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Jamboree Results
Notebook
Follow along with the APUS team from the very beginning
Week 1
JUNE 2023
Hardware
Literature review to learn about plug and play microfluidics (Arjavi)
Learned from Sam (PI) about basic motherboard design (Arjavi)
Literature review to learn about designing temperature controllers (Margherita)
Drew up a basic idea for housing all components in a box (Margherita)
Research fluidic hardware options (Kara)
Study homemade syringe pumps from previous lab project (Kara)
Wetware
Literature review on cell communication and synthetic pathways (Olivia)
Search for communicating synthetic cells to test in APUS platform (Olivia)
Software
Made version 1 of program that makes gifs and graphs, but with ND2 stitching issues (Daniel)
Week 2
JUNE 2023
General
Wrote 1st draft of the Team Impact Grant application (Olivia, Arjavi, Kara, Margherita)
Edited Team Impact Grant application (Olivia, Arjavi, Kara, Margherita)
Hardware
Learned how to make CADs in Fusion (Arjavi, Kara, Margherita)
Learned how to design 3D Microfluidics using 3DUF (Arjavi)
Tested PTC heater in an insulate environment (Margherita)
Created first CAD for housing all components (Margherita)
Designed and prototyped first pumping mechanism (Kara)
Wetware
Develop plate reader protocol (Olivia)
Used preliminary cells in lab to practice generating plate reader results up to 8 hours (Olivia)
Search for communicating synthetic cells to test in APUS platform (Olivia)
Software
Made version 2 of program that crops microscope images and automatically normalizes data with control data (Daniel)
Week 3
JUNE 2023
General
Submitted Team Impact Grant (Olivia)
Write and publish Project Description on Wiki (Olivia, Daniel)
Hardware
Created first draft of iGEM motherboard design (Arjavi)
Learned how to make PDMS chips and found leakage issues (Arjavi)
Created new CAD for housing (Margherita)
Literature review for maintaining precise temperature (Margherita)
Created 2nd design for pumping mechanism with better solenoids and optimized syringes and tubing (Kara)
Wetware
Repeat practice plate reader results (Olivia)
Contact labs to test their synthetic pathway and cells in APUS (Olivia)
Software
Created helper tool that can edit and regenerate graphs (Daniel)
Created helper tool that adds an induction input graph for induced synthetic pathways (Daniel)
Week 4
JUNE 2023
General
Research potential clients for APUS platform (Olivia)
Hardware
Designed 2nd draft of motherboard and fabricated with Sam (Arjavi)
Tested solenoid control of motherboard (Arjavi)
Tested different ways to control PDMS chip leakage (Arjavi)
Attempted at fixing temperature overshoot with smaller housing (Margherita)
Created initial prototype for housing (Margherita)
Created 3rd pump prototype that prevents solenoid overheating and has speed/direction control (Kara)
Integrated motherboard and pump Arduinos (Kara, Arjavi)
Wetware
Continue communication with labs to test their cells (Olivia)
Software
Designed APUS logo (Daniel)
Became familiar with Wiki (Daniel)
Week 1
JULY 2023
General
Won the Team Impact Grant
Attend Boston University’s Microbiome event (Olivia)
Hardware
Tested new ways to seal PDMS chips and prevent leakage (Arjavi)
Fabricated solenoid holder (Arjavi)
Adjusting arduino temperature library (Margherita)
Ran overnight tests on temperature heater (Margherita)
Created improved gears for 10uL syringes (Kara)
Wrote overdrive function for pump longevity testing (Kara)
Wetware
Continued contacting labs to characterize their cells in APUS (Olivia)
Learned iGEM registry parts for cells (Olivia)
Software
Tested and optimized program with other research data (Daniel)
Week 2
JULY 2023
General
Attended iGEM’s entrepreneurship workshop (Olivia)
Hardware
Created new sealing method, preventing leakage up to 500uL/min (Arjavi)
Began integrating motherboard with pumps on overnight tests (Arjavi, Kara)
Compared our pumping mechanism to existing dual-syringe systems
Ours ran at small flow rates (2uL/min), existing ones do not (Kara)
Adjusted housing prototype to fit new motherboard and pumps (Margherita)
Implemented leakage detector for motherboard (Margherita)
Wetware
Created growth curves for normalization strains (Olivia)
Learned how to use Nikon Eclipse TI2 for data collection (Olivia)
Software
Tested and optimized program with other research data (Daniel)
Week 3
JULY 2023
General
First experiments in the microscope (Olivia, Arjavi, Kara)
Pumps, motherboard, preliminary cells
Hardware
Final integration of motherboard and pumps (Arjavi, Kara)
No leakage of PDMS chips with new sealing methods, post-centrifuge (Arjavi)
Find solution to airflow and temperature control between housing and PDMS chips (Margherita)
Design new PDMS chip holders for microscope (Margherita)
Wetware
Order cells and plasmids for transformation (Olivia)
Software
Tested and optimized program with other research data (Daniel)
Week 4
JULY 2023
General
4 experiments in the microscope (Olivia, Arjavi, Kara)
Pumps, motherboard, preliminary cells
Gave our first presentation “Project Reveal” to undergraduates and high schoolers (all)
Hardware
Create new motherboard design to implement better with pumps (Arjavi)
Redesign pump system to prevent bubbles (Kara)
Compiling all arduino codes into a library (Margherita)
Learn other protocols related to full experiment (Margherita)
Wetware
Begin cell transformation training (Olivia)
Software
Tested program with preliminary data (Daniel)
Photo Shoot
Augest 2023
General
Filmed Promotion Video
Held Human Practices meetings with Arcaea and Ginkgo Bioworks
full APUS experiments
Hardware
Conduct performance metrics on individual pieces of equipment
Begin back-end integration of temperature and pumps
Compiling all arduino codes into a library (Margherita)
Learn other protocols related to full experiment (Margherita)
Wetware
Conduct 2nd transformation of pC235 into both CFP and YFP cells
Collect more plate reader data
Software
Optimize monolayer chamber capture software
Continue uploading content onto the Wiki