Non-executablebiomodels

Goldbeter1991 - Min Mit Oscil

Albert Goldbeter + 2 others

v0.0.1CC0-1.0Sep 2024

Citation: A minimal cascade model for the mitotic oscillator involving cyclin and cdc2 kinase

A minimal model for the mitotic oscillator in early amphibian embryos, representing cyclin-driven activation of cdc2 kinase, cdc2-driven activation of cyclin protease, and delayed negative feedback through cyclin degradation.

molecular cellular

How this model is classified mathematically and dynamically.

Model class: ordinary differential equation model
Formalism: ODE
Determinism: Deterministic
Time dynamics: Continuous
Spatial: Compartmental
Multiscale: No

Organisms, entities and processes this model represents.

Organisms: Amphibia
Infectious agents: Not recorded
Health conditions: Not recorded
Biological processes: mitotic cell cycle post-translational protein modification phosphorylation dephosphorylation proteolysis
Molecular entities: Not recorded
Proteins / genes: Cyclin CDC-2 Kinase Cyclin Protease

The data this model consumes and produces when executed.

Parameters

Name	Default	Unit	Meaning
VM1	3	dimensionless	kinetic parameter
VM3	1	dimensionless	kinetic parameter
Kc	0.5	dimensionless	kinetic parameter
vi	0.025	dimensionless	rate of reaction
kd	0.01	dimensionless	rate of reaction
vd	0.25	dimensionless	rate of reaction
Kd	0.02	dimensionless	kinetic parameter
K1	0.005	dimensionless	kinetic parameter
V2	1.5	dimensionless	rate of reaction
K2	0.005	dimensionless	kinetic parameter

Initial conditions

Name	Value	Unit
Cyclin (C)	0.01	concentration unit
CDC-2 Kinase (M)	0.01	concentration unit
Cyclin Protease (X)	0.01	concentration unit

Outputs

Name	Quantity	Unit	Format
species and parameter time series	concentration	model-defined concentration	CSV
species trajectories plot	concentration	model-defined concentration	PNG

Experiment protocol

Uniform time-course simulation from time 0 to 10 with 1000 steps using an ODE solver (KISAO:0000694).

Timestep: 0.01 second
Duration: 10 second
Observables: CMXV1V3VM1VM3Kccellreaction1reaction2reaction3reaction4reaction5reaction6reaction7

Runtime environment, dependencies, and compute requirements.

Language: MATLAB
Environment: native

The authoritative executable model is SBML in BIOMD0000000003_url.xml. COPASI v4.5 Build 20 was used for integration and simulation; the SED-ML file specifies the reproducible simulation protocol.

Compute requirements

GPU: Not required
Parallelism: single

Dependencies

system: COPASI 4.5 Build 20

Entry points

matlab BIOMD0000000003-matlab.m
Run the generated MATLAB representation of the model
octave BIOMD0000000003-octave.m
Run the generated Octave-compatible representation of the model
scilab BIOMD0000000003.sci
Run the generated Scilab representation of the model

Artifacts stored with this model.

Download all (zip)

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BIOMD0000000003.pdf
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Identifiers and integrity.

Source: BIOMD0000000003 · revision 3
Size: 188 KB
SHA-256
Metadata review: Approved · eb7b6c55-efae-45b9-9369-668c8a4d7346 · Oct 2026

Contacts: Bruce Shapiro · bshapiro@jpl.nasa.gov
maintainer · NASA Jet Propulsion Laboratory
Vijayalakshmi Chelliah · viji@ebi.ac.uk
maintainer · EMBL-EBI
Related: Is
biomodels:BIOMD0000000003
Has taxon
ncbitaxon:8292
External IDs: biomodels:BIOMD0000000003

Model characterization

Biology

Inputs & outputs