NOTEBOOK
January
Week One:
Our iGEM 2020 team met for the first time and discussed our aims for this year.
Week Two to Four:
Our team met on a daily basis and each person researched a topic with the potential to generate an IGEM project.
Feburary
Week Five:
After continuous discussion, we reached a consensus to use the topic on reducing palladium. Each person was assigned to find literature about the topic.
Week Six:
We shared our literature and divded the jobs for this project.
Week Seven to Eight:
A pandemic broke out and all face to face meetings had to be cancelled. Therefore, we turned to online meetings.
March
Week Nine to Eleven:
After reading several literatures, we designed our peptide sequences and discussed any difficulties that we may encounter.
Week Twelve:
We listed lab equipment and chemicals needed and ordered them from specific retailers.
April
Week Thirteen:
We discussed possible ways to simulate the binding between palladium and our peptide.
Week Fourteen to Sixteen:
We went through papers about ways to simulate the binding between palladium and our proteins and decided on using a Monte Carlo simulation.
May
Week Seventeen:
Due to social distancing measures, we could not start the lab in time. We were also informed that our ordered materials may experience shipping delays due to the pandemic. Therefore, our team put our main focus on the modelling processes.
Week Eighteen to Twenty One:
The team explored ways to use a Monte Carlo simulation and discussed other possible simulation models.
June
Week Twenty Two to Twenty Three:
Our team searched for collaboration teams and reached out to them one by one.
Week Twenty Four:
After contacting collaboration teams we decided on possible ways of collaboration.
July
Week Twenty Five:
Our team tried to use LEMONADE to run the bond fluctuation model - Monte Carlo simulation. https://github.com/LeMonADE-project/LeMonADE
Week Twenty Six:
Our team decided that the bond fluctuation model - Monte Carlo simulation does not apply to our project so we turned to molecular dynamics simulation.
Week Twenty Seven to Twenty Eight:
We researched literature on the molecular dynamics simulation and see how it can apply to our project.
August
Week Twenty Nine to Thirty Two:
We met with Puiching Macao to converse about possible collaboration.
We started working on promotion videos and started working on the modelling work.
September
Week Thirty Three to Thirty Six:
We started working on wiki components and discussed about the poster designs.
We ran some final checking to the molecular dynamics simulations.
October
Week Thirty Seven:
We started working on the poster and continue to work on the wiki. We also created a workshop talking about synthetic biology.