iGEM Distribution 2022 Finalization

[jcahill]

TODOs

Parts

• [x] Add ApaLI restriction site flankers.
• [x] All of Isaac L's list of parts.
• [x] All preexisting bsub designs
• [x] review isaac G's draft

Description

• [x] Create a README.md file
  • [x] Describe components of AllClo
  • [x] Describe parts collection
  • [x] Attribution and so forth

Package / Submission

• [x] Finalize parts lists and template in Benchling and GSheets
• [x] Add and double-check metadata, ex. authors
• [ ] Export to our github fork.
• [x] Submit merge request of our github fork to iGEM-distribution repo.

2022-02-10 Submission Roundup

Links

• Package WIP
  • top-level directory: github, google drive
  • views subdirectory: github, google drive
• Benchling Drafts
  • AllCloPartsAndOverhangsSummary
  • Finalized Parts: benchling/@friendzymes/iGEM Distribution Kit 2022 - Friendzymes Collection

Preliminary list of parts to design and submit for synthesis in the iGEM Distro

• [x] FiveClo/ThreeClo recombination sites
• [x] Ribozyme insulator parts - google spreadsheet
• [x] Part type switching linkers and an expanded level 2 assembly linker set (using BbsI and mBsaI)
• [x] Universal dropout cassette + DOclo linkers
• [x] HpaII and MspI CDS/TU parts
  • Partially completed. Full set deferred to subsequent submission.
• [x] Split E. coli selection markers - benchling template files: 8, 9
  • Partially completed. Full set deferred to subsequent submission.
• [x] More homology arms for Bsub, Pichia and E. coli
• [x] More constitutive and inducible promoters for Bsub and Pichia
• [x] More Bsub RBSs
• [x] CDSs for auxotrophic selection markers in Bsub and Pichia (+Pichia ku70)
• [x] CDSs for recombinases to go with the FiveClo/ThreeClo recombination sites
• [x] All our existing Bsub wetware part designs, adapted as needed for AllClo
• [x] CDSs for Bsub and Pichia counterselection markers

Stuff from this list that's new

• FiveClo/ThreeClo recombination sites
• More ribozyme insulator parts
• Part type switching linkers and an expanded level 2 assembly linker set
• Universal dropout cassette and DOclo linkers
• HpaII and MspI CDS/TU parts
• More split E. coli selection markers?
• More homology arms for Bsub, Pichia and E. coli
• More constitutive and inducible promoters for Bsub and Pichia
• More Bsub RBSs
• CDSs for auxotrophic selection markers in Bsub and Pichia (+Pichia ku70)
• CDSs for recombinases to go with the FiveClo/ThreeClo recombination sites
• CDSs for Bsub and Pichia counterselection markers
• Homology arms to knock out Pichia proteases PEP4 and PRB1

2022-02-06 Weekly Meet

Action Items

• iGEM Distribution collection discussion.
• Parts / Design Elements
  • Add ApaLI restriction site flankers.
  • All of Isaac L's list of parts.
  • review isaac G's draft, particularly overhangs
  • https://benchling.com/s/seq-jMwf7EKrH4fuXvHc7FqD?m=slm-vezjnWGtCBHLA3h1sWyo
• Description
  • Create a README.md file referencing the authors of each part
  • Ask in github issues about including our own non-automated README for collection.
• Submission workflow:
  1. Finalize parts lists and template in Benchling and GSheets
  2. Export to our github fork.
  3. Submit merge request of our github fork to iGEM-distribution repo.

---

[jcahill]

Source	Prefix	Literal Part
AddGene	AG:	F
Local	Local:	F
PubMed	PMID:	F
GenBank	GB:	T
iGEM	iGEM:	T
Seva	SEVA:	T
URL FASTA	ExtFA:	T
URL GB	ExtGB:	T

[jcahill]

https://github.com/iGEM-Engineering/iGEM-distribution/pull/238

[jcahill]

Internal target for wrapping up final release candidate (soft): 2022-02-21