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[WIP] Costa et al. 2020 model #6

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3c286f2
Add Costa et al. 2020 simulation files
jpgill86 Jun 15, 2020
5aa38e7
Add initial parser support for At type 4
jpgill86 Jun 7, 2020
5a6a0b1
Add initial parser support for Xt type 2
jpgill86 Jun 7, 2020
4364804
Update list of sources for examples
jpgill86 Jun 15, 2020
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60 changes: 60 additions & 0 deletions examples/Costa2020/CPG_Model_01_09_2020/20simsbatch.bch
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>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>> Batch job file: *.bch >>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>


>----------------------->------------------------------->
PARAMETER: > One Parameter >
>----------------------->------------------------------->
CPG_ASW.trt > File containing the param >
>----------------------->------------------------------->
TRT > File type is treatment >
>----------------------->------------------------------->
0 > cinj=0,minj=1,vclmp=2,iclmp=3 >
0 > which inject start from 0 >
2 > start=0, stop=1, magn=2 >
>----------------------->------------------------------->
0 > Manual=0, Auto=1 >
>----------------------->------------------------------->
20 > number of parameter values >
>----------------------->------------------------------->
1.9 > One value >
>----------------------->------------------------------->
1.9 > One value >
>----------------------->------------------------------->
1.9 > One value >
>----------------------->------------------------------->
1.9 > One value >
>----------------------->------------------------------->
1.9 > One value >
>----------------------->------------------------------->
1.9 > One value >
>----------------------->------------------------------->
1.9 > One value >
>----------------------->------------------------------->
1.9 > One value >
>----------------------->------------------------------->
1.9 > One value >
>----------------------->------------------------------->
1.9 > One value >
>----------------------->------------------------------->
1.9 > One value >
>----------------------->------------------------------->
1.9 > One value >
>----------------------->------------------------------->
1.9 > One value >
>----------------------->------------------------------->
1.9 > One value >
>----------------------->------------------------------->
1.9 > One value >
>----------------------->------------------------------->
1.9 > One value >
>----------------------->------------------------------->
1.9 > One value >
>----------------------->------------------------------->
1.9 > One value >
>----------------------->------------------------------->
1.9 > One value >
>----------------------->------------------------------->
1.9 > One value >
>----------------------->------------------------------->
52 changes: 52 additions & 0 deletions examples/Costa2020/CPG_Model_01_09_2020/B20/B20.ion
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>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>> modules name< ION >>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>


>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
Cion: > Concentration of an ion >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

>----------------------->------------------------------------------------------>
> 1 > >
> xxx.xx >Vc< > ------- >
> xxx.xx >K1< > \ >
> xxx.xx >K2< > \ >
> xxx.xx >K3< > dCion CIion - Iu - Id | >
> xxx.xx >Dgain< > ----- = ----------------- | >
> xxx.xx >Dmid< > dt Vc | >
> xxx.xx >p< > | >
> > +-- -+ | >
> > | ------- | | >
> > | \ | | >
> > CIion = K1 x |- > Iion | - K2 | >
> > | / | > (1) >
> > | ------- | | >
> > +-- -+ | >
> > | >
> > Dgain | >
> > Iu = --------------- | >
> > p | >
> > 1+ dmid/Cion | >
> > | >
> > Id = K3 x Cion | >
> > / >
> > / >
> > ------- >
> > >
>----------------------->------------------------------------------------------>
2 > | +- -+ | >
1.0 >K1< > | | ------- | | >
0.2 >K2< > dCion | | \ | | >
> > -----= K1 x |K2 x |- > Iion | -Cion | (2) >
> > dt | | / | | >
> > | | ------- | | >
> > | +- -+ | >
> > +-- --+ >
> > >
>----------------------->------------------------------------------------------>
END


108 changes: 108 additions & 0 deletions examples/Costa2020/CPG_Model_01_09_2020/B20/B20.neu
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>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>> MODELE NAME: neu >>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>



>------------------------------->--------------------------------------->
THRESHOLD: 0.0 > Threshold for transmitter release >
>------------------------------->--------------------------------------->
SPIKDUR: 0.003 > Spike duration. If equal 0 then >
> actual time when presynaptic >
> neuronis above threshold will >
> be measured >
>------------------------------->--------------------------------------->
VMINIT: -60.0 > Initial value of membrane potential. >
>------------------------------->--------------------------------------->
CM: 0.010 > .010 Membrane capacitance >
>------------------------------->--------------------------------------->

>------------------------------->--------------------------------------->
MEM_AREA: > Membrane Area options >
>------------------------------->--------------------------------------->
0 > do not use membrane area >
>------------------------------->--------------------------------------->
> 1 > specify membrane area directly >
> 5.0 >S< > um2 >
>------------------------------->--------------------------------------->
> 2 > sphere >
> 20.0 >D< > um, diameter >
> 1.0 >C< > invagination factor >
>------------------------------->--------------------------------------->
> 3 > cylinder >
> 3.0 >D< > diameter >
> 30.0 >L< > um, length >
> 0 >n< > number of ends closed >
> 1.0 >C< > invagination factor >
>------------------------------->--------------------------------------->
> membrane area is not used >
>------------------------------->--------------------------------------->


>------------------------------->--------------------------------------->
TRNSMTR: > Dynamics of transmitter >
>------------------------------->--------------------------------------->
tr > Name of transmitter >
/cs/B20.tr > File Name >
blue > Color Name >
>------------------------------->--------------------------------------->


>------------------------------->------------------------------->
CONDUCTANCES: > List of Conductances >
>------------------------------->------------------------------->
K_A > Name of conductance >
/B20/B20_K_A.vdg > File Name >
green > Color >
>------------------------------->------------------------------->
leak > Name of conductance >
/B20/B20_leak.vdg > File Name >
green > Color >
>------------------------------->------------------------------->
Na > Name of conductance >
/B20/B20_Na.vdg > File Name >
green > Color >
>------------------------------->------------------------------->
K > Name of conductance >
/B20/B20_K.vdg > File Name >
green > Color >
>------------------------------->------------------------------->
END > >
>------------------------------->------------------------------->

>------------------------------->------------------------------->
LIST_ION: > List of Ion pools >
>------------------------------->------------------------------->
ion > Name of Ion >
/B20/B20.ion > File Name >
blue > Color >
>------------------------------->------------------------------->
END > >
>------------------------------->------------------------------->

>------------------------------->--------------------------------------->
CURRENT_TO_ION: > List of current contributing >
> to ion pools >
>------------------------------->--------------------------------------->
Na > Name of Conductance >
ion > Name of Ion >
blue > Color >
>------------------------------->--------------------------------------->
END > >
>------------------------------->--------------------------------------->


>------------------------------->--------------------------------------->
TRNSMTR_BY_ION: > Regulation of transmitter >
> by ion pools >
>------------------------------->--------------------------------------->
ion > Name of Ion >
/B20/B20_TR.fBR > File Name >
blue > Color >
>------------------------------->--------------------------------------->
END > >
>------------------------------->--------------------------------------->

END
91 changes: 91 additions & 0 deletions examples/Costa2020/CPG_Model_01_09_2020/B20/B20_K.A
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>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>> module's name: A >>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>


>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
A: > Activation function (time constant method) >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

>------------------------------->--------------------------------------->
> > >
> 1 > A = ssA (1) >
> > >
>------------------------------->--------------------------------------->
2 > ssA - A >
-1.0 >IV< > dA/dt= ------------ (2) >
> tA >
>------------------------------->--------------------------------------->

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
ssA: > Steady state value for activation >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

>----------------------->------------------------------------------------------>
1 > 1 >
-25.0 >-25 h< > ssA = -------------------- (1) >
9.0 >9 s< > +- -+ p >
1.0 >1 p< > | (h-V)/s | >
> |1 + e | >
> +- -+ >
> >
>----------------------->------------------------------------------------------>
> 2 > 1 - An >
> 0.0001 >An< > ssA = -------------------- + An >
> 0.0002 >h< > +- -+ p >
> 0.0003 >s< > | (h-V)/s | (2) >
> 0.00004 >p< > |1 + e | >
> > +- -+ >
>----------------------->------------------------------------------------------>


>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
tA: > Time constant for activation >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

>----------------------->------------------------------------------------------>
> > >
> 1 > tA = tx (1)>
> xxxx.xx >tx< > >
>----------------------->------------------------------------------------------>
2 > tx -tn >
0.04 >.04 tx< > tA = -------------------- + tn (2)>
0.004 >.004 tn< > +- -+ p >
-10.0 >-10 h< > | (V-h)/s | >
10.0 >10 s< > |1 + e | >
1.0 >1 p< > +- -+ >
> >
>----------------------->------------------------------------------------------>
> 3 > tx -tn >
> 0.05 >.05 tx< > tA = ----------------------------------- + tn (3)>
> 0.003 >003 tn< > +- -+p1 +- -+p2 >
> -33.0 >-31 h1< > | (V-h1)/s1 | | (V-h2)/s2 | >
> 12.0 >12 s1< > |1+e | |1+e | >
> 1 >1 p1< > +- -+ +- -+ >
> -60.0 >-58 h2< > >
> -11.0 >-11 s2< > >
> 1 >1 p2< > >
>----------------------->------------------------------------------------------>
> > +-- -+ >
> 4 > | 1 - rtn | >
> xxx.xx >tx< > tA = tx | -------------------- + rtn | (4)>
> xxx.xx >rtn< > | +- -+ p | >
> xxx.xx >h< > | | (V-h)/s | | >
> xxx.xx >s< > | |1 + e | | >
> x >p< > | +- -+ | >
> > +-- -+ >
> > >
>----------------------->------------------------------------------------------>
> > +-- --+ >
> 5 > | 1 - rtn | >
> xxx.xx >tx< > tA=tx | ---------------------------------- +rtn | (5)>
> xxx.xx >rtn< > | +- -+p1+- -+p2 | >
> xxx.xx >h1< > | | (V-h1)/s1| | (V-h2)/s2| | >
> xxx.xx >s1< > | |1+e | |1+e | | >
> x >p1< > | +- -+ +- -+ | >
> xxx.xx >h2< > +-- --+ >
> xx.xx >s2< > >
> x >p2< > >
>----------------------->------------------------------------------------------>
55 changes: 55 additions & 0 deletions examples/Costa2020/CPG_Model_01_09_2020/B20/B20_K.vdg
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>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>> modules name: vdg >>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
Ivd: > Current due to a voltage-dependent conductance >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

>------------------------------->--------------------------------------->
> > p >
> 1 > G= g x A x B (1) >
> B20_K.A >A< > >
> B20_K.B >B< > >
> R_VDG.R >R< > >
> XX.0 > g< > >
> X.0 > P< > Ivd = G x (V -E) >
> -XX.0 > E< > >
> > >
>------------------------------->--------------------------------------->
> > p >
> 2 > Ivd= g x m x h (2) >
> model.m >m< > >
> model.h >h< > >
> 0.X >g< > >
> 1 >P< > Ivd = G x (V -E) >
> X >E< > >
> > >
>------------------------------->--------------------------------------->
> p >
3 > G= g x A (3) >
/B20/B20_K.A >A< > >
/R/R_VDG_B20_3.R >R< > >
13.0 >12 g< > >
4 >4 P< > Ivd = G x (V -E) >
-70 >-70 E< > >
> >
>------------------------------->--------------------------------------->
> > p >
> 4 > Ivd= g x m (4) >
> model.m >m< > >
> 0.X >g< > >
> 1 >P< > Ivd = G x (V -E) >
> XX >E< > >
> > >
>------------------------------->--------------------------------------->
> > >
> 5 > Ivd = G x (V -E) (5) >
> 0.X >g< > >
> -XX >E< > >
> > >
>------------------------------->--------------------------------------->

END:
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