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substance units: substance
volume units: volume
length unit: length
creator:
  ORG:
    orgname: NTU
  n:
    given: Nazanin
    family: Saeidi
units def: volume
modified:
  W3 CDTF: Thu Jun 06 12:55:21 BST 2013
species: s5
species: s19
created:
  W3 CDTF: Wed Feb 27 13:22:55 GMT 2013
reaction: re3
species: s42
compartment: default
time units: time
curated: true
species: s1
is version of: GO:0009372
reaction: re14
reaction: re2
is: http://identifiers.org/taxonomy/131567
reaction: re8
name: Saeidi2012 - Quorum sensing device that produces GFP
reaction: re5
species: s45
creator:
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    orgname: EMBL-EBI
  n:
    given: Vijayalakshmi
    family: Chelliah
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notes: Saeidi2012 - Quorum sensing device that produces GFP Saeidi et al. (2012) has modelled a quorum sensing device that produces green fluorescent protein (GFP) as reporter in the presence of Acyl Homoserine Lactone (AHL). This model is described in the article: Characterization of a quorum sensing device for synthetic biology design: Experimental and modeling validation Nazanin Saeidi, Mohamed Arshath, Matthew Wook Chang, Chueh Loo Poh Chemical Engineering Science. December 2012. Abstract: Modeling of biological parts is of crucial importance as it enables the in silico study of synthetic biological systems prior to the actual construction of genetic circuits, which can be time consuming and costly. Because standard biological parts are utilized to build the synthetic systems, it is important that each of these standard parts is well characterized and has a corresponding mathematical model that could simulate the characteristics of the part. These models could be used in computer aided design (CAD) tools during the design stage to facilitate the building of the model of biological systems. This paper describes the development of a mathematical model that is able to simulate both the dynamic and static performance of a biological device created using standard parts. We modeled an example quorum sensing device that produces green fluorescent protein (GFP) as reporter in the presence of Acyl Homoserine Lactone (AHL). The parameters of the model were estimated using experimental results. The simulation results show that the model was able to simulate behavior similar to experimental results. Since it is important that these models and the content in the models can be searchable and readable by machines, standard SBML (system biology markup language) format was used to store the models. All parts and reactions are fully annotated to enable easy searching, and the models follow the Minimum Information Requested In the Annotation of Models (MIRIAM) compliance as well as the M…
is described by: j.ces.2012.12.016
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