SEGA
SEGA_collection Version 1 (Collection)
In the Standardized Genome Architecture (SEGA), genomic integration of DNA fragments is enabled by λ-Red recombineering and so-called landing pads that are a common concept in synthetic biology and typically contain features that i) enable insertion of additional genetic elements and ii) provide well-characterized functional parts such as promoters and genes, and iii) provides insulation against genome context-dependent effects. The SEGA landing pads allow for reusable homology regions and time-efficient construction of parallel genetic designs with a minimal number of reagents and handling steps. SEGA bricks, typically synthetic DNA or PCR fragments, are integrated on the genome simply by combining the two reagents (i.e. competent cells and DNA), followed by incubation steps, and successful recombinants are identified by visual inspection on agar plates. The design of the SEGA standard was heavily influenced by the Standard European Vector Architecture (SEVA). SEGA landing pads typically hosts two major genetic “control elements” that influence gene expression on the transcriptional (C1), and translational (C2) level. Furthermore, landing pads contain gadgets such as selection and counterselection markers.

SBOLDesigner CAD Tool
SBOLDesigner Version 3.1 (Agent)
SBOLDesigner is a simple, biologist-friendly CAD software tool for creating and manipulating the sequences of genetic constructs using the Synthetic Biology Open Language (SBOL) 2 data model. Throughout the design process, SBOL Visual symbols, a system of schematic glyphs, provide standardized visualizations of individual parts. SBOLDesigner completes a workflow for users of genetic design automation tools. It combines a simple user interface with the power of the SBOL standard and serves as a launchpad for more detailed designs involving simulations and experiments. Some new features in SBOLDesigner are the ability to add variant collections to combinatorial derivations, enumerating those collections, and the ability to view sequence features hierarchically. There are also some small changes to the way that preferences work in regards to saving a design with incomplete sequences.

Intein_assisted_Bisection_Mapping
Intein_assisted_Bisection_Mapping_collection Version 1 (Collection)
Split inteins are powerful tools for seamless ligation of synthetic split proteins. Yet, their use remains limited because the already intricate split site identification problem is often complicated by the requirement of extein junction sequences. To address this, we augmented a mini-Mu transposon-based screening approach and devised the intein-assisted bisection mapping (IBM) method. IBM robustly revealed clusters of split sites on five proteins, converting them into AND or NAND logic gates. We further showed that the use of inteins expands functional sequence space for splitting a protein. We also demonstrated the utility of our approach over rational inference of split sites from secondary structure alignment of homologous proteins. Furthermore, the intein inserted at an identified site could be engineered by the transposon again to become partially chemically inducible, and to some extent enabled post-translational tuning on host protein function. Our work offers a generalizable and systematic route towards creating split protein-intein fusions and conditional inteins for protein activity control.

Cello E. Coli Parts
Eco1C1G1T1_collection Version 1 (Collection)
These are the Cello parts for E. Coli circuits

rTT+pR
BBa_K093003 Version 1 (Component)
Convergent Promoter System: Forward Module: rTT+lambda pR

Q04510+RFP
BBa_K131018 Version 1 (Component)
Intermediate for the Response circuit

BBa_K101016
BBa_K101016 Version 1 (Component)
Dually repressed promoter with sites for TetR and P22MNT binding

BBa_K125810
BBa_K125810 Version 1 (Component)
slr2016 signal sequence + GFP fusion for secretion of GFP

OriTR
BBa_J01003 Version 1 (Component)
OriT-R (Origin of transfer for the R-plasmid nic region)

pBSEP1
BBa_K090401 Version 1 (Component)
Gram-positive Shuttle Vector for Episomal Expression

BBa_S04142
BBa_S04142 Version 1 (Component)
The Partial Butanol Operon (Parts I725021+I725022)

BBa_S04143
BBa_S04143 Version 1 (Component)
The Partial Butanol Operon (Parts I725023+I725024)

BBa_S04144
BBa_S04144 Version 1 (Component)
The Partial Butanol Operon (Parts I725024+I725025)

BBa_S04145
BBa_S04145 Version 1 (Component)
The Partial Butanol Operon (Parts I725021+I725022+I725023)

BBa_K106671
BBa_K106671 Version 1 (Component)
GFP, Aar1 AD part

BBa_K106677
BBa_K106677 Version 1 (Component)
Ssn8, Aar1 AD part

BBa_S04147
BBa_S04147 Version 1 (Component)
The Partial Butanol Operon (5 inserts from I725021 to I725025)

BBa_K106692
BBa_K106692 Version 1 (Component)
Sir3, AarI A!D part (A!D variant!)

BBa_K090403
BBa_K090403 Version 1 (Component)
Gram-positive Shuttle Vector for Chromosomal Integration

BBa_C0361
BBa_C0361 Version 1 (Component)
luxI (+LVA) - Codon-optimised for E.coli

BBa_C0378
BBa_C0378 Version 1 (Component)
lasI (+LVA) - Codon-optimised for E.coli

BBa_C0362
BBa_C0362 Version 1 (Component)
luxR - codon-optimised for E.coli

BBa_J24817
BBa_J24817 Version 1 (Component)
dLaRAP firefly luciferase reporter device for promoters

BBa_J24818
BBa_J24818 Version 1 (Component)
dLaRAP firefly luciferase reporter device for promoters

BBa_J24819
BBa_J24819 Version 1 (Component)
dLaRAP firefly luciferase reporter device for promoters with J23101

BBa_K116646
BBa_K116646 Version 1 (Component)
Intermediate part to construct a synchronizer

BBa_K116648
BBa_K116648 Version 1 (Component)
Intermediate part to construct a synchronizer

AD default
BBa_K106400 Version 1 (Component)
Default insert for AarI AD acceptor vectors

BBa_J24820
BBa_J24820 Version 1 (Component)
Renilla luciferase reporter device for DLARAP

BBa_J70100
BBa_J70100 Version 1 (Component)
Library Vector Test Plasmid for J70040

BBa_J70110
BBa_J70110 Version 1 (Component)
Library Vector Test Plasmid for J70034

BBa_J70120
BBa_J70120 Version 1 (Component)
Library Insert Test Plasmid for J70050 and J70052

tetA(C)f
BBa_J31007 Version 1 (Component)
tetracycline resistance protein TetA(C) (forward), [cf. BBa_J31006]

BBa_J70030
BBa_J70030 Version 1 (Component)
A BioScaffold Part (Uses PpiI), Protein Tail Remover see Part Design Page

BBa_J70031
BBa_J70031 Version 1 (Component)
Linker for BioScaffold Parts, example of Gamma BioScaffold part

BBa_J70033
BBa_J70033 Version 1 (Component)
A BioMortar Part for Creating GSGS Protein Fusions (see Design page)

BBa_J70034
BBa_J70034 Version 1 (Component)
A BioScaffold Part (Uses AarI) for Library Vector Preparation (see Part Design page)

BBa_J70036
BBa_J70036 Version 1 (Component)
A BioScaffold Part (Uses AarI) for Library Insert Preparation (see Part Design page)

BBa_J70037
BBa_J70037 Version 1 (Component)
Library Vector Test Part

BBa_J70040
BBa_J70040 Version 1 (Component)
A BioScaffold Part (Uses AarI, MabI) for Library Vector Preparation (see Part Design page)

BBa_J70042
BBa_J70042 Version 1 (Component)
6his part for use with BioScaffold parts ATG-6his-GGATCC (glycine serine)

BBa_J70044
BBa_J70044 Version 1 (Component)
6his part for use with BioScaffold parts (G)GATCC(glycine serine)-6his-TAA

BBa_J70046
BBa_J70046 Version 1 (Component)
6his part for use with BioScaffold parts ATG-6 his-GATCC(glycine serine)-TAA

BBa_J70050
BBa_J70050 Version 1 (Component)
Left Library Insert Preparation Part (To use with J70052, and J70040)

BBa_J70052
BBa_J70052 Version 1 (Component)
Right Library Insert Preparation Part (To use with J70050, and J70040)

BBa_Z00000
BBa_Z00000 Version 1 (Component)
Null Part

BBa_J70048
BBa_J70048 Version 1 (Component)
6his part for use with BioScaffold parts ATG-GGATCC (glycine serine)-6 His-TAA

BBa_J70060
BBa_J70060 Version 1 (Component)
BBa_J70010 (PpiI) protein fusion test part

BBa_J70064
BBa_J70064 Version 1 (Component)
Adds 6 his suffix, using BioScaffold part J70010 (PpiI)

BBa_J70080
BBa_J70080 Version 1 (Component)
BBa_J70030 (PpiI) protein fusion test part