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BIOMD0000000584 - Mandlik2015 - Tristable genetic circuit of Leishmania

 

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Reference Publication
Publication ID: 26264745
Mandlik V, Gurav M, Singh S.
Regulatory dynamics of network architecture and function in Tristable genetic circuit of Leishmania: A Mathematical biology Approach.
J. Biomol. Struct. Dyn. 2015 Aug;
a National Centre for Cell Science , Pune University Campus ,, NCCS Complex, Ganeshkhind, Pune 411007 , India.  [more]
Model
Original Model: BIOMD0000000584.origin
Submitter: Shailza Singh
Submission ID: MODEL1507170000
Submission Date: 17 Jul 2015 18:49:41 UTC
Last Modification Date: 12 Feb 2016 15:21:34 UTC
Creation Date: 26 Oct 2015 12:57:44 UTC
Encoders:  Vijayalakshmi Chelliah
   Shailza Singh
set #1
bqbiol:isVersionOf Gene Ontology sphingolipid metabolic process
set #2
bqbiol:hasTaxon Taxonomy Leishmania
set #3
bqbiol:hasProperty Human Disease Ontology DOID:9065
Notes
Model
Publication ID: 26264745 Submission Date: 17 Jul 2015 18:49:41 UTC Last Modification Date: 12 Feb 2016 15:21:34 UTC Creation Date: 26 Oct 2015 12:57:44 UTC
Mathematical expressions
Reactions
pp1_v1 pp1_v2 pp5_v1 pp5_v2
ia1_bind_forward ia1_bind_reverse pp2_v1 pp2_v2
pp6_v1 pp6_v2 pp3_v1 pp3_v2
pp4_v1 pp4_v2    
Rules
Assignment Rule (variable: rs6) Assignment Rule (variable: rs3) Assignment Rule (variable: rs4) Assignment Rule (variable: rs5)
Assignment Rule (variable: LAMDAR) Assignment Rule (variable: LACI) Assignment Rule (variable: TETR) Assignment Rule (variable: rs1)
Assignment Rule (variable: rs2) Assignment Rule (variable: ope1) Assignment Rule (variable: as1) Assignment Rule (variable: SLS1)
Assignment Rule (variable: SLS4) Assignment Rule (variable: AUR1)    
Physical entities
Compartments Species
DefaultCompartment AUR1 IPTG LACI
LAMDAR SLS1 SLS4
TETR as1 ia1_ActiveTF
ia1_InactiveTF ope1 p1
p2 p3 pAUR1
pSLS1 pSLS4 proAUR1
proLACI proLAMDAR proSLS1
proSLS4 proTETR rs1
rs2 rs3 rs4
rs5 rs6 ter1
ter2 ter3 ter4
ter5 ter6  
Global parameters
tr3_Kd tr3_h tr4_Kd tr4_h
pSLS4_strength tr5_Kd tr5_h tr6_Kd
tr6_h p1_strength p2_strength proLACI_degradation_rate
p3_strength proSLS1_degradation_rate proSLS4_degradation_rate proLAMDAR_degradation_rate
proAUR1_degradation_rate ia1_Kd ia1_repression_Kd ia1_repression_h
pAUR1_strength proTETR_degradation_rate ta1_Kd ta1_h
pp2_translation_rate pp3_translation_rate pp4_translation_rate pp5_translation_rate
pp6_translation_rate tr1_Kd tr1_h pSLS1_strength
tr2_Kd tr2_h    
Reactions (14)
 
 pp1_v1  → [proSLS1];  
 
 pp1_v2 [proSLS1] → ;   {proSLS1}
 
 pp5_v1  → [proLAMDAR];   {LAMDAR} , {LAMDAR}
 
 pp5_v2 [proLAMDAR] → ;   {proLAMDAR}
 
 ia1_bind_forward [IPTG] + [ia1_ActiveTF] → [ia1_InactiveTF];   {IPTG} , {ia1_ActiveTF}
 
 ia1_bind_reverse [ia1_InactiveTF] → [IPTG] + [ia1_ActiveTF];   {ia1_InactiveTF}
 
 pp2_v1  → [proAUR1];   {AUR1} , {AUR1}
 
 pp2_v2 [proAUR1] → ;   {proAUR1}
 
 pp6_v1  → [proTETR];   {TETR} , {TETR}
 
 pp6_v2 [proTETR] → ;   {proTETR}
 
 pp3_v1  → [proSLS4];   {SLS4} , {SLS4}
 
 pp3_v2 [proSLS4] → ;   {proSLS4}
 
 pp4_v1  → [proLACI];   {LACI} , {LACI}
 
 pp4_v2 [proLACI] → ;   {proLACI}
 
Rules (14)
 
 Assignment Rule (name: rs6) rs6 = 1/(1+(proTETR/tr4_Kd)^tr4_h)
 
 Assignment Rule (name: rs3) rs3 = 1/(1+(proLACI/tr6_Kd)^tr6_h)
 
 Assignment Rule (name: rs4) rs4 = 1/(1+(proLAMDAR/tr5_Kd)^tr5_h)
 
 Assignment Rule (name: rs5) rs5 = 1/(1+(proLACI/tr3_Kd)^tr3_h)
 
 Assignment Rule (name: LAMDAR) LAMDAR = p1_strength*rs6
 
 Assignment Rule (name: LACI) LACI = p2_strength*rs4
 
 Assignment Rule (name: TETR) TETR = p3_strength*rs5
 
 Assignment Rule (name: rs1) rs1 = 1/(1+(proSLS1/tr1_Kd)^tr1_h)
 
 Assignment Rule (name: rs2) rs2 = 1/(1+(proAUR1/tr2_Kd)^tr2_h)
 
 Assignment Rule (name: ope1) ope1 = 1/(1+(ia1_ActiveTF/ia1_repression_Kd)^ia1_repression_h)
 
 Assignment Rule (name: as1) as1 = (1+(proSLS4/ta1_Kd)^ta1_h-1)/(1+(proSLS4/ta1_Kd)^ta1_h)
 
 Assignment Rule (name: SLS1) SLS1 = pSLS1_strength*as1*ope1*rs3
 
 Assignment Rule (name: SLS4) SLS4 = pSLS4_strength*rs2
 
 Assignment Rule (name: AUR1) AUR1 = pAUR1_strength*rs1
 
   DefaultCompartment Spatial dimensions: 3.0  Compartment size: 1.0
 
   AUR1
Compartment: DefaultCompartment
Initial concentration: 10.0
 
   IPTG
Compartment: DefaultCompartment
Initial concentration: 10000.0
 
   LACI
Compartment: DefaultCompartment
Initial concentration: 10.0
 
   LAMDAR
Compartment: DefaultCompartment
Initial concentration: 10.0
 
   SLS1
Compartment: DefaultCompartment
Initial concentration: 10.0
 
   SLS4
Compartment: DefaultCompartment
Initial concentration: 10.0
 
   TETR
Compartment: DefaultCompartment
Initial concentration: 10.0
 
   as1
Compartment: DefaultCompartment
Initial concentration: 10.0
 
   ia1_ActiveTF
Compartment: DefaultCompartment
Initial concentration: 100.0
 
   ia1_InactiveTF
Compartment: DefaultCompartment
Initial concentration: 100.0
 
   ope1
Compartment: DefaultCompartment
Initial concentration: 5.0
 
   p1
Compartment: DefaultCompartment
Initial concentration: 10.0
 
   p2
Compartment: DefaultCompartment
Initial concentration: 10.0
 
   p3
Compartment: DefaultCompartment
Initial concentration: 10.0
 
   pAUR1
Compartment: DefaultCompartment
Initial concentration: 10.0
 
   pSLS1
Compartment: DefaultCompartment
Initial concentration: 10.0
 
   pSLS4
Compartment: DefaultCompartment
Initial concentration: 10.0
 
   proAUR1
Compartment: DefaultCompartment
Initial concentration: 0.0
 
   proLACI
Compartment: DefaultCompartment
Initial concentration: 0.0
 
   proLAMDAR
Compartment: DefaultCompartment
Initial concentration: 0.0
 
   proSLS1
Compartment: DefaultCompartment
Initial concentration: 0.0
 
   proSLS4
Compartment: DefaultCompartment
Initial concentration: 0.0
 
   proTETR
Compartment: DefaultCompartment
Initial concentration: 0.0
 
   rs1
Compartment: DefaultCompartment
Initial concentration: 10.0
 
   rs2
Compartment: DefaultCompartment
Initial concentration: 10.0
 
   rs3
Compartment: DefaultCompartment
Initial concentration: 10.0
 
   rs4
Compartment: DefaultCompartment
Initial concentration: 10.0
 
   rs5
Compartment: DefaultCompartment
Initial concentration: 10.0
 
   rs6
Compartment: DefaultCompartment
Initial concentration: 10.0
 
   ter1
Compartment: DefaultCompartment
Initial concentration: 10.0
 
   ter2
Compartment: DefaultCompartment
Initial concentration: 10.0
 
   ter3
Compartment: DefaultCompartment
Initial concentration: 10.0
 
   ter4
Compartment: DefaultCompartment
Initial concentration: 10.0
 
   ter5
Compartment: DefaultCompartment
Initial concentration: 10.0
 
   ter6
Compartment: DefaultCompartment
Initial concentration: 10.0
 
Global Parameters (34)
 
   tr3_Kd
Value: 1.0
Constant
 
   tr3_h
Value: 2.0
Constant
 
   tr4_Kd
Value: 1.0
Constant
 
   tr4_h
Value: 2.0
Constant
 
   pSLS4_strength
Value: 2.57
Constant
 
   tr5_Kd
Value: 1.0
Constant
 
   tr5_h
Value: 2.0
Constant
 
   tr6_Kd
Value: 1.0
Constant
 
   tr6_h
Value: 2.0
Constant
 
   p1_strength
Value: 2.5
Constant
 
   p2_strength
Value: 2.4
Constant
 
   proLACI_degradation_rate
Value: 0.07
Constant
 
   p3_strength
Value: 2.5
Constant
 
   proSLS1_degradation_rate
Value: 0.07
Constant
 
   proSLS4_degradation_rate
Value: 0.04
Constant
 
   proLAMDAR_degradation_rate
Value: 0.0415
Constant
 
   proAUR1_degradation_rate
Value: 0.1
Constant
 
   ia1_Kd
Value: 0.001
Constant
 
   ia1_repression_Kd
Value: 1.0
Constant
 
   ia1_repression_h
Value: 2.0
Constant
 
   pAUR1_strength
Value: 2.014
Constant
 
   proTETR_degradation_rate
Value: 0.08
Constant
 
   ta1_Kd
Value: 1.0
Constant
 
   ta1_h
Value: 2.0
Constant
 
   pp2_translation_rate
Value: 1.0
Constant
 
   pp3_translation_rate
Value: 1.0
Constant
 
   pp4_translation_rate
Value: 1.0
Constant
 
   pp5_translation_rate
Value: 1.0
Constant
 
   pp6_translation_rate
Value: 1.0
Constant
 
   tr1_Kd
Value: 1.0
Constant
 
   tr1_h
Value: 2.0
Constant
 
   pSLS1_strength
Value: 2.5
Constant
 
   tr2_Kd
Value: 1.0
Constant
 
   tr2_h
Value: 2.0
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000584

Curator's comment: (updated: 10 Sep 2015 13:45:52 GMT)

Figure 5 of the reference publication has been reproduced using SBML odeSolver. The plots were generated using Gnuplot.

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