ChenXF2008_CICR
Ontology highlight
ABSTRACT:
SUBMITTER: 
Harish Dharuri
PROVIDER: BIOMD0000000202 | BioModels | 2008-11-24
REPOSITORIES: BioModels
Publications
Dynamic simulation of the effect of calcium-release activated calcium channel on cytoplasmic Ca2+ oscillation.
Chen Xiao-fang XF Li Cong-xin CX Wang Peng-ye PY Li Ming M Wang Wei-chi WC
Biophysical chemistry 20080506 2-3
A mathematical model is proposed to illustrate the activation of STIM1 (stromal interaction molecule 1) protein, the assembly and activation of calcium-release activated calcium (CRAC) channels in T cells. In combination with De Young-Keizer-Li-Rinzel model, we successfully reproduce a sustained Ca(2+) oscillation in cytoplasm. Our results reveal that Ca(2+) oscillation dynamics in cytoplasm can be significantly affected by the way how the Orai1 CRAC channel are assembled and activated. A low su ...[more]
Similar Datasets
Project description:The model reproduces the time profile of species depicted in Figure 12a and 12 b. The authors communicated to the curator that there is a typo in the paper, the values of kd1 and kd2 are reversed. Model successfully reproduced using MathSBML.
2008-08-12 | BIOMD0000000181 | BioModels
Project description:Model reproduces the various plots in the publication for "Control" concentrations. Model successfully tested on MathSBML.
2008-11-27 | BIOMD0000000205 | BioModels
Project description:NCBS Curation Comments
This model shows the control mechanism of Jak-Stat pathway, here SOCS1 (Suppressor of cytokine signaling-I) was identified as the negative regulator of Jak and STAT signal transduction pathway. Note: There are a few ambiguities in the paper like initial concentration of IFN and some reactions were missing in the paper that were employed for obtaining the results. The graphs are almost similar to the graphs as shown in the paper but still some ambiguities regarding the concentration are there. Thanks to Dr Satoshi Yamada for clarifying some of those ambiguities and providing the values used in simulations.
Biomodels Curation Comments
The model reproduces Fig 2 (A,C,E,G,I,K,M) of the paper. The set of equations present in the paper are inadequate to reproduce the figures mentioned . The model appears to have been fine tuned after correspondence between the curators at NCBS and the authors. There is however a slight discrepancy between the simulation results and the plots in the paper. The model was tested on MathSBML.
This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2006 The BioModels Team.
For more information see the terms of use
.
2007-03-07 | BIOMD0000000093 | BioModels
Project description:The model reproduces the time profiles of Calcium in the spine and dendrites as depicted in Fig 8 and Fig 9 of the paper for CF activation.
The model was reproduced using MathSBML.
Please note that the units of volume species is molecules/micrometer cubed as against the units of microMolar given in the paper. To convert the units to microMolar multiply the species concentration by the conversion factor 1/602.
This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2010 The BioModels Team.
For more information see the terms of use
.
To cite BioModels Database, please use Le Novère N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J.L., Hucka M. (2006) BioModels Database: A Free, Centralized Database of Curated, Published, Quantitative Kinetic Models of Biochemical and Cellular Systems Nucleic Acids Res., 34: D689-D691.
2008-01-28 | BIOMD0000000162 | BioModels
Project description:SBML
level 2 code originaly generated for the JWS Online project by Jacky Snoep using PySCeS
Run this model online at http://jjj.biochem.sun.ac.za
To cite JWS Online please refer to: Olivier, B.G. and Snoep, J.L. (2004) Web-based
modelling using JWS Online
, Bioinformatics, 20:2143-2144
BioModels Curation
: The model reproduces Fig 3 of the publication. By substituting a value of 1.4 for Tex it is possible to reproduce Fig 3C and 3D(iii), Fig 3A and 3D(i), are obtained by setting Tex=0. Also, note that the tryptophan concentrations have been normalized by 82 micromolar in the figures; the normalized concetrations can be obtained via the parameters To/s/t_norm. The model was successfully tested on MathSBML and Copasi.
This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2010 The BioModels Team.
For more information see the terms of use
.
To cite BioModels Database, please use Le Novère N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J.L., Hucka M. (2006) BioModels Database: A Free, Centralized Database of Curated, Published, Quantitative Kinetic Models of Biochemical and Cellular Systems Nucleic Acids Res., 34: D689-D691.
2010-02-04 | BIOMD0000000062 | BioModels
Project description:A Synthetic Gene-Metabolic Oscillator
Reference:
Fung et al; Nature (2005) 435:118-122
Name of kinetic law
Reaction
Glycolytic flux, V_gly:
nil -> AcCoA;
Flux to TCA cycle/ETOH, V_TCA:
AcCoA -> TCA/EtOH;
HOAc ex/import,reversible, V_out:
HOAc -> HOAc_E
V_Pta:
AcCoA + Pi -> AcP + CoA
reversible, V_Ack:
AcP + ADP -> OAc + ATP
V_Acs:
OAC + ATP -> AcCoA +PPi
Acetic acid-base equillibrium, reversible, V_Ace:
OAC + H -> HOAc
Expression of LacI, R_LacI:
nil -> LacI
Expression of Acs, R_Acs:
nil -> Acs
Expression of Pta, R_Pta:
nil -> Pta
LacI degradation, R_dLacI:
LacI -> nil
Acs degradation, R_dAcs:
Acs -> nil
Pta degradation, R_dPta:
Pta -> nil
For this model the differential equation for V_Ace was changed from:
C*(AcP*H-K_eq*OAC) with C = 100 in the supplemental material
to C*(OAc*H-K_eq*HOAc) with C = 100, as in
Bulter et. al; PNAS(2004),101,2299-2304
, and a value for K_eq of 5*10^-4 after communication with the authors.
translated to SBML by:
Lukas Endler(luen at tbi.univie.ac.at), Christoph Flamm (xtof at tbi.univie.ac.at)
Biomodels Curation
The model reproduces 3a of the paper for glycolytic flux Vgly = 0.5. The authors have agreed that the values on Y-axis are marked wrong and hence there is a discrepancy between model simulation results and the figure. Also, note that the values of concentration and time are in dimensionless units. The model was successfully tested on MathSBML and Jarnac.
2006-08-28 | BIOMD0000000067 | BioModels
Project description:The model reproduces the time profiles of Golgi Ras-GTP and plasma membrane Ras-GTP, subjected to a palmitoylation rate of 0.00015849 second inverse. This is depicted in Fig 5a and 5b for various palmitolylation rates, however the value used in this model is not present in the figure in the paper but corresponds to Fig S2 of the supplement. Model successfully reproduced using MathSBML. Please note that the units of volumetric species in this model are molecules/micrometer cubed, to convert this to microMolar as given in the paper, multiply the simulation result by 1/602.
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.
2008-01-29 | BIOMD0000000161 | BioModels
Project description:This a model from the article:
Mathematical model predicts a critical role for osteoclast autocrine regulation in the control of bone remodeling.
Komarova SV, Smith RJ, Dixon SJ, Sims SM, Wahl LM Bone2003 Aug;33(2):206-15 14499354,
Abstract:
Bone remodeling occurs asynchronously at multiple sites in the adult skeleton and involves resorption by osteoclasts, followed by formation of new bone by osteoblasts. Disruptions in bone remodeling contribute to the pathogenesis of disorderssuch as osteoporosis, osteoarthritis, and Paget's disease. Interactions among cells of osteoblast and osteoclast lineages are critical in the regulation of bone remodeling. We constructed a mathematical model of autocrine and paracrine interactions among osteoblasts and osteoclasts that allowed us to calculate cell population dynamics and changes in bone mass at a discrete site of bone remodeling. Themodel predicted different modes of dynamic behavior: a single remodeling cycle in response to an external stimulus, a series of internally regulated cycles of bone remodeling, or unstable behavior similar to pathological bone remodeling in Paget's disease. Parametric analysis demonstrated that the mode of dynamic behaviorin the system depends strongly on the regulation of osteoclasts by autocrine factors, such as transforming growth factor beta. Moreover, simulations demonstratedthat nonlinear dynamics of the system may explain the differing effects of immunosuppressants on bone remodeling in vitro and in vivo. In conclusion, the mathematical model revealed that interactions among osteoblasts and osteoclasts result in complex, nonlinear system behavior, which cannot be deduced from studies of each cell type alone. The model will be useful in future studies assessing the impact of cytokines, growth factors, and potential therapies on the overall process ofremodeling in normal bone and in pathological conditions such as osteoporosis and Paget's disease.
The model reproduces Fig 2A and Fig 2B of the paper. Note that the Y-axis scale is not right, the osteoblast steadystate is approximatley 212 and not 0 as depicted in the figure. Also, there is atypo in the equation for x2_bar which has been corrected here. Model successfully tested on MathSBML.
This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2009 The BioModels Team.For more information see the terms of use.To cite BioModels Database, please use Le Novère N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J.L., Hucka M. (2006) BioModels Database: A Free, Centralized Database of Curated, Published, Quantitative Kinetic Models of Biochemical and Cellular Systems Nucleic Acids Res., 34: D689-D691.
2007-07-30 | BIOMD0000000148 | BioModels
Project description:Mass spectrometry-based proteomics is increasingly employed in biology and medicine. To generate reliable information from large data sets and ensure comparability of results it is crucial to implement and standardize the quality control of the raw data, the data processing steps and the statistical analyses. The MSPypeline provides a platform for the import of MaxQuant output tables, the generation of quality control reports, the preprocessing of data including normalization and exploratory analyses by statistical inference plots. These standardized steps assess data quality, provide customizable figures and enable the identification of differentially expressed proteins to reach biologically relevant conclusions.
2021-07-22 | PXD025792 | Pride
Project description:This model corresponds to the IkB-NFkB signaling in wild type cells and reproduces the dynamics of the species as depicted in Figure 2 F of the paper. The authors mention that the simulation is carried out in three phases, where the steady state values of the species in one phase are fed to the succeding phase. This model captures the simulation dynamics of two phases and makes use of the event section to introduce the stimulus and thereby transition to the next phase. Accordingly, a few terms have been introduced that make this transition possible, this in no way compromises the original model. Also, the simulation plots are not an exact reproduction of the figures in the paper, they do however match the simulation results that the authors shared with us. Model was successfully tested on MathSBML.
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.
2007-05-16 | BIOMD0000000140 | BioModels