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System TypeStatesParametersInputsEquationsDescriptionsLast Modified DateGenetic Circuit DiagramDownloadSettings
BMSS, ConstantInduction, Inducible['m', 'p']['n', 'k_ind', 'synm', 'degm', 'synp', 'degp']['ind']['dm = synm*(ind**n)/(ind**n + k_ind**n) - degm*m',
'dp = synp*m - degp*p']
Description:
This model describes a simple gene expression for mRNA and protein driven by an inducible promoter with constant induction.,
Definition of states:
          m: mRNA
          p: protein,
Definition of parameters:
          k_ind: half-activation constant
          synm: mRNA synthesis rate
          degm: mRNA degradation rate
          synp: protein synthesis rate
          degp: protein degradation rate/dilution rate,
Definition of inputs:
          ind: inducer level,
Reference:
          Title: An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs.
          Authors: Yeoh, Jing Wui, Kai Boon Ivan Ng, Ai Ying Teh, JingYun Zhang, Wai Kit David Chee, and Chueh Loo Poh.
          Journal: ACS synthetic biology 8, no. 7 (2019): 1484-1497.
          DOI: https://doi.org/10.1021/acssynbio.8b00523
05/01/2021Genetic Circuit DiagramDownloadSettings
BMSS, ConstantInduction, Inducible, MaturationTime['m', 'p', 'p_mat']['n', 'k_ind', 'synm', 'degm', 'synp', 'degp', 'k_mat']['ind']['dm = synm*(ind**n)/(ind**n + k_ind**n) - degm*m',
'dp = synp*m - k_mat*p',
'dp_mat = k_mat*p - degp*p_mat']
Description:
This model describes the gene expression for mRNA and protein driven by an inducible promoter with constant induction. An additional term is considered to account for the maturation of the protein.,
Definition of states:
          m: mRNA
          p: peptide/protein
          p_mat: matured protein,
Definition of parameters:
          k_ind: half-activation constant
          synm: mRNA synthesis rate
          degm: mRNA degradation rate
          synp: protein synthesis rate
          degp: protein degradation rate/dilution rate
          k_mat: protein maturation rate,
Definition of inputs:
          ind: inducer level,
Reference:
          Title: An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs.
          Authors: Yeoh, Jing Wui, Kai Boon Ivan Ng, Ai Ying Teh, JingYun Zhang, Wai Kit David Chee, and Chueh Loo Poh.
          Journal: ACS synthetic biology 8, no. 7 (2019): 1484-1497.
          DOI: https://doi.org/10.1021/acssynbio.8b00523
05/01/2021Genetic Circuit DiagramDownloadSettings
BMSS, InducerDegradation, Inducible['ind', 'm', 'p']['n', 'degind', 'k_ind', 'synm', 'degm', 'synp', 'degp'][]['dind = -degind*ind',
'dm = synm*(ind**n)/(ind**n + k_ind**n) - degm*m',
'dp = synp*m - degp*p']
Description:
This model describes the gene expression for mRNA and protein driven by an inducible promoter. The inducer is assumed to be unstable and undergoing degradation.,
Definition of states:
          ind: inducer dynamics
          m: mRNA
          p: peptide/protein,
Definition of parameters:
          degind: degradation rate of inducer
          k_ind: half-activation constant
          synm: mRNA synthesis rate
          degm: mRNA degradation rate
          synp: protein synthesis rate
          degp: protein degradation rate/dilution rate,
Definition of inputs:
          ind: inducer level is used as initial condition,
Reference:
          Title: An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs.
          Authors: Yeoh, Jing Wui, Kai Boon Ivan Ng, Ai Ying Teh, JingYun Zhang, Wai Kit David Chee, and Chueh Loo Poh.
          Journal: ACS synthetic biology 8, no. 7 (2019): 1484-1497.
          DOI: https://doi.org/10.1021/acssynbio.8b00523
05/01/2021Genetic Circuit DiagramDownloadSettings
BMSS, InducerDegradation, Inducible, MaturationTime['ind', 'm', 'p', 'p_mat']['n', 'degind', 'k_ind', 'synm', 'degm', 'synp', 'degp', 'k_mat'][]['dind = -degind*ind',
'dm = synm*(ind**n)/(ind**n + k_ind**n) - degm*m',
'dp = synp*m - k_mat*p',
'dp_mat = k_mat*p - degp*p_mat']
Description:
This model describes the gene expression for mRNA and protein driven by an inducible promoter. The inducer is assumed to be unstable and undergoing degradation. An additional term is considered to account for the maturation of the protein.,
Definition of states:
          ind: inducer dynamics
          m: mRNA
          p: peptide/protein
          p_mat: matured protein,
Definition of parameters:
          degind: degradation rate of inducer
          k_ind: half-activation constant
          synm: mRNA synthesis rate
          degm: mRNA degradation rate
          synp: protein synthesis rate
          degp: protein degradation rate/dilution rate
          k_mat: protein maturation rate,
Definition of inputs:
          ind: inducer level is used as initial condition,
Reference:
          Title: An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs.
          Authors: Yeoh, Jing Wui, Kai Boon Ivan Ng, Ai Ying Teh, JingYun Zhang, Wai Kit David Chee, and Chueh Loo Poh.
          Journal: ACS synthetic biology 8, no. 7 (2019): 1484-1497.
          DOI: https://doi.org/10.1021/acssynbio.8b00523
05/01/2021Genetic Circuit DiagramDownloadSettings
BMSS, DelayActivation, Inducible, ActiveTransport['inde', 'indi', 'm', 'p']['vm', 'n_trans', 'k_trans', 'n', 'k_ind', 'synm', 'degm', 'synp', 'degp'][]['dinde = -vm*(inde**n_trans)/(inde**n_trans + k_trans**n_trans)',
'dindi = vm*(inde**n_trans)/(inde**n_trans + k_trans**n_trans)',
'dm = synm*(indi**n)/(indi**n + k_ind**n) - degm*m',
'dp = synp*m - degp*p']
Description:
This model describes the gene expression for mRNA and protein driven by an inducible promoter. There is a delay in induction possibly due to active transport.,
Definition of states:
          inde: extracellular inducer concentration
          indi: intracellular inducer concentration
          m: mRNA
          p: peptide/protein,
Definition of parameters:
          vm: transport rate
          k_trans: half-activation constant for transport
          k_ind: half-activation constant
          synm: mRNA synthesis rate
          degm: mRNA degradation rate
          synp: protein synthesis rate
          degp: protein degradation rate/dilution rate,
Definition of inputs:
          inde: inducer level is used as initial condition,
Reference:
          Title: An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs.
          Authors: Yeoh, Jing Wui, Kai Boon Ivan Ng, Ai Ying Teh, JingYun Zhang, Wai Kit David Chee, and Chueh Loo Poh.
          Journal: ACS synthetic biology 8, no. 7 (2019): 1484-1497.
          DOI: https://doi.org/10.1021/acssynbio.8b00523
05/01/2021Genetic Circuit DiagramDownloadSettings
BMSS, DelayActivation, Inducible, ActiveTransport, MaturationTime['inde', 'indi', 'm', 'p', 'p_mat']['vm', 'n_trans', 'k_trans', 'n', 'k_ind', 'synm', 'degm', 'synp', 'degp', 'k_mat'][]['dinde = -vm*(inde**n_trans)/(inde**n_trans + k_trans**n_trans)',
'dindi = vm*(inde**n_trans)/(inde**n_trans + k_trans**n_trans)',
'dm = synm*(indi**n)/(indi**n + k_ind**n) - degm*m',
'dp = synp*m - k_mat*p',
'dp_mat = k_mat*p - degp*p_mat']
Description:
This model describes the gene expression for mRNA and protein driven by an inducible promoter. There is a delay in induction possibly due to active transport. An additional term is considered to account for the maturation of the protein.,
Definition of states:
          inde: extracellular inducer concentration
          indi: intracellular inducer concentration
          m: mRNA
          p: peptide/protein
          p_mat: matured protein,
Definition of parameters:
          vm: transport rate
          k_trans: half-activation constant for transport
          k_ind: half-activation constant
          synm: mRNA synthesis rate
          degm: mRNA degradation rate
          synp: protein synthesis rate
          degp: protein degradation rate/dilution rate
          k_mat: protein maturation rate,
Definition of inputs:
          inde: inducer level is used as initial condition,
Reference:
          Title: An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs.
          Authors: Yeoh, Jing Wui, Kai Boon Ivan Ng, Ai Ying Teh, JingYun Zhang, Wai Kit David Chee, and Chueh Loo Poh.
          Journal: ACS synthetic biology 8, no. 7 (2019): 1484-1497.
          DOI: https://doi.org/10.1021/acssynbio.8b00523
05/01/2021Genetic Circuit DiagramDownloadSettings
BMSS, ConstantInduction, Inducible, SingleEquation['p']['n', 'k_ind', 'synp', 'degp']['ind']['dp = synp*(ind**n)/(ind**n + k_ind**n) - degp*p']Description:
This model describes a simple gene expression for protein driven by an inducible promoter with constant induction.,
Definition of states:
          p: peptide/protein,
Definition of parameters:
          k_ind: half-activation constant
          synp: protein synthesis rate
          degp: protein degradation rate/dilution rate,
Definition of inputs:
          ind: inducer level,
Reference:
          Title: An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs.
          Authors: Yeoh, Jing Wui, Kai Boon Ivan Ng, Ai Ying Teh, JingYun Zhang, Wai Kit David Chee, and Chueh Loo Poh.
          Journal: ACS synthetic biology 8, no. 7 (2019): 1484-1497.
          DOI: https://doi.org/10.1021/acssynbio.8b00523
05/01/2021Genetic Circuit DiagramDownloadSettings
BMSS, InducerDegradation, Inducible, SingleEquation['ind', 'p']['n', 'degind', 'k_ind', 'synp', 'degp'][]['dind = -degind*ind',
'dp = synp*(ind**n)/(ind**n + k_ind**n) - degp*p']
Description:
This model describes the gene expression for protein driven by an inducible promoter. The inducer is assumed to be unstable and undergoing degradation.,
Definition of states:
          ind: inducer dynamics
          p: peptide/protein,
Definition of parameters:
          degind: degradation rate of inducer
          k_ind: half-activation constant
          synp: protein synthesis rate
          degp: protein degradation rate/dilution rate,
Definition of inputs:
          ind: inducer level is used as initial condition,
Reference:
          Title: An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs.
          Authors: Yeoh, Jing Wui, Kai Boon Ivan Ng, Ai Ying Teh, JingYun Zhang, Wai Kit David Chee, and Chueh Loo Poh.
          Journal: ACS synthetic biology 8, no. 7 (2019): 1484-1497.
          DOI: https://doi.org/10.1021/acssynbio.8b00523
05/01/2021Genetic Circuit DiagramDownloadSettings
BMSS, DelayActivation, Inducible, ActiveTransport, SingleEquation['inde', 'indi', 'p']['vm', 'n_trans', 'k_trans', 'n', 'k_ind', 'synp', 'degp'][]['dinde = -vm*(inde**n_trans)/(inde**n_trans + k_trans**n_trans)',
'dindi = vm*(inde**n_trans)/(inde**n_trans + k_trans**n_trans)',
'dp = synp*(indi**n)/(indi**n + k_ind**n) - degp*p']
Description:
This model describes the gene expression for protein driven by an inducible promoter. There is a delay in induction possibly due to active transport.,
Definition of states:
          inde: extracellular inducer concentration
          indi: intracellular inducer concentration
          p: peptide/protein,
Definition of parameters:
          vm: transport rate
          k_trans: half-activation constant for transport
          k_ind: half-activation constant
          synp: protein synthesis rate
          degp: protein degradation rate/dilution rate,
Definition of inputs:
          inde: inducer level is used as initial condition,
Reference:
          Title: An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs.
          Authors: Yeoh, Jing Wui, Kai Boon Ivan Ng, Ai Ying Teh, JingYun Zhang, Wai Kit David Chee, and Chueh Loo Poh.
          Journal: ACS synthetic biology 8, no. 7 (2019): 1484-1497.
          DOI: https://doi.org/10.1021/acssynbio.8b00523
05/01/2021Genetic Circuit DiagramDownloadSettings
BMSS, ConstantInduction, Inducible, Inhibition['m', 'p']['k_leak', 'synm', 'degm', 'n', 'k_ind', 'k_inhmax', 'n_inh', 'k_inh', 'synp', 'degp']['inducer']['dm = k_leak + (synm*(inducer**n)/(inducer**n + k_ind**n))*(1 - k_inhmax*(inducer**n_inh)/(inducer**n_inh + k_inh**n_inh)) - degm*m',
'dp = synp*m - degp*p']
Description:
This model describes a simple gene expression for mRNA and protein driven by an inducible promoter with constant induction. The model also includes the inhibitory effect at high inducer concentrations.,
Definition of states:
          m: mRNA
          p: peptide/protein,
Definition of parameters:
          k_leak: basal leakiness for promoter activation
          synm: mRNA synthesis rate
          degm: mRNA degradation rate
          k_ind: half-activation constant
          k_inhmax: maximum inhibition rate
          k_inh: half-inhibition constant
          synp: protein synthesis rate
          degp: protein degradation rate/dilution rate,
Definition of inputs:
          inducer: inducer level,
Reference:
          Title: An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs.
          Authors: Yeoh, Jing Wui, Kai Boon Ivan Ng, Ai Ying Teh, JingYun Zhang, Wai Kit David Chee, and Chueh Loo Poh.
          Journal: ACS synthetic biology 8, no. 7 (2019): 1484-1497.
          DOI: https://doi.org/10.1021/acssynbio.8b00523
05/01/2021Genetic Circuit DiagramDownloadSettings
BMSS, DelayActivation, Inducible, ActiveTransport, Inhibition['inde', 'indi', 'm', 'p']['vm', 'n_trans', 'k_trans', 'k_leak', 'n', 'k_ind', 'synm', 'degm', 'k_inhmax', 'n_inh', 'k_inh', 'synp', 'degp'][]['dinde = -vm*(inde**n_trans)/(inde**n_trans + k_trans**n_trans)',
'dindi = vm*(inde**n_trans)/(inde**n_trans + k_trans**n_trans)',
'dm = k_leak + (synm*(indi**n)/(indi**n + k_ind**n))*(1 - k_inhmax*(inde**n_inh)/(inde**n_inh + k_inh**n_inh)) - degm*m',
'dp = synp*m - degp*p']
Description:
This model describes the gene expression for mRNA and protein driven by an inducible promoter. There is a delay in induction possibly due to active transport. The model also includes the inhibitory effect at high inducer concentrations.,
Definition of states:
          inde: extracellular inducer concentration
indi: intracellular inducer concentration
          m: mRNA
          p: peptide/protein,
Definition of parameters:
          vm: transport rate
          k_trans: half-activation constant for transport
          k_leak: basal leakiness for promoter activation
          k_ind: half-activation constant
          synm: mRNA synthesis rate
          degm: mRNA degradation rate
          k_inhmax: maximum inhibition rate
          k_inh: half-inhibition constant
          synp: protein synthesis rate
          degp: protein degradation rate/dilution rate,
Definition of inputs:
          inde: inducer level is used as initial condition,
Reference:
          Title: An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs.
          Authors: Yeoh, Jing Wui, Kai Boon Ivan Ng, Ai Ying Teh, JingYun Zhang, Wai Kit David Chee, and Chueh Loo Poh.
          Journal: ACS synthetic biology 8, no. 7 (2019): 1484-1497.
          DOI: https://doi.org/10.1021/acssynbio.8b00523
05/01/2021Genetic Circuit DiagramDownloadSettings
BMSS, DelayActivation, Inducible, ActiveTransport, InducerDegradation['inde', 'indi', 'm', 'p']['vm', 'n_trans', 'k_trans', 'degind', 'n', 'k_ind', 'synm', 'degm', 'synp', 'degp'][]['dinde = -vm*(inde**n_trans)/(inde**n_trans + k_trans**n_trans)',
'dindi = vm*(inde**n_trans)/(inde**n_trans + k_trans**n_trans) - degind*indi',
'dm = synm*(indi**n)/(indi**n + k_ind**n) - degm*m',
'dp = synp*m - degp*p']
Description:
This model describes the gene expression for mRNA and protein driven by an inducible promoter. There is possibly a degradation of extracellular inducer followed by delay in induction due to active transport.
Definition of states:
          inde: extracellular inducer concentration
          indi: intracellular inducer concentration
          m: mRNA
          p: peptide/protein,
Definition of parameters:
          vm: transport rate
          k_trans: half-activation constant for transport
          degind: degradation rate of inducer
          k_ind: half-activation constant
          synm: mRNA synthesis rate
          degm: mRNA degradation rate
          synp: protein synthesis rate
          degp: protein degradation rate/dilution rate,
Definition of inputs:
          inde: inducer level is used as initial condition, Reference:
          Title: An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs.
          Authors: Yeoh, Jing Wui, Kai Boon Ivan Ng, Ai Ying Teh, JingYun Zhang, Wai Kit David Chee, and Chueh Loo Poh.
          Journal: ACS synthetic biology 8, no. 7 (2019): 1484-1497.
          DOI: https://doi.org/10.1021/acssynbio.8b00523
05/01/2021Genetic Circuit DiagramDownloadSettings
BMSS, InducerDegradation, DelayActivation, Inducible, ActiveTransport['inde', 'indi', 'm', 'p']['vm', 'n_trans', 'k_trans', 'degind', 'n', 'k_ind', 'synm', 'degm', 'synp', 'degp'][]['dinde = -degind*inde -vm*(inde**n_trans)/(inde**n_trans + k_trans**n_trans)',
'dindi = vm*(inde**n_trans)/(inde**n_trans + k_trans**n_trans)',
'dm = synm*(indi**n)/(indi**n + k_ind**n) - degm*m',
'dp = synp*m - degp*p']
Description:
This model describes a simple gene expression for mRNA and protein driven by a constitutive promoter with constant mRNA synthesis rate.,
Definition of states:
          m: mRNA
          p: peptide/protein,
Definition of parameters:
          synm: mRNA synthesis rate
          degm: mRNA degradation rate
          synp: protein synthesis rate
          degp: protein degradation rate/dilution rate,
Definition of inputs:
          [],
Reference:
          Title: An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs.
          Authors: Yeoh, Jing Wui, Kai Boon Ivan Ng, Ai Ying Teh, JingYun Zhang, Wai Kit David Chee, and Chueh Loo Poh.
          Journal: ACS synthetic biology 8, no. 7 (2019): 1484-1497.
          DOI: https://doi.org/10.1021/acssynbio.8b00523
05/01/2021Genetic Circuit DiagramDownloadSettings
BMSS, ConstitutivePromoter, DoubleEquation['m', 'p']['synm', 'degm', 'synp', 'degp'][]['dm = synm - degm*m',
'dp = synp*m - degp*p']
Description:
This model describes the gene expression for mRNA and protein driven by an inducible promoter. There is a delay in induction possibly due to active transport followed by intracellular inducer degradation.,
Definition of states:
          inde: extracellular inducer concentration
          indi: intracellular inducer concentration
          m: mRNA
          p: peptide/protein,
Definition of parameters:
          vm: transport rate
          k_trans: half-activation constant for transport
          degind: degradation rate of inducer
          k_ind: half-activation constant
          synm: mRNA synthesis rate
          degm: mRNA degradation rate
          synp: protein synthesis rate
          degp: protein degradation rate/dilution rate,
Definition of inputs:
          inde: inducer level is used as initial condition,
Reference:
          Title: An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs.
          Authors: Yeoh, Jing Wui, Kai Boon Ivan Ng, Ai Ying Teh, JingYun Zhang, Wai Kit David Chee, and Chueh Loo Poh.
          Journal: ACS synthetic biology 8, no. 7 (2019): 1484-1497.
          DOI: https://doi.org/10.1021/acssynbio.8b00523
05/01/2021Genetic Circuit DiagramDownloadSettings
BMSS, ConstitutivePromoter, DoubleEquation, MaturationTime['m', 'p', 'p_mat']['synm', 'degm', 'synp', 'degp', 'k_mat'][]['dm = synm - degm*m',
'dp = synp*m - k_mat*p',
'dp_mat = k_mat*p - degp*p_mat']
Description:
This model describes a simple gene expression for mRNA and protein driven by a constitutive promoter with constant mRNA synthesis rate. An additional term is considered to account for the maturation of the protein.,
Definition of states:
          m: mRNA
          p: peptide/protein
          p_mat: matured protein,
Definition of parameters:
          synm: mRNA synthesis rate
          degm: mRNA degradation rate
          synp: protein synthesis rate
          degp: protein degradation rate/dilution rate
          k_mat: protein maturation rate,
Definition of inputs:
          [],
Reference:
          Title: An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs.
          Authors: Yeoh, Jing Wui, Kai Boon Ivan Ng, Ai Ying Teh, JingYun Zhang, Wai Kit David Chee, and Chueh Loo Poh.
          Journal: ACS synthetic biology 8, no. 7 (2019): 1484-1497.
          DOI: https://doi.org/10.1021/acssynbio.8b00523
05/01/2021Genetic Circuit DiagramDownloadSettings
BMSS, ConstitutivePromoter, SingleEquation['p']['synp', 'degp'][]['dp = synp - degp*p']Description:
This model describes a simple gene expression for protein driven by a constitutive promoter with constant lumped protein synthesis rate.,
Definition of states:
          p: peptide/protein,
Definition of parameters:
          synp: protein synthesis rate
          degp: protein degradation rate/dilution rate,
Definition of inputs:
          [],
Reference:
          Title: An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs.
          Authors: Yeoh, Jing Wui, Kai Boon Ivan Ng, Ai Ying Teh, JingYun Zhang, Wai Kit David Chee, and Chueh Loo Poh.
          Journal: ACS synthetic biology 8, no. 7 (2019): 1484-1497.
          DOI: https://doi.org/10.1021/acssynbio.8b00523
05/01/2021Genetic Circuit DiagramDownloadSettings
BMSS, ConstitutivePromoter, SingleEquation, MaturationTime['p', 'p_mat']['synp', 'degp', 'k_mat'][]['dp = synp - k_mat*p',
'dp_mat = k_mat*p - degp*p_mat']
Description:
This model describes a simple gene expression for protein driven by a constitutive promoter with constant lumped protein synthesis rate. An additional term is considered to account for the maturation of the protein.,
Definition of states:
          p: peptide/protein
          p_mat: matured protein,
Definition of parameters:
          synp: protein synthesis rate
          degp: protein degradation rate/dilution rate
          k_mat: protein maturation rate,
Definition of inputs:
          [],
Reference:
          Title: An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs.
          Authors: Yeoh, Jing Wui, Kai Boon Ivan Ng, Ai Ying Teh, JingYun Zhang, Wai Kit David Chee, and Chueh Loo Poh.
          Journal: ACS synthetic biology 8, no. 7 (2019): 1484-1497.
          DOI: https://doi.org/10.1021/acssynbio.8b00523
05/01/2021Genetic Circuit DiagramDownloadSettings
BMSS, Multiple, ConstitutivePromoter, DoubleEquation, FixedRBS['mx', 'px']['synmx', 'degm', 'synp', 'degp'][]['dmx = synmx - degm*mx',
'dpx = synp*mx - degp*px']
Description:
This model describes gene expressions for multiple proteins and their corresponding mRNAs driven by the same RBS but different constitutive promoters.,
Definition of states:
          mx: mRNAs for x = 1,2,n
          px: peptides/proteins for x = 1,2,n,
Definition of parameters:
          synmx: mRNA synthesis rate for x = 1,2,n
          degm: mRNA degradation rate
          synp: protein synthesis rate
          degp: protein degradation rate/dilution rate,
Definition of inputs:
          [],
Reference:
          Title: An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs.
          Authors: Yeoh, Jing Wui, Kai Boon Ivan Ng, Ai Ying Teh, JingYun Zhang, Wai Kit David Chee, and Chueh Loo Poh.
          Journal: ACS synthetic biology 8, no. 7 (2019): 1484-1497.
          DOI: https://doi.org/10.1021/acssynbio.8b00523
05/01/2021Genetic Circuit DiagramDownloadSettings
BMSS, Multiple, ConstitutivePromoter, DoubleEquation, FixedRBS, MaturationTime['mx', 'px', 'px_mat']['synmx', 'degm', 'synp', 'degp', 'k_mat'][]['dmx = synmx - degm*mx',
'dpx = synp*mx - k_mat*px',
'dpx_mat = k_mat*px - degp*px_mat']
Description:
This model describes gene expressions for multiple proteins and their corresponding mRNAs driven by the same RBS but different constitutive promoters. An additional term is considered to account for the delayed maturation of the protein.,
Definition of states:
          mx: mRNAs for x = 1,2,n
          px: peptides/proteins for x = 1,2,n
          px_mat: matured proteins for x = 1,2,n,
Definition of parameters:
          synmx: mRNA synthesis rate for x = 1,2,n
          degm: mRNA degradation rate
          synp: protein synthesis rate
          degp: protein degradation rate/dilution rate
          k_mat: protein maturation rate,
Definition of inputs:
          [],
Reference:
          Title: An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs.
          Authors: Yeoh, Jing Wui, Kai Boon Ivan Ng, Ai Ying Teh, JingYun Zhang, Wai Kit David Chee, and Chueh Loo Poh.
          Journal: ACS synthetic biology 8, no. 7 (2019): 1484-1497.
          DOI: https://doi.org/10.1021/acssynbio.8b00523
05/01/2021Genetic Circuit DiagramDownloadSettings
BMSS, Multiple, ConstitutivePromoter, SingleEquation, FixedRBS['px']['synpx', 'degp'][]['dpx = synpx - degp*px']Description:
This model describes gene expressions for multiple proteins driven by the same RBS but different constitutive promoters.,
Definition of states:
          px: peptides/proteins for x = 1,2,n,
Definition of parameters:
          synpx: protein synthesis rate for x = 1,2,n
          degp: protein degradation rate/dilution rate,
Definition of inputs:
          [],
Reference:
          Title: An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs.
          Authors: Yeoh, Jing Wui, Kai Boon Ivan Ng, Ai Ying Teh, JingYun Zhang, Wai Kit David Chee, and Chueh Loo Poh.
          Journal: ACS synthetic biology 8, no. 7 (2019): 1484-1497.
          DOI: https://doi.org/10.1021/acssynbio.8b00523
05/01/2021Genetic Circuit DiagramDownloadSettings
BMSS, Multiple, ConstitutivePromoter, SingleEquation, FixedRBS, MaturationTime['px', 'px_mat']['synpx', 'degp', 'k_mat'][]['dpx = synpx - k_mat*px',
'dpx_mat = k_mat*px - degp*px_mat']
Description:
This model describes gene expressions for multiple proteins driven by the same RBS but different constitutive promoters. An additional term is considered to account for the delayed maturation of the protein.,
Definition of states:
          px: peptides/proteins for x = 1,2,n
          px_mat: matured proteins for x = 1,2,n,
Definition of parameters:
          synpx: protein synthesis rate for x = 1,2,n
          degp: protein degradation rate/dilution rate
          k_mat: protein maturation rate,
Definition of inputs:
          [],
Reference:
          Title: An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs.
          Authors: Yeoh, Jing Wui, Kai Boon Ivan Ng, Ai Ying Teh, JingYun Zhang, Wai Kit David Chee, and Chueh Loo Poh.
          Journal: ACS synthetic biology 8, no. 7 (2019): 1484-1497.
          DOI: https://doi.org/10.1021/acssynbio.8b00523
05/01/2021Genetic Circuit DiagramDownloadSettings
BMSS, Multiple, ConstitutivePromoter, DoubleEquation, FixedPromoter, DifferentRBS1['mx', 'px']['synm', 'degm', 'synpx', 'degp'][]['dmx = synm - degm*mx',
'dpx = synpx*mx - degp*px']
Description:
This model describes gene expressions for multiple proteins and their corresponding mRNAs driven by the same constitutive promoter but different RBSs.,
Definition of states:
          mx: mRNAs for x = 1,2,n
          px: peptides/proteins for x = 1,2,n,
Definition of parameters:
          synm: mRNA synthesis rate
          degm: mRNA degradation rate
synpx: protein synthesis rate for x = 1,2,n
          degp: prote          in degradation rate/dilution rate,
Definition of inputs:
          [],
Reference:
          Title: An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs.
          Authors: Yeoh, Jing Wui, Kai Boon Ivan Ng, Ai Ying Teh, JingYun Zhang, Wai Kit David Chee, and Chueh Loo Poh.
          Journal: ACS synthetic biology 8, no. 7 (2019): 1484-1497.
          DOI: https://doi.org/10.1021/acssynbio.8b00523
05/01/2021Genetic Circuit DiagramDownloadSettings
BMSS, Multiple, ConstitutivePromoter, DoubleEquation, FixedPromoter, DifferentRBS, MaturationTime1['mx', 'px', 'px_mat']['synm', 'degm', 'synpx', 'degp', 'k_mat'][]['dmx = synm - degm*mx',
'dpx = synpx*mx - k_mat*px',
'dpx_mat = k_mat*px - degp*px_mat']
Description:
This model describes gene expressions for multiple proteins and their corresponding mRNAs driven by the same constitutive promoter but different RBSs. An additional term is considered to account for the delayed maturation of the protein.,
Definition of states:
          mx: mRNAs for x = 1,2,n
          px: peptides/proteins for x = 1,2,n
          px_mat: matured proteins for x = 1,2,n,
Definition of parameters:
          synm: mRNA synthesis rate
          degm: mRNA degradation rate
          synpx: protein synthesis rate for x = 1,2,n
          degp: protein degradation rate/dilution rate
          k_mat: protein maturation rate,
Definition of inputs:
          [],
Reference:
          Title: An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs.
          Authors: Yeoh, Jing Wui, Kai Boon Ivan Ng, Ai Ying Teh, JingYun Zhang, Wai Kit David Chee, and Chueh Loo Poh.
          Journal: ACS synthetic biology 8, no. 7 (2019): 1484-1497.
          DOI: https://doi.org/10.1021/acssynbio.8b00523
05/01/2021Genetic Circuit DiagramDownloadSettings
BMSS, NOTgate, DoubleEquation['m1', 'p1', 'm2', 'p2']['synm1', 'degm', 'synp', 'degp', 'synm2', 'k_maxrep', 'p_max']['state']['dm1 = synm1*state - degm*m1',
'dp1 = synp*m1 - degp*p1',
'dm2 = synm2*(1 - k_maxrep*(p1/p_max)) - degm*m2',
'dp2 = synp*m2 - degp*p2']
Description:
This model describes gene expressions for a NOT gate or repressible system. The ODEs include the dynamics of the proteins and the corresponding mRNAs.,
Definition of states:
          m1: mRNA of repressor
          p1: peptide/protein/repressor
          m2: mRNA
          p2: peptide/protein,
Definition of parameters:
          synm1: mRNA synthesis rate for repressor
          degm: mRNA degradation rate
synp: protein synthesis rate
          degp: protein degradation rate/dilution rate
          synm2: mRNA synthesis rate
          k_maxrep: maximum repressible capacity
          p_max: constant for normalization,
Definition of inputs:
          state: input to turn on or off the repressor production,
Reference:
          Title: An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs.
          Authors: Yeoh, Jing Wui, Kai Boon Ivan Ng, Ai Ying Teh, JingYun Zhang, Wai Kit David Chee, and Chueh Loo Poh.
          Journal: ACS synthetic biology 8, no. 7 (2019): 1484-1497.
          DOI: https://doi.org/10.1021/acssynbio.8b00523
05/01/2021Genetic Circuit DiagramDownloadSettings
BMSS, NOTgate, DoubleEquation, MaturationTime['m1', 'p1', 'm2', 'p2', 'p2_mat']['synm1', 'degm', 'synp', 'degp', 'synm2', 'k_maxrep', 'p_max', 'k_mat']['state']['dm1 = synm1*state - degm*m1',
'dp1 = synp*m1 - degp*p1',
'dm2 = synm2*(1 - k_maxrep*(p1/p_max)) - degm*m2',
'dp2 = synp*m2 - k_mat*p2',
'dp2_mat = k_mat*p2 - degp*p2_mat']
Description:
This model describes gene expressions for a NOT gate or repressible system. The ODEs include the dynamics of the proteins and the corresponding mRNAs. An additional term is considered to account for the delayed maturation of the protein.,
Definition of states:
          m1: mRNA of repressor
          p1: peptide/protein/repressor
          m2: mRNA
          p2: peptide/protein
          p2_mat: matured protein,
Definition of parameters:
          synm1: mRNA synthesis rate for repressor
          degm: mRNA degradation rate
          synp: protein synthesis rate
          degp: protein degradation rate/dilution rate
          synm2: mRNA synthesis rate
          k_maxrep: maximum repressible capacity
          p_max: constant for normalization
          k_mat: protein maturation rate,
Definition of inputs:
          state: input to turn on or off the repressor production,
Reference:
          Title: An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs.
          Authors: Yeoh, Jing Wui, Kai Boon Ivan Ng, Ai Ying Teh, JingYun Zhang, Wai Kit David Chee, and Chueh Loo Poh.
          Journal: ACS synthetic biology 8, no. 7 (2019): 1484-1497.
          DOI: https://doi.org/10.1021/acssynbio.8b00523
05/01/2021Genetic Circuit DiagramDownloadSettings
BMSS, NOTgate, SingleEquation['m1', 'p1']['synm', 'degm', 'synp', 'degp', 'k_maxrep']['state']['dm1 = synm*(1-(k_maxrep*state)) - degm*m1',
'dp1 = synp*m1 - degp*p1']
Description:
This model describes gene expressions for a NOT gate or repressible system using a simplified ODE with only one protein and the corresponding mRNA.,
Definition of states:
          m1: mRNA of repressor
          p1: peptide/protein/repressor,
Definition of parameters:
          synm: mRNA synthesis rate
          degm: mRNA degradation rate
          synp: protein synthesis rate
          degp: protein degradation rate/dilution rate
          k_maxrep: maximum repressible capacity,
Definition of inputs:
          state: input to turn on or off the repressor production,
Reference:
          Title: An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs.
          Authors: Yeoh, Jing Wui, Kai Boon Ivan Ng, Ai Ying Teh, JingYun Zhang, Wai Kit David Chee, and Chueh Loo Poh.
          Journal: ACS synthetic biology 8, no. 7 (2019): 1484-1497.
          DOI: https://doi.org/10.1021/acssynbio.8b00523
05/01/2021Genetic Circuit DiagramDownloadSettings
BMSS, NOTgate, SingleEquation, MaturationTime['m1', 'p1', 'p1_mat']['synm', 'degm', 'synp', 'degp', 'k_maxrep', 'k_mat']['state']['dm1 = synm*(1-(k_maxrep*state)) - degm*m1',
'dp1 = synp*m1 - k_mat*p1',
'dp1_mat = k_mat*p1 - degp*p1_mat']
Description:
This model describes gene expressions for a NOT gate or repressible system using a simplified ODE with only one protein and the corresponding mRNA. An additional term is considered to account for the delayed maturation of the protein.,
Definition of states:
          m1: mRNA of repressor
          p1: peptide/protein/repressor
          p1_mat: matured protein,
Definition of parameters:
          synm: mRNA synthesis rate
          degm: mRNA degradation rate
          synp: protein synthesis rate
          degp: protein degradation rate/dilution rate
          k_maxrep: maximum repressible capacity
          k_mat: protein maturation rate,
Definition of inputs:
          state: input to turn on or off the repressor production,
Reference:
          Title: An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs.
          Authors: Yeoh, Jing Wui, Kai Boon Ivan Ng, Ai Ying Teh, JingYun Zhang, Wai Kit David Chee, and Chueh Loo Poh.
          Journal: ACS synthetic biology 8, no. 7 (2019): 1484-1497.
          DOI: https://doi.org/10.1021/acssynbio.8b00523
05/01/2021Genetic Circuit DiagramDownloadSettings
BMSS, LogicGate, ANDgate['m1', 'p1', 'm2', 'p2', 'm3', 'p3']['synm1', 'degm', 'synp', 'degp', 'synm2', 'synm3', 'p1_max', 'p2_max']['state1', 'state2']['dm1 = synm1*state1 - degm*m1',
'dp1 = synp*m1 - degp*p1',
'dm2 = synm2*state2 - degm*m2',
'dp2 = synp*m2 - degp*p2',
'dm3 = synm3*(p1/p1_max)*(p2/p2_max) - degm*m3',
'dp3 = synp*m3 - degp*p3']
Description:
This model describes gene expressions for an AND logic gate. The ODEs include the dynamics of the proteins and the corresponding mRNAs driven by two inputs.,
Definition of states:
          m1: mRNA of p1
          p1: peptide/protein 1
          m2: mRNA of p2
          p2: peptide/protein 2
          m3: mRNA of p3
          p3: peptide/protein 3,
Definition of parameters:
          synm1: mRNA synthesis rate for protein 1
          degm: mRNA degradation rate
          synp: protein synthesis rate
          degp: protein degradation rate/dilution rate
          synm2: mRNA synthesis rate for protein 2
          synm3: mRNA synthesis rate for protein 3
          p1_max: constant for normalization of protein 1
          p2_max: constant for normalization of protein 2,
Definition of inputs:
   &nbnbsp      state1: input1 to control p1 expression
          state2: input2 to control p2 expression,
Reference:
          Title: An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs.
          Authors: Yeoh, Jing Wui, Kai Boon Ivan Ng, Ai Ying Teh, JingYun Zhang, Wai Kit David Chee, and Chueh Loo Poh.
          Journal: ACS synthetic biology 8, no. 7 (2019): 1484-1497.
          DOI: https://doi.org/10.1021/acssynbio.8b00523
05/01/2021Genetic Circuit DiagramDownloadSettings
BMSS, LogicGate, ANDgate, BasalLeakinessP1['m1', 'p1', 'm2', 'p2', 'm3', 'p3']['k_leak', 'synm1', 'degm', 'synp', 'degp', 'synm2', 'synm3', 'p1_max', 'p2_max']['state1', 'state2']['dm1 = k_leak + synm1*state1 - degm*m1',
'dp1 = synp*m1 - degp*p1',
'dm2 = synm2*state2 - degm*m2',
'dp2 = synp*m2 - degp*p2',
'dm3 = synm3*(p1/p1_max)*(p2/p2_max) - degm*m3',
'dp3 = synp*m3 - degp*p3']
Description:
This model describes gene expressions for an AND logic gate. The ODEs include the dynamics of the proteins and the corresponding mRNAs driven by two inputs with basal leakiness for protein 1.,
Definition of states:
          m1: mRNA of p1
          p1: peptide/protein 1
          m2: mRNA of p2
          p2: peptide/protein 2
          m3: mRNA of p3
          p3: peptide/protein 3,
Definition of parameters:
          k_leak: basal leakiness for protein 1
          synm1: mRNA synthesis rate for protein 1
          degm: mRNA degradation rate
          synp: protein synthesis rate
          degp: protein degradation rate/dilution rate
          synm2: mRNA synthesis rate for protein 2
          synm3: mRNA synthesis rate for protein 3
          p1_max: constant for normalization of protein 1
          p2_max: constant for normalization of protein 2,
Definition of inputs:
          state1: input1 to control p1 expression
          state2: input2 to control p2 expression,
Reference:
          Title: An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs.
          Authors: Yeoh, Jing Wui, Kai Boon Ivan Ng, Ai Ying Teh, JingYun Zhang, Wai Kit David Chee, and Chueh Loo Poh.
          Journal: ACS synthetic biology 8, no. 7 (2019): 1484-1497.
          DOI: https://doi.org/10.1021/acssynbio.8b00523
05/01/2021Genetic Circuit DiagramDownloadSettings
BMSS, LogicGate, ANDgate, BasalLeakinessP2['m1', 'p1', 'm2', 'p2', 'm3', 'p3']['k_leak', 'synm1', 'degm', 'synp', 'degp', 'synm2', 'synm3', 'p1_max', 'p2_max']['state1', 'state2']['dm1 = synm1*state1 - degm*m1',
'dp1 = synp*m1 - degp*p1',
'dm2 = k_leak + synm2*state2 - degm*m2',
'dp2 = synp*m2 - degp*p2',
'dm3 = synm3*(p1/p1_max)*(p2/p2_max) - degm*m3',
'dp3 = synp*m3 - degp*p3']
Description:
This model describes gene expressions for an AND logic gate. The ODEs include the dynamics of the proteins and the corresponding mRNAs driven by two inputs with basal leakiness for protein 2.,
Definition of states:
          m1: mRNA of p1
          p1: peptide/protein 1
          m2: mRNA of p2
          p2: peptide/protein 2
          m3: mRNA of p3
          p3: peptide/protein 3,
Definition of parameters:
          k_leak: basal leakiness for protein 2
          synm1: mRNA synthesis rate for protein 1
          degm: mRNA degradation rate
          synp: protein synthesis rate
          degp: protein degradation rate/dilution rate
          synm2: mRNA synthesis rate for protein 2
          synm3: mRNA synthesis rate for protein 3
          p1_max: constant for normalization of protein 1
          p2_max: constant for normalization of protein 2,
Definition of inputs:
          state1: input1 to control p1 expression
          state2: input2 to control p2 expression,
Reference:
          Title: An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs.
          Authors: Yeoh, Jing Wui, Kai Boon Ivan Ng, Ai Ying Teh, JingYun Zhang, Wai Kit David Chee, and Chueh Loo Poh.
          Journal: ACS synthetic biology 8, no. 7 (2019): 1484-1497.
          DOI: https://doi.org/10.1021/acssynbio.8b00523
05/01/2021Genetic Circuit DiagramDownloadSettings
BMSS, LogicGate, ANDgate, BasalLeakinessP3['m1', 'p1', 'm2', 'p2', 'm3', 'p3']['k_leak', 'synm1', 'degm', 'synp', 'degp', 'synm2', 'synm3', 'p1_max', 'p2_max']['state1', 'state2']['dm1 = synm1*state1 - degm*m1',
'dp1 = synp*m1 - degp*p1',
'dm2 = synm2*state2 - degm*m2',
'dp2 = synp*m2 - degp*p2',
'dm3 = k_leak + synm3*(p1/p1_max)*(p2/p2_max) - degm*m3',
'dp3 = synp*m3 - degp*p3']
Description:
This model describes gene expressions for an AND logic gate. The ODEs include the dynamics of the proteins and the corresponding mRNAs driven by two inputs with basal leakiness for protein 3.,
Definition of states:
          m1: mRNA of p1
          p1: peptide/protein 1
          m2: mRNA of p2
          p2: peptide/protein 2
          m3: mRNA of p3
          p3: peptide/protein 3,
Definition of parameters:
          k_leak: basal leakiness for protein 2
          synm1: mRNA synthesis rate for protein 1
          degm: mRNA degradation rate
          synp: protein synthesis rate
          degp: protein degradation rate/dilution rate
          synm2: mRNA synthesis rate for protein 2
          synm3: mRNA synthesis rate for protein 3
          p1_max: constant for normalization of protein 1
          p2_max: constant for normalization of protein 2,
Definition of inputs:
          state1: input1 to control p1 expression
          state2: input2 to control p2 expression,
Reference:
          Title: An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs.
          Authors: Yeoh, Jing Wui, Kai Boon Ivan Ng, Ai Ying Teh, JingYun Zhang, Wai Kit David Chee, and Chueh Loo Poh.
          Journal: ACS synthetic biology 8, no. 7 (2019): 1484-1497.
          DOI: https://doi.org/10.1021/acssynbio.8b00523
05/01/2021Genetic Circuit DiagramDownloadSettings
BMSS, LogicGate, ANDgate, BasalLeakinessP1, BasalLeakinessP3['m1', 'p1', 'm2', 'p2', 'm3', 'p3']['k_leak1', 'k_leak', 'synm1', 'degm', 'synp', 'degp', 'synm2', 'synm3', 'p1_max', 'p2_max']['state1', 'state2']['dm1 = k_leak1 + synm1*state1 - degm*m1',
'dp1 = synp*m1 - degp*p1',
'dm2 = synm2*state2 - degm*m2',
'dp2 = synp*m2 - degp*p2',
'dm3 = k_leak + synm3*(p1/p1_max)*(p2/p2_max) - degm*m3',
'dp3 = synp*m3 - degp*p3']
Description:
This model describes gene expressions for an AND logic gate. The ODEs include the dynamics of the proteins and the corresponding mRNAs driven by two inputs with basal leakiness for protein 1 and 3.,
Definition of states:
          m1: mRNA of p1
          p1: peptide/protein 1
          m2: mRNA of p2
          p2: peptide/protein 2
          m3: mRNA of p3
          p3: peptide/protein 3,
Definition of parameters:
          k_leak1: basal leakiness for protein 1
          k_leak: basal leakiness for protein 3
          synm1: mRNA synthesis rate for protein 1
          degm: mRNA degradation rate
          synp: protein synthesis rate
          degp: protein degradation rate/dilution rate
          synm2: mRNA synthesis rate for protein 2
          synm3: mRNA synthesis rate for protein 3
          p1_max: constant for normalization of protein 1
          p2_max: constant for normalization of protein 2,
Definition of inputs:
          state1: input1 to control p1 expression
          state2: input2 to control p2 expression,
Reference:
          Title: An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs.
          Authors: Yeoh, Jing Wui, Kai Boon Ivan Ng, Ai Ying Teh, JingYun Zhang, Wai Kit David Chee, and Chueh Loo Poh.
          Journal: ACS synthetic biology 8, no. 7 (2019): 1484-1497.
          DOI: https://doi.org/10.1021/acssynbio.8b00523
05/01/2021Genetic Circuit DiagramDownloadSettings
BMSS, LogicGate, ANDgate, BasalLeakinessP1, BasalLeakinessP3, MaturationTime['m1', 'p1', 'm2', 'p2', 'm3', 'p3', 'p3_mat']['k_leak1', 'k_leak', 'synm1', 'degm', 'synp', 'degp', 'synm2', 'synm3', 'p1_max', 'p2_max', 'k_mat']['state1', 'state2']['dm1 = k_leak1 + synm1*state1 - degm*m1',
'dp1 = synp*m1 - degp*p1',
'dm2 = synm2*state2 - degm*m2',
'dp2 = synp*m2 - degp*p2',
'dm3 = k_leak + synm3*(p1/p1_max)*(p2/p2_max) - degm*m3',
'dp3 = synp*m3 - k_mat*p3',
'dp3_mat = k_mat*m3 - degp*p3_mat']
Description:
This model describes gene expressions for an AND logic gate. The ODEs include the dynamics of the proteins and the corresponding mRNAs driven by two inputs with basal leakiness for protein 1 and 3. An additional term is included to describe the delay protein maturation time.,
Definition of states:
          m1: mRNA of p1
          p1: peptide/protein 1
          m2: mRNA of p2
          p2: peptide/protein 2
          m3: mRNA of p3
          p3: peptide/protein 3
          p3_mat: matured protein 3,
Definition of parameters:
          k_leak1: basal leakiness for protein 1
          k_leak: basal leakiness for protein 3
          synm1: mRNA synthesis rate for protein 1
          degm: mRNA degradation rate
          synp: protein synthesis rate
          degp: protein degradation rate/dilution rate
          synm2: mRNA synthesis rate for protein 2
          synm3: mRNA synthesis rate for protein 3
          p1_max: constant for normalization of protein 1
          p2_max: constant for normalization of protein 2
          k_mat: maturation rate for protein 3,
Definition of inputs:
          state1: input1 to control p1 expression
          state2: input2 to control p2 expression,
Reference:
          Title: An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs.
          Authors: Yeoh, Jing Wui, Kai Boon Ivan Ng, Ai Ying Teh, JingYun Zhang, Wai Kit David Chee, and Chueh Loo Poh.
          Journal: ACS synthetic biology 8, no. 7 (2019): 1484-1497.
          DOI: https://doi.org/10.1021/acssynbio.8b00523
05/01/2021Genetic Circuit DiagramDownloadSettings
BMSS, LogicGate, ORgate['mRNA1', 'Pep1', 'mRNA2', 'Pep2', 'mRNA3', 'Pep3']['syn_mRNA1', 'syn_mRNA2', 'syn_mRNA3', 'deg_mRNA', 'syn_Pep', 'deg_Pep', 'Pepmax']['state1', 'state2']['dmRNA1 = syn_mRNA1*(state1) - (deg_mRNA *mRNA1)',
'dPep1 = (syn_Pep*mRNA1) - (deg_Pep*Pep1)',
'dmRNA2 = syn_mRNA2*(state2) - (deg_mRNA *mRNA2)',
'dPep2 = (syn_Pep*mRNA2) - (deg_Pep*Pep2)',
'dmRNA3 = (syn_mRNA3*((Pep1+Pep2)/Pepmax))-(deg_mRNA *mRNA3)',
'dPep3 = (syn_Pep*mRNA3)-(deg_Pep*Pep3)']
Description:
This model describes gene expressions for an OR logic gate. The ODEs include the dynamics of the proteins and the corresponding mRNAs driven by two inputs.,
Definition of states:
          mRNA1: mRNA of p1
          Pep1: peptide/protein 1
          mRNA2: mRNA of p2
          Pep2: peptide/protein 2
          mRNA3: mRNA of p3
          Pep3: peptide/protein 3,
Definition of parameters:
          synmRNA1: mRNA synthesis rate for protein 1
          synmRNA2: mRNA synthesis rate for protein 2
          synmRNA3: mRNA synthesis rate for protein 3
          deg_mRNA: mRNA degradation rate
          syn_Pep: protein synthesis rate
          deg_Pep: protein degradation rate/dilution rate
          Pepmax: normalization constant,
Definition of inputs:
          state1: input1 to control p1 expression
          state2: input2 to control p2 expression,
Reference:
          Title: An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs.
          Authors: Yeoh, Jing Wui, Kai Boon Ivan Ng, Ai Ying Teh, JingYun Zhang, Wai Kit David Chee, and Chueh Loo Poh.
          Journal: ACS synthetic biology 8, no. 7 (2019): 1484-1497.
          DOI: https://doi.org/10.1021/acssynbio.8b00523
05/01/2021Genetic Circuit DiagramDownloadSettings
BMSS, LogicGate, ORgate, InducerDegradation['Ind', 'mRNA1', 'Pep1', 'mRNA2', 'Pep2', 'mRNA3', 'Pep3']['syn_mRNA1', 'syn_mRNA2', 'syn_mRNA3', 'deg_mRNA', 'syn_Pep', 'deg_Pep', 'Pepmax', 'deg_Ind']['state1', 'state2']['dInd = -deg_Ind*Ind',
'dmRNA1 = syn_mRNA1*(Ind)*(state1) - (deg_mRNA *mRNA1)',
'dPep1 = (syn_Pep*mRNA1) - (deg_Pep*Pep1)',
'dmRNA2 = syn_mRNA2*(state2) - (deg_mRNA *mRNA2)',
'dPep2 = (syn_Pep*mRNA2) - (deg_Pep*Pep2)',
'dmRNA3 = (syn_mRNA3*((Pep1+Pep2)/Pepmax))-(deg_mRNA *mRNA3)',
'dPep3 = (syn_Pep*mRNA3)-(deg_Pep*Pep3)']
Description:
This model describes gene expressions for an OR logic gate. The ODEs include the dynamics of the proteins and the corresponding mRNAs driven by two inputs. The inducer for input 1 is assumed to be slowly degrading over time.,
Definition of states:
          Ind: Inducer dynamics
          mRNA1: mRNA of p1
          Pep1: peptide/protein 1
          mRNA2: mRNA of p2
          Pep2: peptide/protein 2
          mRNA3: mRNA of p3
          Pep3: peptide/protein 3,
Definition of parameters:
          synmRNA1: mRNA synthesis rate for protein 1
          synmRNA2: mRNA synthesis rate for protein 2
          synmRNA3: mRNA synthesis rate for protein 3
          deg_mRNA: mRNA degradation rate
          syn_Pep: protein synthesis rate
          deg_Pep: protein degradation rate/dilution rate
          Pepmax: normalization constant
          deg_Ind: inducer degradation rate,
Definition of inputs:
          state1: input1 to control p1 expression
          state2: input2 to control p2 expression,
Reference:
          Title: An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs.
          Authors: Yeoh, Jing Wui, Kai Boon Ivan Ng, Ai Ying Teh, JingYun Zhang, Wai Kit David Chee, and Chueh Loo Poh.
          Journal: ACS synthetic biology 8, no. 7 (2019): 1484-1497.
          DOI: https://doi.org/10.1021/acssynbio.8b00523
05/01/2021Genetic Circuit DiagramDownloadSettings
BMSS, LogicGate, ORgate, InducerDegradation, DelayActivation['Inde', 'Indi', 'Ind', 'mRNA1', 'Pep1', 'mRNA2', 'Pep2', 'mRNA3', 'Pep3']['syn_mRNA1', 'syn_mRNA2', 'syn_mRNA3', 'deg_mRNA', 'syn_Pep', 'deg_Pep', 'Pepmax', 'Km', 'deg_Ind']['state1', 'state2']['dInde = -(Inde/(Inde+Km))*Inde',
'dIndi = (Inde/(Inde+Km))*Inde',
'dInd = -deg_Ind*Ind',
'dmRNA1 = syn_mRNA1*(Ind)*(state1) - (deg_mRNA *mRNA1)',
'dPep1 = (syn_Pep*mRNA1) - (deg_Pep*Pep1)',
'dmRNA2 = syn_mRNA2*Indi*(state2) - (deg_mRNA *mRNA2)',
'dPep2 = (syn_Pep*mRNA2) - (deg_Pep*Pep2)',
'dmRNA3 = (syn_mRNA3*((Pep1+Pep2)/Pepmax))-(deg_mRNA *mRNA3)',
'dPep3 = (syn_Pep*mRNA3)-(deg_Pep*Pep3)']
Description:
This model describes gene expressions for an OR logic gate. The ODEs include the dynamics of the proteins and the corresponding mRNAs driven by two inputs. The inducer for input 2 is assumed to have delay in induction whereas the inducer for input 1 is assumed to be slowly degrading over time.,
Definition of states:
          Inde: extracellular inducer concentration
          Indi: intracellular inducer concentration
          Ind: Inducer dynamics
          mRNA1: mRNA of p1
          Pep1: peptide/protein 1
          mRNA2: mRNA of p2
          Pep2: peptide/protein 2
          mRNA3: mRNA of p3
          Pep3: peptide/protein 3,
Definition of parameters:
          synmRNA1: mRNA synthesis rate for protein 1
          synmRNA2: mRNA synthesis rate for protein 2
          synmRNA3: mRNA synthesis rate for protein 3
          deg_mRNA: mRNA degradation rate
          syn_Pep: protein synthesis rate
          deg_Pep: protein degradation rate/dilution rate
          Pepmax: normalization constant
          Km: half-activation for active transport
          deg_Ind: inducer degradation rate,
Definition of inputs:
          state1: input1 to control p1 expression
          state2: input2 to control p2 expression,
Reference:
          Title: An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs.
          Authors: Yeoh, Jing Wui, Kai Boon Ivan Ng, Ai Ying Teh, JingYun Zhang, Wai Kit David Chee, and Chueh Loo Poh.
          Journal: ACS synthetic biology 8, no. 7 (2019): 1484-1497.
          DOI: https://doi.org/10.1021/acssynbio.8b00523
05/01/2021Genetic Circuit DiagramDownloadSettings
BMSS, LogicGate, ORgate, InducerDegradation, DelayActivation, ResourceCompetition['Inde', 'Indi', 'Ind', 'mRNA1', 'Pep1', 'mRNA2', 'Pep2', 'mRNA3', 'Pep3']['syn_mRNA1', 'syn_mRNA2', 'syn_mRNA3', 'deg_mRNA', 'syn_Pep', 'deg_Pep', 'Pepmax', 'Km', 'deg_Ind', 'Ratio']['state1', 'state2']['dInde = -(Inde/(Inde+Km))*Inde',
'dIndi = (Inde/(Inde+Km))*Inde',
'dInd = -deg_Ind*Ind',
'dmRNA1 = syn_mRNA1*(Ind)*(state1) - (deg_mRNA *mRNA1)',
'dPep1 = (syn_Pep*mRNA1) - (deg_Pep*Pep1)',
'dmRNA2 = syn_mRNA2*Indi*(state2) - (deg_mRNA *mRNA2)',
'dPep2 = (syn_Pep*mRNA2) - (deg_Pep*Pep2)',
'dmRNA3 = (syn_mRNA3*((Pep1+Pep2)/Pepmax))-(deg_mRNA *mRNA3)',
'dPep3 = (syn_Pep*(1-state1*state2*Ratio)*mRNA3)-(deg_Pep*Pep3)']
Description:
This model describes gene expressions for an OR logic gate. The ODEs include the dynamics of the proteins and the corresponding mRNAs driven by two inputs. The inducer for input 2 is assumed to have delay in induction whereas the inducer for input 1 is assumed to be slowly degrading over time. Resource competition is assumed to cause reduction in protein synthesis rate in the presence of both input 1 and 2 (state = 11).,
Definition of states:
          Inde: extracellular inducer concentration
          Indi: intracellular inducer concentration
          Ind: Inducer dynamics
          mRNA1: mRNA of p1
          Pep1: peptide/protein 1
          mRNA2: mRNA of p2
          Pep2: peptide/protein 2
          mRNA3: mRNA of p3
          Pep3: peptide/protein 3,
Definition of parameters:
          synmRNA1: mRNA synthesis rate for protein 1
          synmRNA2: mRNA synthesis rate for protein 2
          synmRNA3: mRNA synthesis rate for protein 3
          deg_mRNA: mRNA degradation rate
          syn_Pep: protein synthesis rate
          deg_Pep: protein degradation rate/dilution rate
          Pepmax: normalization constant
          Km: half-activation for active transport
          deg_Ind: inducer degradation rate
          Ratio: Reduction capacity when both inputs are ON.,
Definition of inputs:
          state1: input1 to control p1 expression
          state2: input2 to control p2 expression,
Reference:
          Title: An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs.
          Authors: Yeoh, Jing Wui, Kai Boon Ivan Ng, Ai Ying Teh, JingYun Zhang, Wai Kit David Chee, and Chueh Loo Poh.
          Journal: ACS synthetic biology 8, no. 7 (2019): 1484-1497.
          DOI: https://doi.org/10.1021/acssynbio.8b00523
05/01/2021Genetic Circuit DiagramDownloadSettings
BMSS, LogicGate, ORgate, InducerDegradationInput2['Ind', 'mRNA1', 'Pep1', 'mRNA2', 'Pep2', 'mRNA3', 'Pep3']['syn_mRNA1', 'syn_mRNA2', 'syn_mRNA3', 'deg_mRNA', 'syn_Pep', 'deg_Pep', 'Pepmax', 'deg_Ind']['state1', 'state2']['dInd = -deg_Ind*Ind',
'dmRNA1 = syn_mRNA1*(state1) - (deg_mRNA *mRNA1)',
'dPep1 = (syn_Pep*mRNA1) - (deg_Pep*Pep1)',
'dmRNA2 = syn_mRNA2*Ind*(state2) - (deg_mRNA *mRNA2)',
'dPep2 = (syn_Pep*mRNA2) - (deg_Pep*Pep2)',
'dmRNA3 = (syn_mRNA3*((Pep1+Pep2)/Pepmax))-(deg_mRNA *mRNA3)',
'dPep3 = (syn_Pep*mRNA3)-(deg_Pep*Pep3)']
Description:
This model describes gene expressions for an OR logic gate. The ODEs include the dynamics of the proteins and the corresponding mRNAs driven by two inputs. The inducer for input 2 is assumed to be slowly degrading over time.,
Definition of states:
          Ind: Inducer dynamics
          mRNA1: mRNA of p1
          Pep1: peptide/protein 1
          mRNA2: mRNA of p2
          Pep2: peptide/protein 2
          mRNA3: mRNA of p3
          Pep3: peptide/protein 3,
Definition of parameters:
          synmRNA1: mRNA synthesis rate for protein 1
          synmRNA2: mRNA synthesis rate for protein 2
          synmRNA3: mRNA synthesis rate for protein 3
          deg_mRNA: mRNA degradation rate
          syn_Pep: protein synthesis rate
          deg_Pep: protein degradation rate/dilution rate
          Pepmax: normalization constant
          deg_Ind: inducer degradation rate,
Definition of inputs:
          state1: input1 to control p1 expression
          state2: input2 to control p2 expression,
Reference:
          Title: An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs.
          Authors: Yeoh, Jing Wui, Kai Boon Ivan Ng, Ai Ying Teh, JingYun Zhang, Wai Kit David Chee, and Chueh Loo Poh.
          Journal: ACS synthetic biology 8, no. 7 (2019): 1484-1497.
          DOI: https://doi.org/10.1021/acssynbio.8b00523
05/01/2021Genetic Circuit DiagramDownloadSettings
BMSS, LogicGate, ORgate, DelayActivation['Inde', 'Indi', 'mRNA1', 'Pep1', 'mRNA2', 'Pep2', 'mRNA3', 'Pep3']['syn_mRNA1', 'syn_mRNA2', 'syn_mRNA3', 'deg_mRNA', 'syn_Pep', 'deg_Pep', 'Pepmax', 'Km']['state1', 'state2']['dInde = -(Inde/(Inde+Km))*Inde',
'dIndi = (Inde/(Inde+Km))*Inde',
'dmRNA1 = syn_mRNA1*(Indi)*(state1) - (deg_mRNA *mRNA1)',
'dPep1 = (syn_Pep*mRNA1) - (deg_Pep*Pep1)',
'dmRNA2 = syn_mRNA2*(state2) - (deg_mRNA *mRNA2)',
'dPep2 = (syn_Pep*mRNA2) - (deg_Pep*Pep2)',
'dmRNA3 = (syn_mRNA3*((Pep1+Pep2)/Pepmax))-(deg_mRNA *mRNA3)',
'dPep3 = (syn_Pep*mRNA3)-(deg_Pep*Pep3)']
Description:
This model describes gene expressions for an OR logic gate. The ODEs include the dynamics of the proteins and the corresponding mRNAs driven by two inputs. The inducer for input 1 is assumed to have delay in induction.,
Definition of states:
          Inde: extracellular inducer concentration
          Indi: intracellular inducer concentration
          mRNA1: mRNA of p1
          Pep1: peptide/protein 1
          mRNA2: mRNA of p2
          Pep2: peptide/protein 2
          mRNA3: mRNA of p3
          Pep3: peptide/protein 3,
Definition of parameters:
          synmRNA1: mRNA synthesis rate for protein 1
          synmRNA2: mRNA synthesis rate for protein 2
          synmRNA3: mRNA synthesis rate for protein 3
          deg_mRNA: mRNA degradation rate
          syn_Pep: protein synthesis rate
          deg_Pep: protein degradation rate/dilution rate
          Pepmax: normalization constant
          Km: half-activation for active transport,
Definition of inputs:
          state1: input1 to control p1 expression
          state2: input2 to control p2 expression,
Reference:
          Title: An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs.
          Authors: Yeoh, Jing Wui, Kai Boon Ivan Ng, Ai Ying Teh, JingYun Zhang, Wai Kit David Chee, and Chueh Loo Poh.
          Journal: ACS synthetic biology 8, no. 7 (2019): 1484-1497.
          DOI: https://doi.org/10.1021/acssynbio.8b00523
05/01/2021Genetic Circuit DiagramDownloadSettings
BMSS, LogicGate, ORgate, DelayActivation, InducerDegradation['Inde', 'Indi', 'Ind', 'mRNA1', 'Pep1', 'mRNA2', 'Pep2', 'mRNA3', 'Pep3']['syn_mRNA1', 'syn_mRNA2', 'syn_mRNA3', 'deg_mRNA', 'syn_Pep', 'deg_Pep', 'Pepmax', 'Km', 'deg_Ind']['state1', 'state2']['dInde = -(Inde/(Inde+Km))*Inde',
'dIndi = (Inde/(Inde+Km))*Inde',
'dInd = -deg_Ind*Ind',
'dmRNA1 = syn_mRNA1*(Indi)*(state1) - (deg_mRNA *mRNA1)',
'dPep1 = (syn_Pep*mRNA1) - (deg_Pep*Pep1)',
'dmRNA2 = syn_mRNA2*Ind*(state2) - (deg_mRNA *mRNA2)',
'dPep2 = (syn_Pep*mRNA2) - (deg_Pep*Pep2)',
'dmRNA3 = (syn_mRNA3*((Pep1+Pep2)/Pepmax))-(deg_mRNA *mRNA3)',
'dPep3 = (syn_Pep*mRNA3)-(deg_Pep*Pep3)']
Description:
This model describes gene expressions for an OR logic gate. The ODEs include the dynamics of the proteins and the corresponding mRNAs driven by two inputs. The inducer for input 1 is assumed to have delay in induction whereas the inducer for input 2 is assumed to be slowly degrading over time.,
Definition of states:
          Inde: extracellular inducer concentration
          Indi: intracellular inducer concentration
          Ind: Inducer dynamics
          mRNA1: mRNA of p1
          Pep1: peptide/protein 1
          mRNA2: mRNA of p2
          Pep2: peptide/protein 2
          mRNA3: mRNA of p3
          Pep3: peptide/protein 3,
Definition of parameters:
          synmRNA1: mRNA synthesis rate for protein 1
          synmRNA2: mRNA synthesis rate for protein 2
          synmRNA3: mRNA synthesis rate for protein 3
          deg_mRNA: mRNA degradation rate
          syn_Pep: protein synthesis rate
          deg_Pep: protein degradation rate/dilution rate
          Pepmax: normalization constant
          Km: half-activation for active transport
          deg_Ind: inducer degradation rate,
Definition of inputs:
          state1: input1 to control p1 expression
          state2: input2 to control p2 expression,
Reference:
          Title: An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs.
          Authors: Yeoh, Jing Wui, Kai Boon Ivan Ng, Ai Ying Teh, JingYun Zhang, Wai Kit David Chee, and Chueh Loo Poh.
          Journal: ACS synthetic biology 8, no. 7 (2019): 1484-1497.
          DOI: https://doi.org/10.1021/acssynbio.8b00523
05/01/2021Genetic Circuit DiagramDownloadSettings
BMSS, LogicGate, ORgate, DelayActivation, InducerDegradation, ResourceCompetition['Inde', 'Indi', 'Ind', 'mRNA1', 'Pep1', 'mRNA2', 'Pep2', 'mRNA3', 'Pep3']['syn_mRNA1', 'syn_mRNA2', 'syn_mRNA3', 'deg_mRNA', 'syn_Pep', 'deg_Pep', 'Pepmax', 'Km', 'deg_Ind', 'Ratio']['state1', 'state2']['dInde = -(Inde/(Inde+Km))*Inde',
'dIndi = (Inde/(Inde+Km))*Inde',
'dInd = -deg_Ind*Ind',
'dmRNA1 = syn_mRNA1*(Indi)*(state1) - (deg_mRNA *mRNA1)',
'dPep1 = (syn_Pep*mRNA1) - (deg_Pep*Pep1)',
'dmRNA2 = syn_mRNA2*(Ind)*(state2) - (deg_mRNA *mRNA2)',
'dPep2 = (syn_Pep*mRNA2) - (deg_Pep*Pep2)',
'dmRNA3 = (syn_mRNA3*((Pep1+Pep2)/Pepmax))-(deg_mRNA *mRNA3)',
'dPep3 = (syn_Pep*(1-state1*state2*Ratio)*mRNA3)-(deg_Pep*Pep3)']
Description:
This model describes gene expressions for an OR logic gate. The ODEs include the dynamics of the proteins and the corresponding mRNAs driven by two inputs. The inducer for input 1 is assumed to have delay in induction whereas the inducer for input 2 is assumed to be slowly degrading over time. Resource competition is assumed to cause reduction in protein synthesis rate in the presence of both input 1 and 2 (state = 11).,
Definition of states:
          Inde: extracellular inducer concentration
          Indi: intracellular inducer concentration
          Ind: Inducer dynamics
          mRNA1: mRNA of p1
          Pep1: peptide/protein 1
          mRNA2: mRNA of p2
          Pep2: peptide/protein 2
          mRNA3: mRNA of p3
          Pep3: peptide/protein 3,
Definition of parameters:
          synmRNA1: mRNA synthesis rate for protein 1
          synmRNA2: mRNA synthesis rate for protein 2
          synmRNA3: mRNA synthesis rate for protein 3
          deg_mRNA: mRNA degradation rate
          syn_Pep: protein synthesis rate
          deg_Pep: protein degradation rate/dilution rate
          Pepmax: normalization constant
          Km: half-activation for active transport
          deg_Ind: inducer degradation rate
          Ratio: Reduction capacity when both inputs are ON.,
Definition of inputs:
          state1: input1 to control p1 expression
          state2: input2 to control p2 expression,
Reference:
          Title: An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs.
          Authors: Yeoh, Jing Wui, Kai Boon Ivan Ng, Ai Ying Teh, JingYun Zhang, Wai Kit David Chee, and Chueh Loo Poh.
          Journal: ACS synthetic biology 8, no. 7 (2019): 1484-1497.
          DOI: https://doi.org/10.1021/acssynbio.8b00523
05/01/2021Genetic Circuit DiagramDownloadSettings
BMSS, LogicGate, ORgate, DelayActivation, DelayActivation['Inde1', 'Indi1', 'Inde2', 'Indi2', 'mRNA1', 'Pep1', 'mRNA2', 'Pep2', 'mRNA3', 'Pep3']['syn_mRNA1', 'syn_mRNA2', 'syn_mRNA3', 'deg_mRNA', 'syn_Pep', 'deg_Pep', 'Pepmax', 'Km1', 'Km2']['state1', 'state2']['dInde1 = -(Inde1/(Inde1+Km1))*Inde1',
'dIndi1 = (Inde1/(Inde1+Km1))*Inde1',
'dInde2 = -(Inde2/(Inde2+Km2))*Inde2',
'dIndi2 = (Inde2/(Inde2+Km2))*Inde2',
'dmRNA1 = syn_mRNA1*(Indi1)*(state1) - (deg_mRNA *mRNA1)',
'dPep1 = (syn_Pep*mRNA1) - (deg_Pep*Pep1)',
'dmRNA2 = syn_mRNA2*(Indi2)*(state2) - (deg_mRNA *mRNA2)',
'dPep2 = (syn_Pep*mRNA2) - (deg_Pep*Pep2)',
'dmRNA3 = (syn_mRNA3*((Pep1+Pep2)/Pepmax))-(deg_mRNA *mRNA3)',
'dPep3 = (syn_Pep*mRNA3)-(deg_Pep*Pep3)']
Description:
This model describes gene expressions for an OR logic gate. The ODEs include the dynamics of the proteins and the corresponding mRNAs driven by two inputs. The inducer for both inputs are assumed to have delay in induction.,
Definition of states:
          Inde1: extracellular inducer concentration
          Indi1: intracellular inducer concentration
          Inde2: extracellular inducer concentration
          Indi2: intracellular inducer concentration
          mRNA1: mRNA of p1
          Pep1: peptide/protein 1
          mRNA2: mRNA of p2
          Pep2: peptide/protein 2
          mRNA3: mRNA of p3
          Pep3: peptide/protein 3,
Definition of parameters:
          synmRNA1: mRNA synthesis rate for protein 1
          synmRNA2: mRNA synthesis rate for protein 2
          synmRNA3: mRNA synthesis rate for protein 3
          deg_mRNA: mRNA degradation rate
          syn_Pep: protein synthesis rate
          deg_Pep: protein degradation rate/dilution rate
          Pepmax: normalization constant
          Km1: half-activation for active transport for inducer 1
          Km2: half-activation for active transport for inducer 2,
Definition of inputs:
          state1: input1 to control p1 expression
          state2: input2 to control p2 expression,
Reference:
          Title: An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs.
          Authors: Yeoh, Jing Wui, Kai Boon Ivan Ng, Ai Ying Teh, JingYun Zhang, Wai Kit David Chee, and Chueh Loo Poh.
          Journal: ACS synthetic biology 8, no. 7 (2019): 1484-1497.
          DOI: https://doi.org/10.1021/acssynbio.8b00523
05/01/2021Genetic Circuit DiagramDownloadSettings
BMSS, LogicGate, ORgate, DelayActivation, DelayActivation, ResourceCompetition['Inde1', 'Indi1', 'Inde2', 'Indi2', 'mRNA1', 'Pep1', 'mRNA2', 'Pep2', 'mRNA3', 'Pep3']['syn_mRNA1', 'syn_mRNA2', 'syn_mRNA3', 'deg_mRNA', 'syn_Pep', 'deg_Pep', 'Pepmax', 'Km1', 'Km2', 'Ratio']['state1', 'state2']['dInde1 = -(Inde1/(Inde1+Km1))*Inde1',
'dIndi1 = (Inde1/(Inde1+Km1))*Inde1',
'dInde2 = -(Inde2/(Inde2+Km2))*Inde2',
'dIndi2 = (Inde2/(Inde2+Km2))*Inde2',
'dmRNA1 = syn_mRNA1*(Indi1)*(state1) - (deg_mRNA *mRNA1)',
'dPep1 = (syn_Pep*mRNA1) - (deg_Pep*Pep1)',
'dmRNA2 = syn_mRNA2*(Indi2)*(state2) - (deg_mRNA *mRNA2)',
'dPep2 = (syn_Pep*mRNA2) - (deg_Pep*Pep2)',
'dmRNA3 = (syn_mRNA3*((Pep1+Pep2)/Pepmax))-(deg_mRNA *mRNA3)',
'dPep3 = (syn_Pep*(1-state1*state2*Ratio)*mRNA3)-(deg_Pep*Pep3)']
Description:
This model describes gene expressions for an OR logic gate. The ODEs include the dynamics of the proteins and the corresponding mRNAs driven by two inputs. The inducer for both inputs are assumed to have delay in induction. Resource competition is assumed to cause reduction in protein synthesis rate in the presence of both input 1 and 2 (state = 11).,
Definition of states:
          Inde1: extracellular inducer concentration
          Indi1: intracellular inducer concentration
          Inde2: extracellular inducer concentration
          Indi2: intracellular inducer concentration
          mRNA1: mRNA of p1
          Pep1: peptide/protein 1
          mRNA2: mRNA of p2
          Pep2: peptide/protein 2
          mRNA3: mRNA of p3
          Pep3: peptide/protein 3,
Definition of parameters:
          synmRNA1: mRNA synthesis rate for protein 1
          synmRNA2: mRNA synthesis rate for protein 2
          synmRNA3: mRNA synthesis rate for protein 3
          deg_mRNA: mRNA degradation rate
          syn_Pep: protein synthesis rate
          deg_Pep: protein degradation rate/dilution rate
          Pepmax: normalization constant
          Km1: half-activation for active transport for inducer 1
          Km2: half-activation for active transport for inducer 2
          Ratio: Reduction capacity when both inputs are ON.,
Definition of inputs:
          state1: input1 to control p1 expression
          state2: input2 to control p2 expression,
Reference:
          Title: An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs.
          Authors: Yeoh, Jing Wui, Kai Boon Ivan Ng, Ai Ying Teh, JingYun Zhang, Wai Kit David Chee, and Chueh Loo Poh.
          Journal: ACS synthetic biology 8, no. 7 (2019): 1484-1497.
          DOI: https://doi.org/10.1021/acssynbio.8b00523
05/01/2021Genetic Circuit DiagramDownloadSettings
BMSS, LogicGate, ORgate, DelayActivationInput2['Inde', 'Indi', 'mRNA1', 'Pep1', 'mRNA2', 'Pep2', 'mRNA3', 'Pep3']['syn_mRNA1', 'syn_mRNA2', 'syn_mRNA3', 'deg_mRNA', 'syn_Pep', 'deg_Pep', 'Pepmax', 'Km']['state1', 'state2']['dInde = -(Inde/(Inde+Km))*Inde',
'dIndi = (Inde/(Inde+Km))*Inde',
'dmRNA1 = syn_mRNA1*(state1) - (deg_mRNA *mRNA1)',
'dPep1 = (syn_Pep*mRNA1) - (deg_Pep*Pep1)',
'dmRNA2 = syn_mRNA2*Indi*(state2) - (deg_mRNA *mRNA2)',
'dPep2 = (syn_Pep*mRNA2) - (deg_Pep*Pep2)',
'dmRNA3 = (syn_mRNA3*((Pep1+Pep2)/Pepmax))-(deg_mRNA *mRNA3)',
'dPep3 = (syn_Pep*mRNA3)-(deg_Pep*Pep3)']
Description:
This model describes gene expressions for an OR logic gate. The ODEs include the dynamics of the proteins and the corresponding mRNAs driven by two inputs. The inducer for input 2 is assumed to have delay in induction.,
Definition of states:
          Inde: extracellular inducer concentration
          Indi: intracellular inducer concentration
          mRNA1: mRNA of p1
          Pep1: peptide/protein 1
          mRNA2: mRNA of p2
          Pep2: peptide/protein 2
          mRNA3: mRNA of p3
          Pep3: peptide/protein 3,
Definition of parameters:
          synmRNA1: mRNA synthesis rate for protein 1
          synmRNA2: mRNA synthesis rate for protein 2
          synmRNA3: mRNA synthesis rate for protein 3
          deg_mRNA: mRNA degradation rate
          syn_Pep: protein synthesis rate
          deg_Pep: protein degradation rate/dilution rate
          Pepmax: normalization constant
          Km: half-activation for active transport,
Definition of inputs:
          state1: input1 to control p1 expression
          state2: input2 to control p2 expression,
Reference:
          Title: An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs.
          Authors: Yeoh, Jing Wui, Kai Boon Ivan Ng, Ai Ying Teh, JingYun Zhang, Wai Kit David Chee, and Chueh Loo Poh.
          Journal: ACS synthetic biology 8, no. 7 (2019): 1484-1497.
          DOI: https://doi.org/10.1021/acssynbio.8b00523
05/01/2021Genetic Circuit DiagramDownloadSettings
BMSS, GrowthModel, Verhulst, LogisticModel['OD']['r', 'N_asymp'][]['dOD = (r) * (OD) * (1 - (OD / N_asymp))']Description:
This is the most commonly used phenomenological model to describe the growth rate of cells. The model captures the population dynamics of growth in a closed habitat constrained by the maximum carrying capacity of the habitat which corresponds to the stationary phase. This equation assumed that a momentary or instant growth rate is proportional to its momentary size and the momentary fraction of the remaining resources.,
Definition of states:
          OD: optical density of the bacterial cells,
Definition of parameters:
          r: rate constant which depends on ambient factors.
          N_asymp: carrying capacity of the habitat/asymptotic growth level,
Definition of inputs:
          [],
Reference:
          Title: Microbial growth curves: what the models tell us and what they cannot.
          Authors: Peleg, Micha, and Maria G. Corradini
          Journal: Critical reviews in food science and nutrition 51, no. 10 (2011): 917-945.
          DOI: https://doi.org/10.1080/10408398.2011.570463
05/01/2021Genetic Circuit DiagramDownloadSettings
BMSS, GrowthModel, GeneralizedVerhulst, LogisticModel['OD']['r', 'N_asymp', 'alpha', 'beta'][]['dOD = (r) * ((OD) ** alpha) * ((1 - (OD / N_asymp)) ** (beta))']Description:
This is the generalized version of the logistic model to describe the growth rate of cells with added power terms. The model captures the population dynamics of growth in a closed habitat constrained by the maximum carrying capacity of the habitat which corresponds to the stationary phase. This model assumed that the momentary growth rate is not exactly proportional to the momentary cell number or density and the carrying capacity of the habitat.,
Definition of states:
          OD: optical density of the bacterial cells,
Definition of parameters:
          r: rate constant which depends on ambient factors.
          N_asymp: carrying capacity of the habitat/asymptotic growth level
          alpha: coefficient that depends on temperature or other ambient factors
          beta: coefficient that depends on temperature or other ambient factors,
Definition of inputs:
          [],
Reference:
          Title: Microbial growth curves: what the models tell us and what they cannot.
          Authors: Peleg, Micha, and Maria G. Corradini
          Journal: Critical reviews in food science and nutrition 51, no. 10 (2011): 917-945.
          DOI: https://doi.org/10.1080/10408398.2011.570463
05/01/2021Genetic Circuit DiagramDownloadSettings
BMSS, GrowthModel, LogisticModel, LongLagTime['OD']['r', 'N_asymp', 't_lag', 'a']['t']['dOD = (r * OD * (1 - (OD / N_asymp))) / (1 + (2.7183**(a * (t_lag - t))))']Description:
This is a modified version of the logistic model to describe the growth rate of cells with an added term to capture the long-lag time during the initial growth phase. Similarly to the logistic model, the growth profile is constrained by the carrying capacity of the habitat.,
Definition of states:
          OD: optical density of the bacterial cells,
Definition of parameters:
          r: rate constant which depends on ambient factors.
          N_asymp: carrying capacity of the habitat/asymptotic growth level
          t_lag: lag time
          a: an arbitrary large number,
Definition of inputs:
          t: time,
Reference:
          Title: Microbial growth curves: what the models tell us and what they cannot.
          Authors: Peleg, Micha, and Maria G. Corradini
          Journal: Critical reviews in food science and nutrition 51, no. 10 (2011): 917-945.
          DOI: https://doi.org/10.1080/10408398.2011.570463
05/01/2021Genetic Circuit DiagramDownloadSettings
BMSS, GrowthModel, LogisticModel, VerhulstDeviation['OD']['r', 'N_max', 'N_mini', 'n'][]['dOD = (r) * (OD) * (1 - (OD / N_max)) * ((1 - (N_mini / OD)) ** (n))']Description:
This is a deviation of the logistic model to describe the growth rate of cells with an added term to better capture the transition region between the adjustment regime and exponential growth phase. Similarly to the logistic model, the growth profile is constrained by the carrying capacity of the habitat.,
Definition of states:
          OD: optical density of the bacterial cells,
Definition of parameters:
          r: rate constant which depends on ambient factors.
          N_max: carrying capacity of the habitat/asymptotic growth level
          N_mini: the instantaneuous population when time = 0
          n: temperature and condition-dependent coefficient,
Definition of inputs:
          [],
Reference:
          Title: Microbial growth curves: what the models tell us and what they cannot.
          Authors: Peleg, Micha, and Maria G. Corradini
          Journal: Critical reviews in food science and nutrition 51, no. 10 (2011): 917-945.
          DOI: https://doi.org/10.1080/10408398.2011.570463
05/01/2021Genetic Circuit DiagramDownloadSettings
BMSS, GrowthModel, LogisticModel, BaranyiRobertsModel, ShortLagTime['OD']['mu_max', 'N_max', 'm', 'q0']['t']['dOD = ((q0 * (2.7183**(mu_max * t))) / (1 + (q0 * (2.7183**(mu_max * t))))) * mu_max * OD * (1 - ((OD / N_max) ** m))']Description:
The Baranyi-Roberts Model is a popular logistic model to describe the growth rate of cells which can be better used to capture short lag time or no lag time. Similarly to the logistic model, the growth profile is constrained by the carrying capacity of the habitat.,
Definition of states:
          OD: optical density of the bacterial cells,
Definition of parameters:
          mu_max: maximum specific growth rate
          N_max: maximum cell density or carrying capacity of the habitat/asymptotic growth level
          m: deceleration parameter
          q0: constant for the physiological state of the initial population,
Definition of inputs:
          t: time,
Reference:
          Title: Microbial growth curves: what the models tell us and what they cannot.
          Authors: Peleg, Micha, and Maria G. Corradini
          Journal: Critical reviews in food science and nutrition 51, no. 10 (2011): 917-945.
          DOI: https://doi.org/10.1080/10408398.2011.570463
05/01/2021Genetic Circuit DiagramDownloadSettings
BMSS, GrowthModel, MortalityPhase['OD']['N0', 'm1', 'm2', 'tc1', 'tc2']['t']['a = 1 / (tc1 ** m1)',
'b = 1 / (tc2 ** m2)',
'',
'dOD = N0 * (a * m1 * (t ** (m1-1)) - b * m2 * (t ** (m2-1))) * (2.7183**(a * (t ** m1) - b * (t ** m2))) ']
Description:
This model is to capture the growth profile with mortality phase. A crowded habitat depleted of resources and polluted by discarded metabolites could not support a large population indefinitely, thus the population may decline at some point instead of reaching stationary phase.,
Definition of states:
          OD: optical density of the bacterial cells,
Definition of parameters:
          N0: initial number or cell density
          m1: steepness of the growth phase
          m2: steepness of the mortality phase
          tc1: the characteristic time of the exponential growth had it been unimpeded
          tc2: the characteristic time of the mortality stage,
Definition of inputs:
          t: time,
Reference:
          Title: Microbial growth curves: what the models tell us and what they cannot.
          Authors: Peleg, Micha, and Maria G. Corradini
          Journal: Critical reviews in food science and nutrition 51, no. 10 (2011): 917-945.
          DOI: https://doi.org/10.1080/10408398.2011.570463
05/01/2021Genetic Circuit DiagramDownloadSettings