Online model checking approach based parameter estimation to a neuronal fate decision simulation model in Caenorhabditis elegans with hybrid functional Petri net with extension

2011 ◽  
Vol 7 (5) ◽  
pp. 1576 ◽  
Author(s):  
Chen Li ◽  
Masao Nagasaki ◽  
Chuan Hock Koh ◽  
Satoru Miyano
Keyword(s):  
Parameter Estimation ◽  
Caenorhabditis Elegans ◽  
Model Checking ◽  
Simulation Model ◽  
Petri Net ◽  
Hybrid Functional ◽  
Neuronal Fate ◽  
Fate Decision

scholarly journals Automated parameter estimation for biological models using Bayesian statistical model checking

2015 ◽  
Vol 16 (S17) ◽  
Author(s):  
Faraz Hussain ◽  
Christopher J Langmead ◽  
Qi Mi ◽  
Joyeeta Dutta-Moscato ◽  
Yoram Vodovotz ◽  
...  
Keyword(s):  
Parameter Estimation ◽  
Model Checking ◽  
Statistical Model ◽  
Biological Models ◽  
Statistical Model Checking

Model checking workflow net based on Petri net

2006 ◽  
Vol 11 (5) ◽  
pp. 1297-1301 ◽  
Author(s):  
Zhou Conghua ◽  
Chen Zhenyu
Keyword(s):  
Model Checking ◽  
Petri Net ◽  
Workflow Net

scholarly journals PARAMETER ESTIMATION OF MACROSCOPIC TRAFFIC SIMULATION MODEL

2001 ◽  
Vol 18 ◽  
pp. 747-754
Author(s):  
Chumchoke NANTHAWICHIT ◽  
Takashi NAKATSUJI
Keyword(s):  
Parameter Estimation ◽  
Simulation Model ◽  
Traffic Simulation

Multi-scale assimilation of SMAP data: comparison between land surface and land surface-subsurface model

2020 ◽  
Author(s):  
Haojin Zhao ◽  
Roland Baatz ◽  
Carsten Montzka ◽  
Harry Vereecken ◽  
Harrie-Jan Hendricks Franssen
Keyword(s):  
Parameter Estimation ◽  
Soil Moisture ◽  
Data Assimilation ◽  
Simulation Model ◽  
Land Surface ◽  
Cosmic Ray ◽  
Remotely Sensed ◽  
Surface Model ◽  
Systematic Bias

<p>Soil moisture plays an important role in the coupled water and energy cycles of the terrestrial system. However, the characterization of soil moisture at the large spatial scale is far from trivial. To cope with this challenge, the combination of data from different sources (in situ measurements by cosmic ray neutron sensors, remotely sensed soil moisture and simulated soil moisture by models) is pursued. This is done by multiscale data assimilation, to take the different resolutions of the data into account. A large number of studies on the assimilation of remotely sensed soil moisture in land surface models has been published, which show in general only a limited improvement in the characterization of root zone soil moisture, and no improvement in the characterization of evapotranspiration. In this study it was investigated whether an improved modelling of soil moisture content, using a simulation model where the interactions between the land surface, surface water and groundwater are better represented, can contribute to extracting more information from SMAP data. In this study over North-Rhine-Westphalia, the assimilation of remotely sensed soil moisture from SMAP in the coupled land surface-subsurface model TSMP was tested. Results were compared with the assimilation in the stand-alone land surface model CLM. It was also tested whether soil hydraulic parameter estimation in combination with state updating could give additional skill compared to assimilation in CLM stand-alone and without parameter updating. Results showed that modelled soil moisture by TSMP did not show a systematic bias compared to SMAP, whereas CLM was systematically wetter than TSMP. Therefore, no prior bias correction was needed in the data assimilation. The results illustrate how the difference in simulation model and parameter estimation result in significantly different estimated soil moisture contents and evapotranspiration.  </p>

scholarly journals Simulated Cell Division Processes of the Xenopus Cell Cycle Pathway by Genomic Object Net

2004 ◽  
Vol 1 (1) ◽  
pp. 27-37 ◽  
Author(s):  
Mika Matsui ◽  
Sachie Fujita ◽  
Shunichi Suzuki ◽  
Hiroshi Matsuno ◽  
Satoru Miyano
Keyword(s):  
Cell Cycle ◽  
Cell Division ◽  
Notch Signaling ◽  
Signaling Pathway ◽  
Petri Net ◽  
Notch Signaling Pathway ◽  
Hybrid Functional ◽  
Dynamic Cell ◽  
Cell Cycle Pathway ◽  
Cell Division Control

Summary Matsuno et al.[1] modeled and simulated that multicellular patterning by the Drosophila Delta-Notch signaling pathway by using the software “Genomic Object Net” which was developed based on hybrid functional Petri net (HFPN) architecture. In this model, cellular formation is fixed throughout the simulation. This paper constructs an HFPN model of the Xenopus cell cycle pathway, which includes the mechanism for cell division control as well as checkpoint processes. This model simulates dynamic cell division processes of the early Xenopus embryo, including the changes in cell division cycles from synchronous to asynchronous.

Sign in / Sign up

Export Citation Format

Share Document