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Assembly lvl2 - #103

Merged

Gonza10V merged 45 commits into

full_buildfrom

assembly_lvl2

Jul 9, 2026

Merged

Assembly lvl2#103
Gonza10V merged 45 commits into
full_buildfrom
assembly_lvl2

Commits on Apr 6, 2026
- backbone now listed last in product
  doublergreer
  committed
  1ad96f2
Commits on Apr 7, 2026
- type correction on ligation products
  doublergreer
  committed
  fd65c9a
- function to simplify complex plasmid part representation to a scar-TU-scar-bb representation
  doublergreer
  committed
  ee7451f
Commits on Apr 8, 2026
- intermediate w/ annos not working
  doublergreer
  committed
  5640cd8
Commits on Apr 14, 2026
Commits on Apr 21, 2026
- remove todo
  doublergreer
  committed
  2747758
- ligase and RE flow optimized + domestication added if not found
  doublergreer
  committed
  494ddcf
- definition->identity
  doublergreer
  committed
  69fea09
Commits on Apr 27, 2026
- lvl2 and multi-design lvl1 drafts
  doublergreer
  committed
  d9fbdf2
- docstring updates
  doublergreer
  committed
  88a3b44
Commits on Apr 28, 2026
- get referencing CD in extract toplevel definition
  doublergreer
  committed
  230f2ba
- ironing out iterative lvl1
  doublergreer
  committed
  de292b8
Commits on Apr 29, 2026
- better doc search in get_or_pull
  doublergreer
  committed
  a0f395c
- added combinatorial design support to lvl1
  doublergreer
  committed
  fb76b9c
Commits on May 7, 2026
- new tests for digestion and ligation
  doublergreer
  committed
  79b6b3a
- combinatorial test
  doublergreer
  committed
  e622941
Commits on May 8, 2026
Commits on May 12, 2026
- activity tests for digestion and ligation
  doublergreer
  committed
  4e9f961
- test buildcompiler draft
  doublergreer
  committed
  3dc25ee
- level 1 and first comb test complete
  doublergreer
  committed
  7d346cf
- removed superfluous prints
  doublergreer
  committed
  da38668
- new test suite
  doublergreer
  committed
  d2fe409
Commits on May 13, 2026
- synbiohub.org->api.synbiohub.org
  doublergreer
  committed
  feb64fa
- secret access for github job
  doublergreer
  committed
  3384148
- api for pulls only
  doublergreer
  committed
  cecf73f
- api for collections
  doublergreer
  committed
  26e638d
- revert api for collections
  doublergreer
  committed
  f91e490
- added server mode flag to add api. to canonical sbh registry uris
  doublergreer
  committed
  bb8d338
- notebooks for creating various implementations used in buildcompiler
  doublergreer
  committed
  776bc73
Commits on May 16, 2026
- decouple forward and reverse fusion site matching to fix skipped backbone match + composite numbering adjustment
  doublergreer
  committed
  767fa6b
- lvl2 working
  doublergreer
  committed
  0454cfe
Commits on May 17, 2026
- lvl2 test draft
  doublergreer
  committed
  307f61c
Commits on May 18, 2026
- lvl1 TU tests for lvl2 assembly
  doublergreer
  committed
  9cebf0d
- transformation test
  doublergreer
  committed
  207b68c
- notebook updates
  doublergreer
  committed
  1c67d56
- added transformation
  doublergreer
  committed
  2237123
Commits on Jul 9, 2026
- Merge branch 'full_build' into assembly_lvl2
  Gonza10V
  authored
  28cebdc
- Fix domestication BsaI implementation reference
  Gonza10V
  committed
  2ed6001
- Respect supplied level 2 backbone
  Gonza10V
  committed
  f10a5b4
- Select top-level design for lvl2 TU extraction
  Gonza10V
  committed
  de4387a

Commits

Commits on Apr 6, 2026

Commits on Apr 7, 2026

Commits on Apr 8, 2026

Commits on Apr 14, 2026

Commits on Apr 21, 2026

Commits on Apr 27, 2026

Commits on Apr 28, 2026

Commits on Apr 29, 2026

Commits on May 7, 2026

Commits on May 8, 2026

Commits on May 12, 2026

Commits on May 13, 2026

Commits on May 16, 2026

Commits on May 17, 2026

Commits on May 18, 2026

Commits on Jul 9, 2026