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cello-AND-circuits.js
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cello-AND-circuits.js
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// one-or-more(<PhlF TU> or <SrpR TU> or <AmtR TU>)
let oneOrMoreTU =
'one-or-more((' +
'(pSrpR then pAmtR) or ' +
'(pAmtR then pSrpR) then RiboJ53 then P3 then PhlF then ECK120033737) or ' +
'(pTet then RiboJ10 then S2 then SrpR then ECK120029600) or ' +
'(pTac then BydvJ then A1 then AmtR then L3S2P55))';
let exactlyOnePhlf =
'zero-or-more(Cello_minus_PhlF) then PhlF then zero-or-more(Cello_minus_PhlF)';
let exactlyOneSrpr =
'zero-or-more(Cello_minus_SrpR) then SrpR then zero-or-more(Cello_minus_SrpR)';
let exactlyOneAmtr =
'zero-or-more(Cello_minus_AmtR) then AmtR then zero-or-more(Cello_minus_AmtR)';
// Architecture for Cello-like circuit with no roadblocking
// one-or-more(<TU with no roadblocking>)
let noRoadblocking =
'one-or-more(any_promoter then zero-or-one(Cello_promoter_2) then ' +
'any_ribozyme then any_RBS then any_CDS then any_terminator)';
// Architecture for Cello-like circuit with roadblocking
// zero-or-more(<TU with no roadblocking>) then <TU with roadblocking> then zero-or-more(<TU with roadblocking> or <TU with no roadblocking>)
let withRoadblocking =
'zero-or-more(any_promoter then zero-or-one(Cello_promoter_2) then ' +
'any_ribozyme then any_RBS then any_CDS then any_terminator) then ' +
'any_promoter then Cello_RB_promoter then any_ribozyme then any_RBS then any_CDS then any_terminator then ' +
'zero-or-more((any_promoter then Cello_RB_promoter then any_ribozyme then any_RBS then any_CDS then any_terminator) or ' +
'(any_promoter then zero-or-one(Cello_promoter_2) then any_ribozyme then any_RBS then any_CDS then any_terminator))';
/*******************************
* AND tolerance=0: Refinement *
*******************************/
// Cello AND circuit with single copy number TUs in any order
let and0GOLDBAR = `(${oneOrMoreTU}) and0 (${exactlyOnePhlf}) and0 (${exactlyOneSrpr}) and0 (${exactlyOneAmtr})`;
/*****************************************
* AND tolerance=1: Querying, Validation *
*****************************************/
// Cello AND circuit variants with NO roadblocking
let and1GOLDBAR_NORB = `(${noRoadblocking}) and1 ((${oneOrMoreTU}) and0 (${exactlyOnePhlf}) and0 (${exactlyOneSrpr}) and0 (${exactlyOneAmtr}))`;
// Cello AND circuit variants WITH roadblocking
let and1GOLDBAR_RB = `(${withRoadblocking}) and1 ((${oneOrMoreTU}) and0 (${exactlyOnePhlf}) and0 (${exactlyOneSrpr}) and0 (${exactlyOneAmtr}))`;
/**********************************************
* AND tolerance=2: Composition/Instantiation *
**********************************************/
// Cello circuit with variable copy number PhlF TU
let variablePhlf = 'one-or-more((((pSrpR then pAmtR) or (pAmtR then pSrpR)) then RiboJ53 then P3 then PhlF then ECK120033737) or ' +
'(any_promoter then zero-or-one(any_promoter) then any_ribozyme then any_RBS then any_CDS then any_terminator))';
// Cello circuit with variable copy number SrpR TU
let variableSrpr = 'one-or-more((pTet then RiboJ10 then S2 then SrpR then ECK120029600) or ' +
'(any_promoter then zero-or-one(any_promoter) then any_ribozyme then any_RBS then any_CDS then any_terminator))';
// Cello circuit with variable copy number AmtR TU
let variableAmtr = 'one-or-more((pTac then BydvJ then A1 then AmtR then L3S2P55) or ' +
'(any_promoter then zero-or-one(any_promoter) then any_ribozyme then any_RBS then any_CDS then any_terminator))';
let and2GOLDBAR = `(${variablePhlf} and2 ${variableSrpr}) and1 ${variableAmtr}`;