Our team’s main goal for collaboration this year was to facilitate the sharing of knowledge, whether that be our own team’s knowledge, or that of other iGEM teams. We accomplished this through organizing and hosting this year’s Mid-Atlantic Meetup event, participating in the SDG Impact Challenge collaboration run by TAS Taipei, collaborating with OSU’s modeling team, participating in the Dusseldorf Postcard Project, and completing surveys for several other teams.
iGEM MidAtlantic Meetup 2021
The Mid-Atlantic Meetup is a yearly event where iGEM teams from throughout the Mid-Atlantic region meet to present their projects, provide feedback to each other, learn more about various aspects of synthetic biology, and generally grow as synthetic biologists. This year, our team hosted the meetup as a hybrid event, with the Virginia team attending in-person, and Johns Hopkins, Pittsburgh, UMaryland, Baltimore Biocrew, and Gaston Day School attending virtually. We hosted several speakers, including a notable keynote speaker, and had each team present their project and respond to questions. We also conducted two workshops.
Keynote - Dr. Anne Meyer
"Dr. Anne S. Meyer is an Associate Professor of Biology at the University of Rochester, USA. Dr. Meyer received her Ph.D. in Biological Sciences at Stanford University (USA) in 2005. She was a postdoctoral fellow in the Department of Biology at the Massachusetts Institute of Technology (USA). Dr. Meyer served as an Assistant Professor in the Department of Bionanoscience at TU Delft in The Netherlands, prior to moving her research group to the University of Rochester in September, 2018. She has served as the lead advisor for seven iGEM (International Genetically Engineered Organisms) teams, which have won numerous awards including the 2015 Grand Prize. Her research focuses on using quantitative techniques in the fields of biochemistry, microbiology, and biophysics to study structural dynamics, macromolecular interactions, and physiological responses of organisms to environmental stressors. She also uses tools of synthetic biology to engineer novel functions into microorganisms, with a particular focus on the production of improved, tunable biomaterials and the development of new tools for 3D patterning of bacteria."
Dr. Meyer spoke for an hour about her fascinating current research designing photosynthetic living materials. She used visual aids to explain the various properties her team hoped to generate in their biomaterial and gave an engaging presentation filled with images showcasing the durability of her creations. After her presentation, attendees were able to ask questions about her career and research. Dr. Meyer and her work provided a great example of the amazing potential of a career in synthetic biology, which was invaluable for the students in attendance hoping to eventually go into the field.
iGEM Diversity & Inclusion Committee - Lore Leclerc
"Lore Leclerc is a freelance artist that received a Masters in Biological Sciences at Concordia University (Canada) in 2018. They have participated in iGEM as a contestant during their undergraduate studies as well as a judge in 2019, and now serve as part of the Diversity and Inclusion committee. Their research interests span between disciplines from coding and microfluidics to soil microbial research, but they aspire to help develop sustainable technology through synthetic biology. Together with their wife they have organized, edited, and published an environmentalism themed queer comics anthology, as well as led a workshop at an LGBTQ+ convention to teach indie video game creators how to use a Python-based coding engine."
Lore Leclerc led an interactive talk challenging teams to think about how they would respond to real-life conflicts in a research lab setting, focusing on how to avoid the bystander effect. They presented hypothetical scenarios that the students then discussed in groups and later shared how they felt they should respond if found in that situation. As a result of Leclerc’s presentation, those in attendance are now better able to ensure that everyone’s unique perspective is valued and stand up for those who may experience discrimination in a lab setting.
During the workshop section of the meetup, we allowed team members to choose between two workshops (Modeling and Animation), so that they could choose to learn something new, or focus on what they’re most passionate about. For both workshops, we created guides for teams to reference later and invited them to contribute any of their prior knowledge as well to make the workshops as collaborative as possible.
For this workshop, we hosted an interactive notebook containing code for an introduction to data analysis using Python tools. Despite having a set of extremely useful tools that are relatively simple to get started with, online tutorials for Python tend to use jargon geared towards students from a more technical background and can thus be intimidating to those who haven’t done any programming before; thus, the goal of this workshop was to be accessible to biologists who may not have any programming experience. We gave a brief overview of some necessary technical knowledge, such as calling commands and assigning variables, before moving on to skills that would be more useful to biologists wanting to streamline their data analysis process. Using a sample dataset with rates of various central dogma processes found in E. coli, we demonstrated how to load datasets from a variety of formats into the pandas package in Python, and how to filter those data frames, calculate correlations, run analysis of variance, and visualize any patterns found in the data.
We hosted the code for the workshop’s content on GitHub in a Jupyter Notebook format, as well as an installation guide for Python and Anaconda, available for all participants to download and run on their local machines. After the introductory section, we encouraged participants to write their own code to find, analyze, or plot any correlations they might have found interesting in the data. Our tutorial freely available to anyone interested on GitHub.
This workshop focused on teaching teams how to communicate scientific concepts visually using Google Drawings and Adobe AfterEffects.
We began the workshop by discussing the importance of not only speaking and writing effectively as a means of scientific communication, but how visual science communication makes science more accessible to the general public. We then looked at examples of graphics from papers published in Nature and discussed what they did well and what they could have done better.
Next, we provided a demonstration of how to create graphics using Google Drawings, an easy-to-use and collaborative software within the Google Drive Suite. We then allowed teams to practice creating graphics with the Google Drawings software.
After that, we showed an example animation of 3G Assembly that our team had put together in AfterEffects to show the capabilities of the program. We explained the basics of 3G Assembly to those who were unfamiliar, and also provided a short demonstration of how to use Adobe AfterEffects to animate graphics into a video.
We were also able to discuss other programs used for animation with members of the Virginia iGEM team such as MathSpace, and came away with ideas that could enhance the visual communication of our own project.
Each team was given 10 minutes to give a presentation on the current state of their project and then were submitted to 5 minutes of questioning by the other teams and sponsors in attendance. This helped teams to practice their pitch in front of other people within the field and helped illuminate new directions for our projects.
Our team learned a great deal from organizing and hosting!
Though the meetup was overall a success, it was difficult to engage teams that attended virtually. Although events like this will hopefully return to being completely in-person in the future, it is important that we work on ways to more effectively include virtual attendees.
SDG Impact Challenge
The SDG Impact Challenge run by TAS Taipei challenged teams to focus on sustainability, specifically through the sustainable development goals (SDGs) outlined by the United Nations. Each team could choose a task that another team could help out with that would allow their project to achieve one of the sustainability goals. Teams will then help each other accomplish these tasks and present their work for the SDG Impact Challenge at a conference in September.
The goal we chose for our team was goal 9.5 : “Enhance scientific research, upgrade the technological capabilities of industrial sectors in all countries, in particular developing countries, including, by 2030, encouraging innovation and substantially increasing the number of research and development workers per 1 million people and public and private research and development spending.” We chose to accomplish this through our team’s survey about interest in and accessibility of the orthogonality system we hope to develop. The task we gave was to “take our survey about orthogonality, crosstalk, or burden of genetic circuits designing & ask 5 other iGEM teams to take it.”
We chose to complete ATG X UMA’s task, which was to “complete [their] survey on questions about whether or not you carry out activities that can harm marine ecosystems [and answer] some questions about the use that you give to the Waste Cooking Oil and more questions about life below water SDG.” Every member of our team filled out the survey, and additionally provided their team with a contact responsible for recycling waste cooking oil with the William & Mary dining program. After taking this survey, our team members have agreed to be more conscientious about what we do with our waste cooking oil.
We sent one of our team members as a representative to the iGEM x SDG Impact Challenge Conference on September 18th, and she gave a short presentation. The conference began with a short introduction to the Sustainable Development Goals by TAS_Taipei, followed by a brief introduction from each team. We were then sent into breakout rooms with six other teams where each team gave a 4 minute presentation describing their project, their chosen SDG and task, and the task they completed for another team followed by a short Q&A period. Our team’s slides are below:
Ultimately, the SDG Impact Challenge was a great way to hold ourselves accountable with regards to sustainability, especially since it is something that William & Mary strives for as an institution. The survey results helped us to assess interest in and accessibility of our orthogonality metric, and gave us a quantitative justification for the direction of our project. The conference was also a great experience, as our team representative was able to interact with teams from all over the world, and hear their unique perspectives on sustainability.
The OSU iGEM Team reached out to us asking if we could explain our model from last year’s project, so we held several Zoom meetings to answer their questions. As they are a relatively new team, our modeling team was able to provide them with pointers about how to delegate workload and approach models in general, as well as some more specific questions pertaining to last year’s model.
Dusseldorf Postcard Project
This year we decided to participate in Dusseldorf’s annual Postcard Project! We designed a fun cartoon representation of orthogonality, wrote up a short description of our project, and sent it off to the Dusseldorf team for them to produce and distribute.
In addition to our larger collaborations, we also filled out a few teams’ surveys. Each member of our team completed Paris Saclay’s endometriosis questionnaire, Athens’ survey about de novo dNTPs, and SUNY Oneonta’s survey about a hardware database.
Collaboration with Gaston Day School iGEM
Our team had a productive collaboration with Gaston Day School. Gaston Day School attended our regional meetup in July and we were able to interact with them on their project. We collaborated on their Outreach Project which was to develop a very easy to use, 3D printable "non-cylinder" measuring cylinder designed for individuals with disabilities. Their "square" cylinder was designed to be very easy to use and much more stable. To help confirm that their design was truly accessible and usable by other teams, we were able to take their code, print their cylinder and the stand into which it fits, and use it to measure a 5 ml volume with great accuracy (using only a thumb and little finger to simulate a diversity of physical abilities. Because our school has a SEAPHAGES and members of our iGEM team participated in SEAPHAGES we were able to offer suggestions to the Gaston Day School team and they also provided us with information on tools for assessing lateral gene transfer.
Collaboration with Virginia iGEM
Our team collaborated with Virginia iGEM to test one of their genetic parts using our orthogonality toolkit.
Our team learned so much from collaborating with other teams, and we hope to have added to their knowledge as well. Through our collaborations, we strove to better ourselves and others in science communication and quantitative skills, managing team dynamics, ensuring accessibility of science, promoting a spirit of scientific innovation, and making informed decisions. Although at the end of the day, iGEM is a competition, it’s important to remember that science is collaborative, and that the ultimate goal is to advance humanity towards a brighter future.