These steps will guide you through the creation of a new Electrophysiology model using the model editor, compile the model on a remote server, solve a problem on that server, using the client/server architecture of Continuity and setup an anatomically accurate rabbit ventricular mesh with orthotropic conductivity using your newly created model.
Continuity Client/Server

Install Continuity on the Cluster (follow “Getting started with Electrophysiology on a cluster”).
 Run Continuity from the server as a client only and load the Electrophysiology module.
Model Editor

Add a new model by Fenton and Karma, 1998, Chaos, 8, 2047.
 Go to Electrophysiology – Edit – Ionic Model – Add new model

Name your model as EP_Fenton_Karma_model
 Add the Author’s name and details about the model

Switch tab to Edit equations and setup your EP model as follows:
 CONSTANTS

u_v = 0.04
u_csi = 0.85
tau_si = 30
k = 10
u_c = 0.13
Cm = 1
g_fi_max = 4
tau_w_plus = 870
tau_w_minus = 41
V_0 = 85
V_fi = 15
tau_v_plus = 3.33
tau_v1_minus = 1250
tau_v2_minus = 19.6
tau_r = 33
tau_0 = 12.5
u_v = 0.04
u_csi = 0.85
tau_d = Cm/g_fi_max

 GATING_PARAMETERS

q = HeavisideEq(uu_v)
p = HeavisideEq(uu_c)
tau_v_minus = q*tau_v1_minus + (1q)*tau_v2_minus

 CURRENTS

J_si = – w * (1 + tanh(k*(uu_csi))) / (2*tau_si)
J_so = u*(1p)/tau_0 + p/tau_r
J_fi = v*p*(1u)*(uu_c)/tau_d
I_fi = J_fi*Cm*(V_fi – V_0)
I_si = J_si * Cm * (V_fi – V_0)
I_so = J_so * Cm * (V_fi – V_0)

 STIMULUS

J_stim = stim_amp * HeavisideEq( t – t_start ) * (1 – HeavisideEq( t – t_end))
I_stim = J_stim * Cm * (V_fi – V_0)

 STATE_VARIABLES

du_dt = – (J_fi + J_so + J_si – J_stim)
dv_dt = ((1p) * (1v)/ tau_v_minus) – (p*v/tau_v_plus) (as spatially coupled variable)
dw_dt = ((1p)*(1w)/tau_w_minus) – (p*w/tau_w_plus)

 CONSTANTS
 Set your Initial Values and Set the Parameters properly

You can also find a text file with the model here

Switch to the Compile tab and Save and Compile your model and Submit
Model Setup

Start with Rabbit_model

Load the file, Send, Calculate Mesh, Render lines
 A few things need to be noticed:
 Integration/collocation points are 2 rather than 3

TriCubic Hermite basis function (should be the first basis selected)

TriLinear Lagrange Basis function should be defined too
 Go to View – Edit Dimensions and Apply Marked Recommendations
 Go to View – Set Divisions to maybe 4
 Go to View – Change Renderer and make sure that you are using Open Mesh

Open the Nodes form and verify that:

Fiber Fields are defined: (Mesh > Edit > Material Coordinates > Mat Coord Standard and the Fiber, Transverse and Sheet parameters are setup to the right Fields)

Field 1 contains the stimuli at the desired nodes. To verify this you can render the Field. To set it up click “Change list” and Apply value 15.0 to node list .*stim.* of Field 1 Value

Field 2 has a TriCubic basis function and is set to the value of the resting Voltage of the cell model

 Render Surfaces (that is necessary to solve)
Diffusion Tensor Transformation
 The Conductivity is a diagonal matrix at the fiber angle orientation and is defined as:

(f11) Dfiber
0
0
0
f(22) Dtransverse
0
0
0
f(33) Dsheet


To Calculate the conductivity tensor (Electrophysiology > Edit > Conductivity Model > Standard Conductivity) and setup the values for f11, f22 and f33 using either a constant value or a field and Submit (If you want to define a higher conductivity for the endocardial nodes, simply define it on a field by clicking “Change list” in the Nodes form and Apply value for all nodes list and then Apply a higher value to node list containing .*endo.* of Field 3 Value. You should setup f22 on Fields 4 and f33 on Field 5 respectively for an orthotropic conduction).
 Recalculate mesh
 Setup Ionic Model

Choose Your Model
 u = Field 2
 Stim_Amp = Field 1


Send

Initialize

Calculate Constraints (Fix out of plane…)

Reset > Save,reset, and reload

Recalculate Mesh

Initialize

Electrophysiology > Solve > Integration Setup the Duration of your stimulus (at least 300ms recommended for this simulation), select the name of your Output file. Go to > Output and increase the number of display solutions to at least 20. Calculate

Retrieve your solution and Render Solution (make sure to use 85.0 and 15.0 for Max and Min value)
Potential Gotchas?
 Must calculate mesh after changing basis functions of fields
 Maybe memory error with too many frames?
 The solution was written at the server and it needs to be retrieved by the client
 Rendering frames is somewhat slow