###### tags: `admin` `wiki`

# Friendzymes - Meets

[TOC]

## 2021-10-03 Team Meet

- Fewer members in attendance than normal due to the hackathon.
- Giovanna:
- Hackathon wrap-up
- Peer review on JOGL
- Friendzymes team members will be needed as evaluators for peer review
- Next week focused on the wiki
- Isaac G:
- Talked with Harry about facilitating the Philippines Genome Center hackathon project
- Have them meet with BioHive and see how the project can be facilitated
- Invite from Jake Beal to the COMBINE meeting
- Talked with Jeremy about software
- Decided on story for how we're using software to automate actions
- Final scope: 3 github actions, 1 repository, and a video walkthrough
- Isaac L:
- BioBlaze has received library plasmids
- Discussion with Isaac G about use of pichia vs subtilis for iGEM results data
- Sarah Ware:
- Discussion with Diego of bioreactor preferences
- Isaac G unable to get a laboratory in Brazil to ship organisms to Diego in time for iGEM
- Isaac G has another lead. He's following up with them.
- Isaac L recommends a call between Sarah, Ahmed, Scott to address strains
- Almiro:
- Reports wiki mostly done, needs tweaks
- Expects to be done on 10-06, the deadline set with Jeremy
- Isaac L and Isaac G:
- Discussion of plate reader development and costs
- Gofundme totals < cost of chow lab materials
- Isaac L wants to approach Sebastian Cocioba about commodity replacements for parts list
- ex. chinese OEM substitutes
- Isaac L and Sarah Ware:
- Benedictine University plate reader access
- Isaac G:
- Keoni Gandall has shared some opentrons software of relevance
- Isaac G will discuss with hardware/software teams
- Isaac G reiterates that we need to double-check the criteria for igem awards and prizes

## 2021-10-01 Wiki Meet

- Last-minute discussions about safety and judging forms

## 2021-09-26 Software Meet

- A new meet schedule was agreed upon.
- Two meetings per week during the iGEM sprint.
- Daily comms will not be calls, i.e. `standups`.
- Instead, progress will be reported in chat.

## 2021-09-26 Team Meet

- Software's new list of deliverables was recapped.
- Wetware's lack of ability to make immediate-term progress for iGEM was underscored.
- A validation experiment with the plasmid of parts at BioBlaze was devised as a means of generating data prior to deadline.
- The need for a lab manager, tracking ongoing wetlab progress across labs, was raised.

## 2021-09-24 Software Meet

IsaacG notes - original: https://cdn.discordapp.com/attachments/854189265596317736/891126256081469501/software_meeting_092421.txt

IsaacG notes - edited for wikification:

### Goals

1. Create software to automate the design phase
2. Create software to automate some protocols for build

### Deliverables for Goal 1

The following deliverables 1-1 through 1-4 represent the iGEM sprint deliverables.

1. Colab Notebooks
- Estimate: 7 days
- Description
1. Get a list of enzymes and return a list of DNA sequences of these enzymes already:
- Codon optimized
- With Coding regions corrected by removing:
- Homopolymers
- Forbidden restriction binding sites
- Harpins
- Repetitions longer than 10-bp
- Repetitions between sequence and host genome.
- OpenYeast Golden Gate standard of overhangs for CDS
- friendzymes_toolkit
2. Get a list of parts and return them using the OpenYeast Golden Gate standard of overhangs
3. Get a list of sequences as Genbank files and return a list of Genbank files with problematic subsequences annotated
2. Github Actions
- Estimate: 5 days
- Description
- Define inputs and outputs
- Generate a executable file
- Running this inside Github actions as artifact
3. Webapp
- Estimate: 14 days
- Description
- A list of enzymes from Free Genes project
- Plasmids for different host organism
- Poly API
- IO/Fasta
- Create codon table
- Codon Optimize
- Design for webapp
- Implement tha page
- List of Codon Tables
- Change some things from the friendzymes for codon optimize and coding region fixes
4. Wiki
- Estimate: none by IsaacG yet.
- Description
- The wiki is an additional deliverable and possible complication.
- Scenario where it's a complication: strict interpretation of iGEM judging guidelines.
- Background
- IsaacG believes that we may be limited by how judges are instructed to view wikis.
- He thinks they are required only to consider what's within the wiki.
- That might mean we have to adapt/constrain the "notebooks, gh actions, webapp" lineup.
- Status
- We are waiting to see if Giovanna can confirm or deny.
- We checked previous iGEM teams' wikis for external javascript libs.
- We only found a small number. Most teams keep everything inside the wiki.
- Regardless of whether Giovanna can clarify, we should probably do an SPA for the webapp.

### Deliverables for Goal 2

1. Golden Gate assembly[^golden-gate-assemb]
1. Explore protocols and translate as Opentron API
- Estimate: 4 days
2. Setup a fake running experiment - Input and Outputs
- Estimate: 3 days
2. Plasmid Extraction[^plasmid-extraction]
1. Explore protocols and translate as Opentron API
- Estimate: 4 days
2. Setup a fake running experiment - Input and Outputs
- Estimate: 3 days
3. Phillipines - Samoh

[^plasmid-extraction]: Create automated protocols for Plasmid Extraction using OT-2 and P300 multichannel pipette
[^golden-gate-assemb]: Update Golden Gate protocol to work with P300 multichannel pipette

## 2021-09-24 Wiki Meet

### structure

- Project is not the landing page.
- add distinct homepage.
- main nav holds core category links.
- burger menu holds Team and other links.
- subpages hold extended copy.

### color

- discussion of whether to use a uniform dark bg
- consensus: yes but not pure black(?)
- giovanna mentions transparency/opacity for page background color

### styles

- need for guide
- need to freeze site style
- almiro and luiza are style owners

### media

- video's target length is 20 minutes
- yan-kay mentions a short video to serve as basis
- who is working on media production?
- luiza has video production experience
- jeremy has video production experience
- **raise the video's production cycle on Sunday**

### logs

- notes go in this channel
- do subteam meetings get recordings?
- jeremy screen-recorded this meet. can upload if team wants that

### links

`snipped - now in the main link index`