" ...Here we present a qualitative analysis of a recent mathematical model of astrocyte calcium responses. We show how the major response types are generated in the model as a result of the underlying bifurcation structure. By varying key channel parameters, mimicking blockers used by experimentalists, we manipulate this underlying bifurcation structure and predict how the distributions of responses can change. We find that store-operated calcium channels, plasma membrane bound channels with little activity during calcium transients, have a surprisingly strong effect, underscoring the importance of considering these channels in both experiments and mathematical settings. ..."
Gregory Handy
Marsa Taheri
This is the readme for the models associated with the paper:
Handy G, Taheri M, White JA, Borisyuk A (2017) Mathematical
investigation of IP3-dependent calcium dynamics in astrocytes.
J Comput Neurosci
These MATLAB and XPP files were contributed by G Handy.
Use example_ca_sim_TH.m to reproduce calcium simulations found in
Fig. 2
Use autoRespTypeDetection_TH.m to generate calcium responses
resulting from multiple (or all 600) underlying IP3 traces, as
well as characterize those calcium and IP3 traces (in terms of,
for example, amplitude, total duration, area under the curves, etc.).
Use ca_bifurcation_xpp.ode with XPPAUT to reproduce the bifurcation
diagrams found J. Computation Neuroscience (submitted)
Supporting_Functions contains all necessary functions to run the
simulations.
Histogram_Figures contains the data base of calcium response types
distributions for a range of parameter values (original figures can be
found in J. Computation Neuroscience (submitted))
Hopefully you have found this code helpful!
--Marsa Taheri and Gregory Handy
Privacy settings
To improve your experience with BioSimulations, we use cookies to store information about your preferences and to track your use of the site. This information does not identify you personally or preserve personal information about you. This allows us to improve the site and gather usage information for funding and development. Because we respect your right to privacy, you can opt-out of this data.
BioSimulations collects limited personal data to credit authors and improve the platform. By using this site, you agree to our terms of service, privacy policy, and use of cookies.
Browse simulation projects
Browse simulator tools
Browse the docs
Re-run Original Simulation
Customize & Re-run Simulation
Project
Download File
Open Modeling and Exchange (OMEX)
autoRespTypeDetection_TH.m
MATLAB
ca_bifurcation_xpp_TH.ode
XPP
ca_bifurcation_xpp_TH.sedml
Simulation Experiment Description Markup Language (SED-ML)
example_ca_sim_TH.m
all_ip3_panel1.fig
MATLAB figure
all_ip3_panel2.fig
all_ip3_panel3.fig
low_ip3_panel1.fig
low_ip3_panel2.fig
low_ip3_panel3.fig
metadata.rdf
OMEX Metadata
README.txt
TEXT
CaRiseAndDecay_TH.m
FourCaResponseTypes_TH.m
GenerateLegend_TH.m
ip_function_TH.m
IP3Dyn_model_TH.m
Official_Params_TH.m
Paper_Ca_ODE_TH.m
PeakLatency_TH.m
PeaksAndTroughs_TH.m
plotCa_TH.m
plotCaAmountVsIP3Amount_TH.m
RunParallelFunc_TH.m
Outputs
JavaScript Object Notation (JSON) in BioSimulators simulator schema
Zip of HDF5 and PDF files
Log
JavaScript Object Notation (JSON) in BioSimulators log schema