How to add long list of ionic parameters in .par file

Question

Hi , I am trying to use BO ionic model in my simulations with modified parameters from this paper (Weber, F. M., et al. "Adaptation of a minimal four-state cell model for reproducing atrial excitation properties." 2008 Computers in Cardiology. IEEE, 2008.).

Before running simulations I verified the availability of model and nomenclature of parameters using 'bench --imp BO --imp-info'

My issue: I am able to run simulations with the standard set of BO parameters available in CARP but when I try to modify the parameters (23 out of 28 parameters require scaling of the BO model parameters) , I get an error. CARP is not allowing allow me to change or scale beyond 16 parameters. Is there any workaround or syntax to overcome this limit of the max number of ionic channel conductance that can be scaled or prescribed by a value in a .par file ?

Please see the MWE extract from my .par file below for further clarity :

#IONIC SETUP

num_imp_regions = 1

#Myocardium

imp_region[0].im = BO

imp_region[0].im_param = "k_s=1.008,k_so=1.748,k_w_minus=135,tau_fi=0.0678,tau_o1=100,tau_o2=64.87,tau_s1=5.406,tau_s2=52.91,tau_si=6.978,tau_so1=53.54,tau_so2=8.03,tau_v1_minus=65.6,tau_v_pls=0.95,tau_w1_minus=170.8,tau_w2_minus=112.4,tau_w_inf=4.97,tau_w_pls=217,th_o=0.06,th_v_minus=0.172,th_w=0.33,u_s=0.814,u_u=1.02,u_w_minus=0.0744"

Once I run this, I am getting error that openCARP doesn't recognize tau_w_pls which is the 17th ionic parameters in the list. If I delete tau_w_pls , I get error regarding the next (17th) parameter in the list. Seems to be some max limit issue.

I would be thankful for your kind guidance and reply.

Answer 1

Hi Ovais,

It seems that there is a spelling mistake in the variable that you are modifying (tau_w_plus not tau_w_pls). The exact names can be obtained using the following command line in the terminal (see below). 

Let me know if this helps or if you are still getting an error.

Cheers,

Jorge

bench.opt --imp Bueno --imp-info

Ionic model:

------------

Metadata:

        Authors: Alfonso Bueno-Orovio, Elizabeth M. Cherry, Flavio H. Fenton

        Year: 2008

        Title: Minimal model for human ventricular action potentials in tissue

        Journal: Journal of Theoretical Biology, 253.3

        DOI: 10.1016/j.jtbi.2008.03.029

        Comment: Script includes the option to switch via flag between the original model (normalized Vm and Iion scale, 0-1) and a transformed version of the model with physiological Vm and Iion scales based on a resting membrane potential of V_0=-84mV. The transformed model is used by default.

Name: Bueno

        Parameters:

                                     V_0        -84

                                    V_mu        85.7

                                     k_s        2.0994

                                    k_so        2

                               k_w_minus        200

                        modelformulation        0

                                  tau_fi        0.1

                                  tau_o1        470

                                  tau_o2        6

                                  tau_s1        2.7342

                                  tau_s2        2

                                  tau_si        2.9013

                                 tau_so1        40

                                 tau_so2        1.2

                            tau_v1_minus        75

                            tau_v2_minus        10

                              tau_v_plus        1.4506

                            tau_w1_minus        6

                            tau_w2_minus        140

                               tau_w_inf        0.0273

                              tau_w_plus        280

                                 theta_o        0.006

                                 theta_v        0.3

                           theta_v_minus        0.2

                                 theta_w        0.13

                                     u_o        0

                                     u_s        0.9087

                                    u_so        0.65

                                     u_u        1.56

                               u_w_minus        0.016

                              w_inf_star        0.78

                                   flags        TRANSFORM|ORIGINAL

        State variables:

                                   s

                                   v

                                   w

Comments

Hi Jorge , thanks for your reply. The cell model name is BO. While making the .par file I check exact cellular nomenclature using bench --imp BO --imp-info , please find screenshot below:Above in view, the spellings of the parameters of ionic model: BO seems correct. I check the model and simulation ran perfect when I don't attempt to modify parameter , however when I try to scale the parameter beyond a fix number (16 parameters) , only then I start to notice this error.

Also one important addition, I am using CARP not openCARP. I use bench.pt --imp BO --imp-info 

Thanks again for your reply.

---

Hi Ovais,

If the spelling is correct I would suggest to ask the team that provided you that executable so they can look into this specific issue that is not related to openCARP.

Cheers,

Jorge