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BIOMD0000000037 - Marwan2003 - Genetics, regulatory hierarchy between genes

 

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Reference Publication
Publication ID: 12750324
Marwan W.
Theory of time-resolved somatic complementation and its use to explore the sporulation control network in Physarum polycephalum.
Genetics 2003 May; 164(1): 105-115
Institut für Biologie III, Albert-Ludwigs-Universität, 79104 Freiburg im Breisgau, Germany. marwan@biologie.uni-freiburg.de  [more]
Model
Original Model: BIOMD0000000037.xml.origin
Submitter: Nicolas Le Novère
Submission ID: MODEL6621175859
Submission Date: 13 Sep 2005 14:20:29 UTC
Last Modification Date: 12 Feb 2014 13:06:14 UTC
Creation Date: 07 Jul 2005 16:16:30 UTC
Encoders:  Nicolas Le Novère
set #1
bqbiol:isVersionOf Gene Ontology regulation of sporulation resulting in formation of a cellular spore
Gene Ontology far-red light signaling pathway
bqbiol:occursIn Taxonomy Physarum polycephalum
Notes

To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

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.

Model
Publication ID: 12750324 Submission Date: 13 Sep 2005 14:20:29 UTC Last Modification Date: 12 Feb 2014 13:06:14 UTC Creation Date: 07 Jul 2005 16:16:30 UTC
Mathematical expressions
Reactions
Photoreceptor_activation Photoreceptor_inactivation Transducer_activation Transducer_inactivation
preS_formation S_generation Glucose_sensor_inactivation S_formation
V_formation S_degradation V_degradation Photoreceptor_decay
Physical entities
Compartments Species
compartment Pfr Pr Xi
Xa prepreS preS
Ya S Gluc
Yi V Pi
Reactions (12)
 
 Photoreceptor_activation [Pfr] → [Pr];  
 
 Photoreceptor_inactivation [Pr] → [Pfr];  
 
 Transducer_activation [Xi] → [Xa];   {Pr}
 
 Transducer_inactivation [Xa] → [Xi];  
 
 preS_formation [prepreS] → [preS];   {Xa}
 
 S_generation [preS] → [S];   {Ya}
 
 Glucose_sensor_inactivation [Ya] + [Gluc] → [Yi];  
 
 S_formation  → [S];   {V}
 
 V_formation  → [V];   {S}
 
 S_degradation [S] → ;  
 
 V_degradation [V] → ;  
 
 Photoreceptor_decay [Pr] → [Pi];  
 
   Spatial dimensions: 3.0  Compartment size: 1.0
 
 Pfr
Compartment: compartment
Initial amount: 10.0
 
 Pr
Compartment: compartment
Initial amount: 0.0
 
   Xi
Compartment: compartment
Initial amount: 6.0
 
   Xa
Compartment: compartment
Initial amount: 0.0
 
   prepreS
Compartment: compartment
Initial amount: 200.0
 
   preS
Compartment: compartment
Initial amount: 0.0
 
   Ya
Compartment: compartment
Initial amount: 0.9
 
   S
Compartment: compartment
Initial amount: 0.0
 
 Gluc
Compartment: compartment
Initial amount: 0.0
 
   Yi
Compartment: compartment
Initial amount: 0.0
 
   V
Compartment: compartment
Initial amount: 30.0
 
   Pi
Compartment: compartment
Initial amount: 0.0
 
Photoreceptor_activation (1)
 
   IfrSfrPfr
Value: 0.1
Constant
 
Photoreceptor_inactivation (1)
 
   IrSrPr
Constant
 
Transducer_activation (1)
 
   kia
Value: 0.1
Constant
 
Transducer_inactivation (1)
 
   kai
Value: 0.8
Constant
 
preS_formation (1)
 
   kx
Value: 0.2
Constant
 
S_generation (1)
 
   ky
Value: 1.0
Constant
 
Glucose_sensor_inactivation (1)
 
   kG
Value: 0.1
Constant
 
S_formation (1)
 
   alpha1
Value: 30.0
Constant
 
V_formation (1)
 
   alpha2
Value: 50.0
Constant
 
S_degradation (1)
 
   kd_s
Value: 1.0
Constant
 
V_degradation (1)
 
   kd_v
Value: 1.0
Constant
 
Photoreceptor_decay (1)
 
   kd
Value: 0.1
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000037

Curator's comment: (updated: 15 Dec 2006 15:29:41 GMT)

Figure 5B reproduced in COPASI 4 build 19. Although the peak is a little bit higher, the bistable switch is exact, wether in intensity or dynamics.

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