Registry of Standard Biological Models/Basic Component Models/BioBrick Plasmid

BioBrick Plasmid Architecture

Description: BioBrick plasmid model to define number of plasmid copies in simulations Hypothesis: the number of plasmid copies is an average among a given population of cells. Inputs: none Outputs: nbPlasmidCopies Characteristic parameters: Unit: copy

File:VBB Plasmid.png Plasmid Brick Architecture

CellML structure (CellML 1.1 spec)

• Component: Plasmid
• Units:
  • copy
• Variables:
  • nbCopiesPlasmid (public interface = out / initial value = 300.)
• MathML
  • none

Examples

BioBricks from Registry	CellML file
not applicable	Media:BioBrick_Plasmid_Model.xml
not applicable	other plasmid

CellML Code

CellML Code

<syntax type = 'xml'>

<?xml version="1.0"?>

<model xmlns="http://www.cellml.org/cellml/1.0#"

      xmlns:cmeta="http://www.cellml.org/metadata/1.0#" 
      xml:base="http://openwetware.org/index.php?title=Registry_of_Standard_Biological_Models/Basic_Component_Models/Plasmid/CellML_Code&action=raw"
      cmeta:id="Plasmid"
      name="Plasmid">
 

<component name="promoter-RBS_constitutive">

<variable name="nbGeneCopiesOut" initial_value="1" public_interface="out" units="dimensionless"/>

</component>

</model> </syntax>

Comments

• This component is used to customize a given circuit to a particular plasmid construct in terms of copy number
• This component defines the average number of gene copies per cell due to the number of plasmid copies.