Chen2000_CellCycle
This a model from the article:
Kinetic analysis of a molecular model of the budding yeast cell cycle.
Chen KC, Csikasz-Nagy A, Gyorffy B, Val J, Novak B, Tyson JJ. Mol Biol Cell
2000 Jan;11(1):369-91 10637314
,
Abstract:
The molecular machinery of cell cycle control is known in more detail for
budding yeast, Saccharomyces cerevisiae, than for any other eukaryotic organism.
In recent years, many elegant experiments on budding yeast have dissected the
roles of cyclin molecules (Cln1-3 and Clb1-6) in coordinating the events of DNA
synthesis, bud emergence, spindle formation, nuclear division, and cell
separation. These experimental clues suggest a mechanism for the principal
molecular interactions controlling cyclin synthesis and degradation. Using
standard techniques of biochemical kinetics, we convert the mechanism into a set
of differential equations, which describe the time courses of three major
classes of cyclin-dependent kinase activities. Model in hand, we examine the
molecular events controlling "Start" (the commitment step to a new round of
chromosome replication, bud formation, and mitosis) and "Finish" (the transition
from metaphase to anaphase, when sister chromatids are pulled apart and the bud
separates from the mother cell) in wild-type cells and 50 mutants. The model
accounts for many details of the physiology, biochemistry, and genetics of cell
cycle control in budding yeast.
This model was taken from the CellML repository
and automatically converted to SBML.
The original model was:
Chen KC, Csikasz-Nagy A, Gyorffy B, Val J, Novak B, Tyson JJ. (2000) - version=1.0
The original CellML model was created by:
Catherine Lloyd
c.lloyd@auckland.ac.nz
The University of Auckland
This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team.
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In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not..
To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
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Kinetic analysis of a molecular model of the budding yeast cell cycle.
- Chen KC, Csikasz-Nagy A, Gyorffy B, Val J, Novak B, Tyson JJ
- Molecular biology of the cell , 1/ 2000 , Volume 11 , Issue 1 , pages: 369-391 , PubMed ID: 10637314
- Department of Biology, Virginia Polytechnic Institute and State University, Blacksburg Virginia 24061, USA.
- The molecular machinery of cell cycle control is known in more detail for budding yeast, Saccharomyces cerevisiae, than for any other eukaryotic organism. In recent years, many elegant experiments on budding yeast have dissected the roles of cyclin molecules (Cln1-3 and Clb1-6) in coordinating the events of DNA synthesis, bud emergence, spindle formation, nuclear division, and cell separation. These experimental clues suggest a mechanism for the principal molecular interactions controlling cyclin synthesis and degradation. Using standard techniques of biochemical kinetics, we convert the mechanism into a set of differential equations, which describe the time courses of three major classes of cyclin-dependent kinase activities. Model in hand, we examine the molecular events controlling "Start" (the commitment step to a new round of chromosome replication, bud formation, and mitosis) and "Finish" (the transition from metaphase to anaphase, when sister chromatids are pulled apart and the bud separates from the mother cell) in wild-type cells and 50 mutants. The model accounts for many details of the physiology, biochemistry, and genetics of cell cycle control in budding yeast.
Submitter of this revision: Krishna Kumar Tiwari
Modellers: administrator, Camille Laibe, Ashley Xavier, Krishna Kumar Tiwari
Metadata information
BioModels Database BIOMD0000000675
BioModels Database MODEL1006230004
isDescribedBy (3 statements)
hasTaxon (1 statement)
isVersionOf (1 statement)
Connected external resources
SBGN view in Newt Editor
| Name | Description | Size | Actions |
|---|---|---|---|
Model files |
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| BIOMD0000000675.xml | SBML L2V4 representation of Chen2000 - Budding yeast cell cycle | 185.09 KB | Preview | Download |
Additional files |
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| BIOMD0000000675-biopax2.owl | Auto-generated BioPAX (Level 2) | 4.52 KB | Preview | Download |
| BIOMD0000000675-biopax3.owl | Auto-generated BioPAX (Level 3) | 4.61 KB | Preview | Download |
| BIOMD0000000675.m | Auto-generated Octave file | 15.81 KB | Preview | Download |
| BIOMD0000000675.pdf | Auto-generated PDF file | 166.71 KB | Preview | Download |
| BIOMD0000000675.png | Auto-generated Reaction graph (PNG) | 4.27 KB | Preview | Download |
| BIOMD0000000675.sci | Auto-generated Scilab file | 67.00 Bytes | Preview | Download |
| BIOMD0000000675.svg | Auto-generated Reaction graph (SVG) | 845.00 Bytes | Preview | Download |
| BIOMD0000000675.vcml | Auto-generated VCML file | 900.00 Bytes | Preview | Download |
| BIOMD0000000675.xpp | Auto-generated XPP file | 11.56 KB | Preview | Download |
| BIOMD0000000675_urn.xml | Auto-generated SBML file with URNs | 182.54 KB | Preview | Download |
| MODEL1006230004.cps | Curated and annotated COPASI file that reproduces figure 3. | 153.62 KB | Preview | Download |
| MODEL1006230004.sedml | SED-ML file for figure 3 of the reference publication. | 9.82 KB | Preview | Download |
- Model originally submitted by : Camille Laibe
- Submitted: Jun 23, 2010 10:11:50 AM
- Last Modified: Aug 22, 2019 2:17:11 PM
Revisions
-
Version: 5
- Submitted on: Aug 22, 2019 2:17:11 PM
- Submitted by: Krishna Kumar Tiwari
- With comment: Automatically added model identifier BIOMD0000000675
-
Version: 3
- Submitted on: Mar 14, 2018 9:37:33 AM
- Submitted by: administrator
- With comment: Current curated version of Chen2000_CellCycle
-
Version: 2
- Submitted on: Jun 25, 2010 1:06:06 PM
- Submitted by: Camille Laibe
- With comment: Current version of Chen2000_CellCycle
-
Version: 1
- Submitted on: Jun 23, 2010 10:11:50 AM
- Submitted by: Camille Laibe
- With comment: Original import of Chen2000_CellCycle
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revisions as only public revisions are displayed here. Any private revisions
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: Variable used inside SBML models
| Species | Initial Concentration/Amount |
|---|---|
| Clb5 Sic1 S-phase entry cyclin-5 ; Protein SIC1 |
0.0207 mol |
| Mcm1 Pheromone receptor transcription factor |
0.512775724968637 mol |
| Sic1 Protein SIC1 |
0.0234 mol |
| Cln3 G1/S-specific cyclin CLN3 |
0.0019841460485227 mol |
| Cdc20 APC/C activator protein CDC20 |
0.6848 mol |
| Bck2 Protein BCK2 |
0.00178416 mol |
| Clb5 T S-phase entry cyclin-5 |
0.0614 mol |
| Clb2 T G2/mitotic-specific cyclin-2 |
0.2342 mol |
| Clb2 Sic1 Protein SIC1 ; G2/mitotic-specific cyclin-2 |
0.079 mol |
| Clb2 G2/mitotic-specific cyclin-2 |
0.1552 mol |
| Reactions | Rate | Parameters |
|---|---|---|
| Clb5_Sic1 = kas_b5*Clb5*Sic1-Clb5_Sic1*(kdi_b5+Vd_b5+kd1_c1+Vd2_c1/(Jd2_c1+Sic1_T)) | kas_b5*Clb5*Sic1-Clb5_Sic1*(kdi_b5+Vd_b5+kd1_c1+Vd2_c1/(Jd2_c1+Sic1_T)) | Vd_b5 = 0.2712; kd1_c1 = 0.01; kas_b5 = 50.0; Jd2_c1 = 0.05; kdi_b5 = 0.05; Vd2_c1 = 0.0306448922911362 |
| Mcm1 = 2*ka_mcm*Clb2*Ji_mcm/(((ki_mcm+ka_mcm*Clb2*Ji_mcm+ki_mcm*Ja_mcm)-ka_mcm*Clb2)+(((ki_mcm+ka_mcm*Clb2*Ji_mcm+ki_mcm*Ja_mcm)-ka_mcm*Clb2)^2-4*(ki_mcm-ka_mcm*Clb2)*ka_mcm*Clb2*Ji_mcm)^(1/2)) | [] | Ji_mcm = 1.0; ka_mcm = 1.0; Ja_mcm = 1.0; ki_mcm = 0.15 |
| Sic1 = Sic1_T-(Clb2_Sic1+Clb5_Sic1) | [] | [] |
| Cln3 = Cln3_max*Dn3*mass/(Jn3+Dn3*mass) | [] | Jn3 = 6.0; Dn3 = 1.0; mass = 0.6608 |
| Cdc20 = ka_20*(Cdc20_T-Cdc20)-Cdc20*(Vi_20+kd_20) | ka_20*(Cdc20_T-Cdc20)-Cdc20*(Vi_20+kd_20) | kd_20 = 0.08; ka_20 = 1.0; Vi_20 = 0.1 |
| Bck2 = Bck2_0*mass | [] | mass = 0.6608 |
| Clb5_T = mass*(ks_b5+ks_b5_*MBF)-Vd_b5*Clb5_T | mass*(ks_b5+ks_b5_*MBF)-Vd_b5*Clb5_T | ks_b5 = 0.006; ks_b5_ = 0.02; Vd_b5 = 0.2712; mass = 0.6608 |
| Clb2_T = mass*(ks_b2+ks_b2_*Mcm1)-Vd_b2*Clb2_T | mass*(ks_b2+ks_b2_*Mcm1)-Vd_b2*Clb2_T | Vd_b2 = 2.023494; ks_b2 = 0.002; ks_b2_ = 0.05; mass = 0.6608 |
| Clb2_Sic1 = kas_b2*Clb2*Sic1-Clb2_Sic1*(kdi_b2+Vd_b2+kd1_c1+Vd2_c1/(Jd2_c1+Sic1_T)) | kas_b2*Clb2*Sic1-Clb2_Sic1*(kdi_b2+Vd_b2+kd1_c1+Vd2_c1/(Jd2_c1+Sic1_T)) | Vd_b2 = 2.023494; kd1_c1 = 0.01; kas_b2 = 50.0; Jd2_c1 = 0.05; kdi_b2 = 0.05; Vd2_c1 = 0.0306448922911362 |
| Clb2 = Clb2_T-Clb2_Sic1 | [] | [] |
(added: 20 Feb 2018, 09:12:50, updated: 20 Feb 2018, 09:12:50)