Team:Stony Brook/Notebook.html

Notebook

Our team was divided into a total of 4 subteams: Design, Modeling, Outreach, and Web Development. In order to keep each other updated on the different aspects of our project, we held weekly meetings every Tuesday afternoons on Zoom. Here is a rundown of what we completed every week as we worked on LightSwitch!

WEEK ONE

Area	Description
Design and Research	Familiarizing ourselves with Bax, HR, and PCD through articles
Outreach and Fundraising	Reaching out to farmers, highschool teachers Prepping for iGEM collabs and challenges Setting up Molecular cloud account Submitting Revive and Restore Grant

WEEK TWO

Area	Description
Design and Research	Finalizing Design and Construct document Meeting with Dr. Balázsi to review our new approach
Outreach and Fundraising	Reaching out to OSU and Oneonta for collaboration opportunities Emailing more farmers Begin prepping an outreach presentation for high schools Working on GMO attitude survey Introducing our project in Social Media Organizing #introGEM challenge
Website Development	Familiarizing ourselves with Github, HTML & CSS

WEEK THREE

Area	Description
Design and Research	Reviewing more articles
Modeling	Coming up with ideas for potential modeling for our project
Outreach and Fundraising	Contacted CSTEP to set up a date for an iGEM presentation Emailing farmers that have not replied back Finalizing meetings with OSU and Oneonta Updating Social Media Reaching out to more high schools we can present to
Website Development	Finishing up skeleton pages for the wiki (no content)

WEEK FOUR

Area	Description
Design and Research	Familiarizing ourselves with Benchling, writing more notes on articles Attempting to finalize BphP1 and Bax constructs
Modeling	Reviewing MATLAB and Python Writing notes on Boolean logic, phylogenetic analysis, fluorescnece microscopy, and import/export ODEs
Outreach and Fundraising	Met with Jen from HeartBeet farms Established scripts for scientists Continuation of #introGEM challenge
Website Development	Establishing a timeline for the Wiki Beginning profile cards for team members

WEEK FIVE

Area	Description
Design and Research	Establishing a flowchart of our current design and reading more papers Updating Design and Construct document
Modeling	Writing up questions for Dr. B meeting Reviewing differential equations
Outreach and Fundraising	Began thinking about possible Human Practice ideas, such as a series of educational YouTube video or a GMO handbook for farmers Considering reaching out to SBU BioEthics Club and Philosophy department
Website Development	Continuing further page development Writing up content for Wiki Researching past teams' Wikis

WEEK SIX

Area	Description
Design and Research	Looking into tissue specific promoter for activation of our switch Worked on improving our project after discussing the points made in the meeting with Dr. Hughes
Modeling	Reviewing meeting with Dr. Balázsi and reading modeling papers
Outreach and Fundraising	Preparing for meeting with Babylon Micro-Farms Established collaboration ideas with OSU and Oneonta. Reaching out to Dr. Kate Creasey
Website Development	Further research into other Wikis and writing up more content

WEEK SEVEN

Area	Description
Design and Research	Looking into locus to insert our construct into, continuing work on gene circuit Meeting with Dr. Verkhusha
Modeling	Preliminary flowchart is done Continuing work on BphP1 shuttling, Bax mRNA and protein production, and formation of the MAC
Outreach and Fundraising	Preparing for CSTEP presentation Reaching out to more farmers Continuing collabs with OSU and Oneonta Beginning new collab with MSP
Website Development	Beginning styling on the website and looking into Bootstrap

Area	Description
Design and Research	Looking into the UVR8 optogenetic system, designing siRNA, and working to have our system target CLV/WUS
Modeling	Looking into new modeling approaches given the improved design
Outreach and Fundraising	Working further into our posters for our collaboration with Oneonta Meeting with David from Babylon Micro-Farms Further collaboration work
Website Development	Looking more into Boostrap, website content, and general styling

Area	Description
Design and Research	Moving forward with UVR8 Weighing advantages and disadvantages of siRNA, miRNA, and CRISPRi Beginning early stages of establshing an experimental protocol
Modeling	More Python tutorials with Justin Looking into prospective modeling approaches
Outreach and Fundraising	Working on expanding our Education initiative by looking into pre-freshman/freshman clubs and organizations at Stony Brook University to present to Reaching out to Square Roots Farms More work with OSU, Oneonta, and MSP Beginning to post facts about vertical farming to engage our social media followers
Website Development	Wiki styling and preliminary Bootstrap implementation

Area	Description
Design and Research	Looking into complications associated with expressing homologous UVR8, if any Working on a light-inducible promoter for our xiRNA construct Organizing a schedule for the Dr. Creasey presentation Working on the Dr. Creasey Experimental Protocol and Strategy presentation
Modeling	Running Tinkercell on GEMini within CoCalc Looking into a way to use GROMACS to stimulate protein protein interactions and determine a few kinetics of our system
Outreach and Fundraising	Contacting more organizations and schools like the Educational Opportunity Program (EOP) to ask if we can present to them and further our educational initiative Looking into contacting the USDA Organizing meeting with Maxwell from Square Root Farms Tweaking OSU video collaboration, brainstorming poster ideas for the Oneonta collaboration, and setting up a timeline to finish the MSP collab
Website Development	Flushing out features for our Wiki, such as a dark vs. light theme and logos Beginning to finalize design decisions

Area	Description
Design and Research	Finalizing experimental protocols Presenting to Dr. Creasey Looking into transient transformation Looking into possible real-life applications for our project
Modeling	Simulating UVR8 dimer in water Going through GROMACS tutorials to become more familiar with the program
Outreach and Fundraising	Beginning Instagram Takeover series to increase engagement with our followers Tweaking our GMO survey and reaching out to faculty that can potentially help us distribute it Reaching out to faculty to see where we can put our GMO poster for the Oneonta collaboration
Website Development	Starting to finalize styling for the Wiki Updating Wiki content Looking into possible logo ideas

Area	Description
Design and Research	Switching our model organism from A. thalina to N. benthamiana Finalizing protocols Starting up MSP Journal Collaboration Revising constructs for N. benthamiana
Modeling	Looking into I-TASSER, a server hub that allows us to process protein structure and templates Continuing work on BagelBot
Outreach and Fundraising	Organizing meeting with Dr. Dickson Despommier, the founder of modern day Vertical Farming Reaching out to Tony from Freight Farms Beginning video production for the OSU video collaboration Starting up Instagram takeovers
Website Development	Reviewing and updating Wiki content Revising schedule to accomodate the new iGEM deadlines

Area	Description
Design and Research	Finalizing experimental protocols in terms of genotyping and phenotyping Looking into the CLAVATA-WUSCHEL pathway in other organisms Continuing article for the MSP collaboration Continuing to revise constructs for N. benthamiana
Modeling	Working with MEGAx, a phylogeny software Debugging BagelBot
Outreach and Fundraising	Writing up questions for the meeting with Dr. Despommier Reaching out to Mike Axelrod, Instructional Support Specialist and Greenhouse Curator at Stony Brook University Finalizing voiceovers for the OSU video collaboration Continuing to write stuff up for the MSP journal collaboration Brainstorming ideas for the Oneonta poster collaboration
Website Development	Reviewing Wiki content Updating more Wiki content

Area	Description
Design and Research	Finalizing plant constructs Reaching out to Stony Brook professors for advice on our constructs
Modeling	Continuing to upgrade BagelBot Looking into gaining SeaWulf access
Outreach and Fundraising	Looking into hosting an event for freshman by reaching out to Stony Brook undergraduate college adviors Making additional changes to our GMO attitude survey Finalizing voiceovers for the OSU video collaboration Committing final changes to the MSP journal collaboration Brainstorming ideas for the Oneonta poster collaboration Editing OSU collaboration video

Area	Description
Modeling	Conducting even more BagelBot updates and looking into possible future features such as advanced plotting functions and conducting BLAST search on a DNA sequence
Outreach and Fundraising	Meeting with Molecular Cloud to reflect on our work and our resilience against COVID-19 Continuing poster collaboration with Oneonta Continuing work for iGEM Promotional and Presentation videos

Area	Description
Modeling	Obtaining access to SeaWulf Updating BagelBot
Outreach and Fundraising	Working on Presentation and Promotion Videos Continuing collaborations

Area	Description
Modeling	Testing SeaWulf
Outreach and Fundraising	Working on iGEM Deliverables
Website Development	Continuing to update the Wiki before it goes live

Area	Description
Design and Research	Completing iGEM Deliverables
Outreach and Fundraising	Completing iGEM Deliverables
Website Development	Making further Wiki edits

Team:Stony Brook/Notebook.html

Stony Brook iGEM 2020