Options

Global
geneticKnockouts
lengthSec (s) 50000
macromoleculeStateInitialization multinomial
seed
stepSizeSec (s) 1
timeStep (h)
verbosity 1
Processes
CentralMetabolismODE
AbsTol (dimensionless)
RelTol (dimensionless)
Vectorized (dimensionless)
ChromosomeCondensation
seed
stepSizeSec (s) 1
verbosity 1
ChromosomeSegregation
seed
stepSizeSec (s) 1
verbosity 1
Cytokinesis
seed
stepSizeSec (s) 1
verbosity 1
DNADamage
seed
stepSizeSec (s) 1
verbosity 1
DNARepair
seed
stepSizeSec (s) 1
verbosity 1
DNASupercoiling
seed
stepSizeSec (s) 1
verbosity 1
FtsZPolymerization
seed
stepSizeSec (s) 1
verbosity 1
GlobalMetabolismRFBA
fluxBoundsEqualThresh (dimensionless)
lpsolver (dimensionless)
HostInteraction
seed
stepSizeSec (s) 1
verbosity 1
MacromolecularComplexation
seed
stepSizeSec (s) 1
verbosity 1
Metabolism
linearProgrammingOptions {'solverOptions': {'linprog': {'Display': u'off'}, 'lp_solve': {'scaling': 195, 'presolve': 0, 'verbose': 0}, 'qsopt': {}, 'glpk': {'presol': 1, 'scale': 1, 'lpsolver': 1, 'msglev': 0, 'tolbnd': 1e-06}}, 'solver': u'glpk'}
macromoleculeStateInitialization multinomial
realmax (dimensionless) 1000000
seed
stepSizeSec (s) 1
tolerance (fraction) 0.001
verbosity 1
ProteinActivation
seed
stepSizeSec (s) 1
verbosity 1
ProteinDecay
seed
stepSizeSec (s) 1
verbosity 1
ProteinFolding
seed
stepSizeSec (s) 1
verbosity 1
ProteinModification
seed
stepSizeSec (s) 1
verbosity 1
ProteinProcessingI
seed
stepSizeSec (s) 1
verbosity 1
ProteinProcessingII
seed
stepSizeSec (s) 1
verbosity 1
ProteinTranslocation
seed
stepSizeSec (s) 1
verbosity 1
Replication
seed
stepSizeSec (s) 1
verbosity 1
ReplicationInitiation
seed
stepSizeSec (s) 1
verbosity 1
RibosomeAssembly
seed
stepSizeSec (s) 1
verbosity 1
RNADecay
seed
stepSizeSec (s) 1
verbosity 1
RNAModification
seed
stepSizeSec (s) 1
verbosity 1
RNAProcessing
seed
stepSizeSec (s) 1
verbosity 1
TerminalOrganelleAssembly
seed
stepSizeSec (s) 1
verbosity 1
Transcription
seed
stepSizeSec (s) 1
verbosity 1
TranscriptionalRegulation
seed
stepSizeSec (s) 1
verbosity 1
Translation
seed
stepSizeSec (s) 1
verbosity 1
tRNAAminoacylation
seed
stepSizeSec (s) 1
verbosity 1
States
Chromosome
seed
verbosity 1
FtsZRing
seed
verbosity 1
Geometry
seed
verbosity 1
Host
seed
verbosity 1
Mass
seed
verbosity 1
MetabolicReaction
seed
verbosity 1
Metabolite
seed
verbosity 1
Polypeptide
seed
verbosity 1
ProteinComplex
seed
verbosity 1
ProteinMonomer
seed
verbosity 1
Ribosome
seed
verbosity 1
Rna
seed
verbosity 1
RNAPolymerase
seed
verbosity 1
Stimulus
seed
verbosity 1
Time
seed
verbosity 1
Transcript
seed
verbosity 1