Flis2015 - Plant clock gene circuit (P2011.2.1 PLM_71 ver 2)

Model Identifier

BIOMD0000000598

Short description

 cL_m_degr, param m1, modified to ensure light rate > dark rate. Parameter set from PLM_67v2_LDLLLDs_newFFT_1, with modification to m1 (= old_m1 - m2).

Format

SBML (L2V4)

Related Publication

Defining the robust behaviour of the plant clock gene circuit with absolute RNA timeseries and open infrastructure.
Anna Flis, Aurora Piñas Fernández, Tomasz Zielinski, Virginie Mengin, Ronan Sulpice, Kevin Stratford, Alastair Hume, Alexandra Pokhilko, Megan M Southern, Daniel D Seaton, Harriet G McWatters, Mark Stitt, Karen J Halliday, Andrew J Millar
Open biology , 10/ 2015 , Volume 5 , Issue 10 , pages: 150042 , PubMed ID: 26468131

Contributors

Submitter of the first revision: Andrew J Millar
Submitter of this revision: Lucian Smith
Curator: Lucian Smith
Modeller: Andrew J Millar

Metadata information

isDerivedFrom (1 statement)

BioModels Database BIOMD0000000412

is (2 statements)

BioModels Database BIOMD0000000598
BioModels Database MODEL1510190001

isDescribedBy (1 statement)

PubMed 26468131

hasTaxon (1 statement)

Taxonomy Arabidopsis thaliana

isVersionOf (1 statement)

Gene Ontology regulation of circadian rhythm

hasProperty (1 statement)

Mathematical Modelling Ontology Ordinary differential equation model

Curation status

Curated

Modelling approach(es)

ordinary differential equation model

Connected external resources

SBGN view in Newt Editor

Name	Description	Size	Actions
Model files (1)
BIOMD0000000598_url.xml	SBML L2V4 representation of Flis2015 - Plant clock gene circuit (P2011.2.1 PLM_71 ver 2)	186.86 KB	Preview \| Download
Additional files (13)
BIOMD0000000598-biopax2.owl	Auto-generated BioPAX (Level 2)	51.16 KB	Preview \| Download
BIOMD0000000598-biopax3.owl	Auto-generated BioPAX (Level 3)	80.83 KB	Preview \| Download
BIOMD0000000598-matlab.m	Auto-generated Matlab file.	31.52 KB	Preview \| Download
BIOMD0000000598-octave.m	Auto-generated Octave file.	31.52 KB	Preview \| Download
BIOMD0000000598.m	Auto-generated Octave file	31.52 KB	Preview \| Download
BIOMD0000000598.ode	Auto-generated ODE file for XPP.	27.94 KB	Preview \| Download
BIOMD0000000598.pdf	Auto-generated PDF file	495.26 KB	Preview \| Download
BIOMD0000000598.png	Auto-generated Reaction graph (PNG)	1.36 MB	Preview \| Download
BIOMD0000000598_url.sedml	CRBM auto-generated "template" SED-ML file.	107.74 KB	Preview \| Download
curation_image.png	Reproduced figure(s) from original curation.	47.29 KB	Preview \| Download
curation_notes.txt	Notes from original curation (describes curation_image).	515.00 Bytes	Preview \| Download
manifest.xml	Auto-generated manifest file for OMEX archives.	1.64 KB	Preview \| Download
metadata.rdf	Auto-generated annotation metadata file.	2.15 KB	Preview \| Download

Model originally submitted by : Andrew J Millar
Submitted: Oct 19, 2015 4:14:59 PM
Last Modified: Aug 21, 2024 11:30:49 PM

Revisions

Version: 3
- Submitted on: Aug 21, 2024 11:30:49 PM
- Submitted by: Lucian Smith
- With comment: CRBM-sponsored manual and automated updates.
Version: 2
- Submitted on: Apr 15, 2016 6:00:00 PM
- Submitted by: Andrew J Millar
- With comment: Current version of Flis2015 - Plant clock gene circuit (P2011.2.1 PLM_71 ver 2)
Version: 1
- Submitted on: Oct 19, 2015 4:14:59 PM
- Submitted by: Andrew J Millar
- With comment: Original import of P2011_PLM_67v6

(*) You might be seeing discontinuous revisions as only public revisions are displayed here. Any private revisions of this model will only be shown to the submitter and their collaborators.

Legends
: Variable used inside SBML models

Species	Initial Concentration/Amount
cCOP1c	0.3269 nmol
cCOP1d	0.2566 nmol
cP7 m	0.4016 nmol
cE3	0.1503 nmol
cT m	0.0977 nmol
cP7	0.1167 nmol
cP9	0.0238 nmol
cT	0.0435 nmol
cZG	0.0755 nmol

Reactions	Rate	Parameters
cCOP1c => ; cCOP1c	defm27cCOP1c(1+p15L)/def	m27 = 0.1; p15 = 3.0; L = 0.5
cCOP1d => ; cCOP1d	defm31(1+m33D)cCOP1d/def	D = 0.5; m33 = 13.0; m31 = 0.3
cP7_m => ; cP7_m	defm14cP7_m/def	m14 = 0.58317183194053
cE3 => cE3n; cE3, cE3n	def(p19cE3-p20*cE3n)/def	p20 = 0.1940717319972; p19 = 1.74107843497564
=> cT_m; cEC, cL, cEC, cL	defn2g4/(cEC+g4)*g5^e/(cL^e+g5^e)/def	g4 = 0.00503234997631; n2 = 0.68148116717556; g5 = 0.20247194961847; e = 2.0
cP7 => ; cP7	def(m15+m23D)*cP7/def	m23 = 0.54491969619247; D = 0.5; m15 = 0.7
cP9 => ; cP9	def(m13+m22D)*cP9/def	m13 = 0.32; D = 0.5; m22 = 0.09605427710298
=> cT; cT_m, cT_m	defp4cT_m/def	p4 = 0.51783935402389
cT_m => ; cT_m	defm5cT_m/def	m5 = 0.3
cG + cZTL => cZG; cG, cZG, cZTL	def(p12LcZTLcG-p13DcZG)/def	p12 = 2.43270583452351; D = 0.5; p13 = 0.16471437958494; L = 0.5

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Curator's comment:
(added: 15 Apr 2016, 17:33:50, updated: 15 Apr 2016, 17:33:50)

Figure 9 (solid lines, that is corresponding to this model P2011.2.1 - PLM_71 ver 2) has been reproduced here.The model was simulated and plots were generated using SimBiology version 5.1 (Matlab R2014b) Note: The SBML model has the kinetic laws in the form of FunctionDefinition, which is not recognized in SimBiology. So, I converted the FunctionDefintion to kinetic law using a tool in libSBML and used SimBiology to simulate the model. The kineticLaw version of the model can be downloaded from below link.