HackMD
tags: admin wiki
Friendzymes - Progress
About
- Isaac G and Jeremy produce project-wide progress reports here.
- Progress reports are scheduled for Wednesday and Sunday.
- After iGEM deadline, frequency may decrease.
2021-10-20
2021, Week 42: Wednesday
Upcoming
2021-10-19
2021, Week 42: Tuesday
Sent
Special Battle Plan Edition
It's iGEM Freeze time.
1. Big Picture content: tagteam takeover
Several 'big picture' items fell largely or solely to Isaac L.
Isaac has very limited availability.
These need to be brought up to MVP by others.
Initial Triage Roster:
- Giovanna
- Harini
- Isaac G
2. Wetware content: sole focus for most knowledgeable
Wetware content is very essential and very far behind.
Those with most knowledge of design and results: focus here!
Wetware pages and parts registry are where we need you.
Initial Triage Roster:
- Ahmed
- Almiro
- Isaac L if available
- Scott
3. Software & Hardware content: firm Wed deadline
Github repositories follow specific submission guidelines.
An administrative transfer is required.
This involves an interaction with iGEM's github organization.
We shouldn't wait much longer than c. midday Wed for this.
It's now or never.
⇒ If necessary, Triage Roster must drop other tasks for this.
Initial Triage Roster:
- Hardware
- Diego if available
- Samoh
- Sarah
- SW team in support
- Software
- Giovanna
- Isaac G
- Jeremy
4. Low-noise comms & clear final drafts
Wiki writing and discussion must be low noise.
Final drafts must be unambiguously identified in comms as such.
Harini must confirm your final contents in gdocs.
5. Bird's Eye View / Taskmaster
Someone needs to be keeping a high-level overview on the situation.
This person is responsible for overall taskmaster responsibilities.
They watch the clock and monitor progress against checklists.
If they ask for updates, it's important to respond ASAP.
Supervisor: Yan-Kay
2021-10-17
2021, Week 41: Sunday
Sent
Admin
Wiki
- Harini re: Friday editathon
- Worked on the project description, contributions.
- Giovanna and Luiza worked on HP
- We brainstormed about illustrations and Sana is at it.
- I'd say it didn't go too bad.
- I'd have liked to get stuff done on the parts side though.
- Almiro told he'll talk to Ahmed
- they'll try to get it done by Saturday
- Software
- Isaac G and Jeremy worked on draft1
- other updates to be discussed at weekly meet
Engineering
Hardware
- iGEM-related work: No update.
- Build added: bixels frugal plate reader / transilluminator.
Software
- Actions
- 3 of 3 initially targeted actions are written.
- All require light editing for english usage and consistency.
- All require docs, which feed directly into wiki > software.
- Notebooks
- 3 of 3 notebooks have code.
- All require further work on the text etc.
- All require being added to the cookbook repo.
- Wiki
- Today we will look at Plan B, using a tool to generate bugfixes.
- PAML Pilot Project
- We have tentatively planned to participate in a pilot project
- The project is for a new https://combine-org.github.io standard.
Wetware
- Plan A
- There have been delays with Plan A.
- Twist parts likely won't be received in time for results by deadline.
- Plan B
- Plan B is on-track at BioBlaze.
2021-10-13
2021, Week 41: Wednesday
Sent
Admin
Human Practices
- No update
Wiki
- Wiki editathon scheduled for this Friday, 2021-10-15.
Engineering
Hardware
- No update
Software
- Actions
- Docs in progress for actions
annotatorandsynthesizable synthesizablein debugging and finalization- third action not yet started
- Docs in progress for actions
- Notebooks
- Still only one person assigned, Giovanna
- Wiki
- Template updated with typography recommendations and non-dummy text
- No bugfix updates
Wetware
- No update
2021-10-10
2021, Week 40: Sunday
Sent
Admin
Human Practices
- The Hackathon is complete. Peer Evaluation forms are pending.
Wiki
- Wiki tasks spreadsheet substantially updated at Friday 10-08 meet.
Engineering
Hardware
- Diego and Luiza coordinated on wiki writing
- Until Monday, 2021-10-11: first part of hardware (design and construction)
- Diego continues the coordination for the tests
- Diego hopes to have more news on Monday
Software
- Actions
- Isaac G has completed action 1 of 3.
- When Isaac says each action is releasable, Jeremy will tidy english usage.
- https://github.com/Open-Science-Global/annotator
- Notebooks
- Giovanna will start to write the codon optimization notebook.
- Webapp
- The webapp has been postponed until post-iGEM.
- Wiki
- The wiki's site code is undergoing revisions.
- Release v0.3 is the MVP for use with iGEM.
- WIP thread
- Site code
- Live site
Wetware
- No update
Events
cGEM 2021
- Ahmed presented at cGEM on 2021-10-03.
COMBINE 2021
- Isaac G and Jeremy are registered for COMBINE 2021.
- See: discord thread and hackmd note.
2021-10-06
2021, Week 40: Wednesday
Sent
Admin
Human Practices
- HP activities are on hold until Thurs, 2021-10-07.
Wiki
- Almiro has completed most of the frontend.
- Almiro has further work to do on
- the hamburger button
- text animation
- dark mode
Engineering
Hardware
- TBD pending update from Diego
- BioBlaze has received shipment of Opentrons OT-2 addons.
- BioBlaze has confirmed order of NEB supplies via NEB's iGEM team support program.
Software
Wetware
- Ahmed is ok with being the interim lab manager, though Scott should be longterm.
- We're finalizing Twist orders today.
- Hopefully we get those delivered before the wiki freeze
- otherwise we won't be able to finish the level 1 assembly.
- 4 of our parts are now working for the level 0 assembly
- digestion-ligation -> transformation -> ** (we are here today) minipreps and restriction mapping -> sequencing
- In parallel: level 0.5 assembly
- (ecoli vector creation: RFP + ecoori + Kan)
- doing miniprep of RFP today
- will be able to make the assembly the day after and use it with bsai for assembly.
- After that we can dropout the RFP and add the rest of our parts.
- And then for the ccDB part, we needed to first remove ccdb from popenv3, we did that and will proceed with ccDB ligation today.
- looks like LacI had a rough time but we'll be finishing up with the ligation+transformation of the rest of the parts now.
- Digested/ligated 11 of our parts, 8 left but those are the non essential ones if we're focused on just building the pHT43 before optimizing.
2021-10-03
2021, Week 39: Sunday
Sent. Note: This update was incomplete due to the hackathon running concurrently.
Subteams List
- Hackathon
- Hardware
- Software
- Wetware
Subteams Updates
- Hackathon
- The hackathon is underway.
- Hardware
- TBD
- Software
- TBD
- Wetware
- The main construct in Scott's Laboratory with Ahmed as lab assistant
- Our strategy is to test the plasmid of parts in Chicago by BioBlaze.
Next iGEM Deadline
The next iGEM deadline is YYYY-MM-DD.
- X must be submitted
- Y must be submitted
- Z must be submitted
