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BIOMD0000000484 - Cao2013 - Application of ABSIS method in birth-death process

 

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Reference Publication
Publication ID: 23862966
Cao Y, Liang J.
Adaptively biased sequential importance sampling for rare events in reaction networks with comparison to exact solutions from finite buffer dCME method.
J Chem Phys 2013 Jul; 139(2): 025101
Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois 60607, USA. youfang@uic.edu  [more]
Model
Original Model: Birth and Death model
Submitter: Youfang Cao
Submission ID: MODEL1308080004
Submission Date: 08 Aug 2013 20:27:48 UTC
Last Modification Date: 28 Apr 2014 15:57:32 UTC
Creation Date: 23 Sep 2013 12:03:19 UTC
Encoders:  Nick Juty
   Vijayalakshmi Chelliah
   Youfang Cao
set #1
bqbiol:isVersionOf Gene Ontology regulation of growth
set #2
bqbiol:hasProperty Mathematical Modelling Ontology MAMO_0000046
set #3
bqmodel:isDerivedFrom PubMed 21280690
PubMed 21054005
set #4
bqbiol:hasTaxon Taxonomy cellular organisms
Notes
Model
Publication ID: 23862966 Submission Date: 08 Aug 2013 20:27:48 UTC Last Modification Date: 28 Apr 2014 15:57:32 UTC Creation Date: 23 Sep 2013 12:03:19 UTC
Mathematical expressions
Reactions
re2 re12    
Physical entities
Compartments Species
default S ES  
Global parameters
k1 k2    
Reactions (2)
 
 re2 [ES] → [S];  
 
 re12 [S] → [ES];   {S}
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 S
Compartment: default
Initial amount: 0.0
 
 ES
Compartment: default
Initial amount: 0.0
 
Global Parameters (2)
 
   k1
Value: 1.0
Constant
 
   k2
Value: 0.025
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000484

Curator's comment: (updated: 23 Sep 2013 13:00:18 BST)

The rare event probability estimation using discrete chemical master equation (dCME) is plotted in the paper. The model as such do not reproduce any of the plots in the paper. However, the steady state
concentrations of the model has been checked and is consistent with that of the paper.
The direct solution of dCME in the paper is obtained
using the author's previous method FBS-dCME based on finite buffer state space enumeration. The software package can be downloaded from https://code.google.com/p/fibose-dcme/downloads/list. Or, the dCME can also be directly solved using the online tool on nanoHub:
https://nanohub.org/tools/fbsdcme. This needs registration. The nanoHub tool is still under developing, so far only steady state distribution can be obtained.

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