Attributions

Avery Bradley

Avery has been a member of the William & Mary iGEM for the past three years, and this year, Avery served as one of the team captains. She led weekly team meetings throughout the iGEM season in which our team developed our project idea and addressed necessary tasks. She headed the IHP committee of our team, which involved contacting individuals for interviews, conducting interviews, and organizing feedback. She assisted with the circuit design and conducted the wetlab testing of our osmY circuits. She, along with Lin Fang, performed 16S sequencing, which involved collecting soil samples, extracting the DNA, optimizing the PCR protocol, performing the PCR experiments, and the PCR purifications. Additionally, she trained many of the other wetlab team members and participated in the InterLab Study. For our education, she designed the Re-terraforming Mars Expansion Pack, developing the game rules, writing the cards, and assisting with the designing of the cards. She presented at the Mid-Atlantic Meetup and at W&M's BioMath Seminar to obtain feedback for our project. She edited several wiki pages and wrote the following pages: IHP, Inclusivity, Home Page, Sustainable Development Impact, and portions of the Education and Description pages.

Lin Fang

Lin conducted a literature search on 16S sequencing and constructed a database containing papers' protocols on soil extraction and 16S PCR. His searches aided his team in picking the optimal soil extraction kit, PCR purification kit, and 16S primers. He worked with Diego Morandi Zerpa on optimizing his lab's 16S PCR settings and worked with Avery Bradley on PCRing soil-extracted DNA and performing PCR product purification. He also contributed to coding his team’s wiki pages.

Megan Fleeharty

Megan designed the initial sequence for the osmY circuit, and assisted in the construction and testing of this circuit for the Improve a Part requirement. She helped collect soil samples for 16S sequencing and assisted with extracting microbial DNA from that soil, having written our lab’s protocol for this. She also participated in circuit transformation and fluorescence testing for the InterLab study. She contributed largely to the Re-Terraforming Earth board game by creating the rules, designing the boards and cards, contributing to the instruction manual, and overseeing the educational events to test the game. Megan also served on the collaborations committee, creating the Chassis Selection video, presenting at the PuiChing Macau and UM Macau iGEM Online Conference, and assisting with other collaborations. She also presented at W&M’s BioMath Seminar. She wrote the following wiki pages: Proposed Implementation, Contributions, Education, and parts of the Improve a Part, Collaboration, Partnership, and Communications pages. She contributed largely to writing and coding the BBa_K4174002 and BBa_K4174001 parts pages on the iGEM registry.

Walker Knapp

Walker primarily worked on the final software package for the W&M 2022 team. They focused on data processing and full stack software development for relative abundance predictions. They developed multi-step applications to collect and clean microbiome information from databases and literature, and applied that data in neural network predictive models. Walker wrote the front-end systems for the software package, including implementation of the web framework and creating networking protocols, and helped to create the back-end software used to generate data provided to end users of the package. They were a member of the collaborations committee, and worked with the Gaston Day School iGEM members to help simulate their therapeutic production system, as well as assisting with other collaborations. Walker presented sections of W&M’s talk at the PuiChing Macau and UM Macau iGEM online conference, as well as the MidAtlantic Meetup.

Krithika Layagala

This year, Krithika helped collect soil samples and extract DNA from them for 16S sequencing. She also participated in the Interlab Study. As a part of the IHP committee, Krithika contacted and interviewed scientists to get feedback and advice on the project including Dr. Wood, Ms. Ezzamouri, Dr. Salerno, and Dr. Schwartz. She assisted in the creation of graphics for the Wiki alongside Alana and Debby. She wrote part of the Education page and contributed to the IHP page. Finally, she assisted in testing the designed osmY circuit for the completion of improving a part.

Zhe Liu

Zhe worked on mathematical and statistical models for this year’s project. He did the processing and cleaning of raw datasets and the exploratory data analysis before fitting data into the model. For the chassis selection model in soil, Zhe was responsible for building the Random Forest regression model and KNN regression and optimizing the validation results. He also developed a performance metric to evaluate the prediction accuracy. Zhe also led the gut microbiome data search tool. He developed a webscraper that downloads data from online and exports it to CSV files. He wrote the codes for ranking bacterial dominance given user inputs of human conditions. He also presented the project in the PuiChing Macau and UM Macau iGEM conference and the W&M Biomath Seminar.

Bjorn Shockey

Bjorn was primarily in charge of the regression analysis as well as the genome-scale metabolic model software. He worked with datasets of over 30,000 different samples to create unique regressions optimized for individual bacteria species growth. Additionally, he participated in dimensionality reduction and data visualization techniques to help make the results of the regression more interpretable and coherent. Bjorn also worked on the genomic-scale metabolic models and researched some of the first ever applications of GEMs in fieldable synthetic biology. Through the Gaston Day School iGEM (GDS iGEM) collaboration he created a collaboratory that helped GDS iGEM visualize their bacterial growth model in different conditions as well as input their own unique circuit. He also participated in the PuiChing Macau and UM Macau iGEM conference, where he presented his team's work.

Alana Thomas

This was Alana’s second year as a member of the W&M iGEM team, and this year she served as one of the team captains. As a captain, she helped with the training of new team members in lab procedures. She helped with design and testing of the osmY circuits to improve a part. Alana also did the animation and graphics for the project promotional video, and worked on the wiki graphics along with Debby and Krithika. She led an education event hosting middle and high school students in the lab, and teaching them about synthetic biology, and wrote the Education Booklet aimed at middle and high school students. She also helped with soil collection and DNA extraction for 16S sequencing, and participated in construct transformation and testing for the InterLab Study. She was a presenter for the W&M team at the MidAtlantic Meetup conference.

Diego Morandi Zerpa

This year, Diego worked on optimizing PCR conditions for 16S testing and developed the literature review on chassis selection in synthetic biology. Further, he assisted in soil sample collection and DNA extraction for 16S sequencing to test the chassis selection software package, and participated in the calibration and experimental portions of the InterLab Study.

Debby Zhong

Debby helped with soil collection and DNA extraction for 16S sequencing. She wrote and coded the Meet the Team page and the Notebook page. She worked on the wiki graphics along with Alana and Krithika. She made the English subtitles for the promotional video. She also participated in the Interlab Study. She aided with searching for soil DNA extractions kits. As a member of the education committee, she helped with an education event hosting middle and high school students in the lab and teaching them about synthetic biology. She designed the graphics for the Re-terraforming Mars Expansion Pack cards. She also helped with “improving a part” sequencing.