFOLD system. This collaboration heightened our knowledge of our own models, while providing UChicago further software checks for them to determine the accuracy of their optimization models.  
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              <b>Fig 1.</b> The introduction to our Code of Ethical Conduct, stating our goals for the document and our hope that other teams can use this framework to document their own efforts and considerations.
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               Over the course of the summer, our team turned our focus internally in order to grapple with the current state of our country and the obligation and responsibility we have as scientists. As it turns out, our team has tons of diverse perspectives, and many of the routes we considered for HP research arose from these differing opinions.  
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               In the age of Covid, we’ve implemented a variety of methods to maintain our team’s workflow and implement the device we've detailed, and through some extra work, we've managed to ensure communication through collaboration. For nearly all of our efforts, we’ve sought out new, digital resources that allow us to work together in real time. This work became the basis for what we call the iGEM Resource Page. After several talks with Nemanja Stijepovic and Leandros Tsiotos of the Video and Remote Technologies Committee, we created a compilation of all the relevant resources and tools iGEM teams should know about. We presented our original list in the Global Meet up, sharing the tools we had found most useful and how they allowed us to adapt to a summer spent outside the lab. Following this presentation, we distributed a survey where other iGEM teams could respond and tell us about the resources they found most useful. We organized and outlined all the resources in one document, talking about function and accessibility, pros and cons, and similar alternatives. We hope this document proves useful to future teams as they continue to work either online or in person.  
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              Protests in late May, and the #ShutDownStem day initially inspired internal discussions about the role of scientists in social movements. We established formal, seminar-style discussions about how we as a team could respond and help to be part of the solution, and out of these discussions came an obvious need for a set of agreed team values. As a result, we sought to solidify our understanding through the writing of our own Code of Ethical Conduct. This document is a collection of our team’s stances and represents our dedication to standing by these principles. In this document, we outline our statement of values, specific laws, Diversity &amp; Inclusion Rules, Safety and Security, and Implementation. We created this as a code applicable to all iGem teams, taking into account differing global perspectives and ideals in the everchanging bioethical landscape. We’ve checked this document through UVA faculty, including bioethicists and biology professors, and after a final review of our team members, it was ratified. Now we present it to all future iGEM teams to edit, debate, and implement as well. We hope you can take the framework this document provides and determine your own team values, all in the pursuit of being better, more conscious, scientists.  
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Revision as of 20:52, 24 October 2020

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Collaborations
Modelling Collaboration with UChicago
Our modeling team orchestrated a collaboration with the University of Chicago modeling team focused on enzyme concentration optimization. Their team created an R-based software which utilizes reaction parameters from a multi-enzyme pathway to find the most efficient enzyme stoichiometry. Through many zoom meetings to share reaction parameters and debug syntax, their software demonstrated the estimated increase in yield of our system with optimized enzyme concentrations (seen below). According to their model, concentrations in our optimized system are 2.05e-07, 4.74e-05, 6.43e-05, and 7.07e-05 M which correspond to ACS, ACC, 4CL, and STS enzymes respectively. Our project allows for direct control of these enzyme ratios due to the zinc-finger domain patterns apparent in our DNA scaffolds. Therefore, we will use these findings in our future DNA scaffold assemblies to further test the efficiency of the MANIFOLD system. This collaboration heightened our knowledge of our own models, while providing UChicago further software checks for them to determine the accuracy of their optimization models.

Fig 1. The introduction to our Code of Ethical Conduct, stating our goals for the document and our hope that other teams can use this framework to document their own efforts and considerations.
iGEM Resource Page
In the age of Covid, we’ve implemented a variety of methods to maintain our team’s workflow and implement the device we've detailed, and through some extra work, we've managed to ensure communication through collaboration. For nearly all of our efforts, we’ve sought out new, digital resources that allow us to work together in real time. This work became the basis for what we call the iGEM Resource Page. After several talks with Nemanja Stijepovic and Leandros Tsiotos of the Video and Remote Technologies Committee, we created a compilation of all the relevant resources and tools iGEM teams should know about. We presented our original list in the Global Meet up, sharing the tools we had found most useful and how they allowed us to adapt to a summer spent outside the lab. Following this presentation, we distributed a survey where other iGEM teams could respond and tell us about the resources they found most useful. We organized and outlined all the resources in one document, talking about function and accessibility, pros and cons, and similar alternatives. We hope this document proves useful to future teams as they continue to work either online or in person.





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