Changeset 11996 in project

Timestamp:

09/25/08 09:56:46 (12 years ago)

Author:

Ivan Raikov

Message:

Added some useful shortcuts for tau/inf to alpha/beta conversion.

Location:

release/3/nemo/trunk

Files:

• examples/AKP06/PotIhCa.scm (modified) (5 diffs)
• examples/AKP06/morphology_mechanisms.hoc (modified) (1 diff)
• extensions/nemo-hh.scm (modified) (2 diffs)
• nemo.scm (modified) (1 diff)
• nmodl.scm (modified) (4 diffs)

release/3/nemo/trunk/examples/AKP06/PotIhCa.scm

@@ -116 +116 @@
                         ) ;; end Kv4 current
              
+
              
              (component (type ion-channel) (name Ih)
@@ -141 +142 @@
                                      (h-power   0)
                                      (m-inf     (Ih_inf v))
-                                     (m-tau     (/ temp_adj (Ih_tau v)))
+                                     (m-tau     (/ (Ih_tau v) temp_adj))
                                      ))
                                    
@@ -147 +148 @@
 
                         (component (type pore)
-                                   (const  gbar_Ih  = 0.2)
+                                   (const  gbar_Ih  = 0.0002)
                                    (output gbar_Ih ))
                         
@@ -156 +157 @@
                         ) ;; end Ih current
 
-             (component (type ion-channel) (name CaP)
-                        
-                        (component (type gate)
-                                   
-                                   ;; rate functions
-                                   (defun CaP_inf (v)  
-                                     (let ((cv  19)
-                                           (ck  5.5))
-                                       (/ 1.0 (+ 1.0 (exp (neg (/ (+ v cv) ck)))))))
-                                   
-                                   (defun CaP_tau (v temp_adj)  
-                                     (if (> v -50) 
-                                         (* 1e3 (+ 0.000191 (* 0.00376 (pow (exp (neg (/ (+ v 41.9) 27.8)))  2))))
-                                         (* 1e3 (+ 0.00026367 (* 0.1278 (exp (* 0.10327 v)))))))
-
-                                   (hh-ionic-conductance 
-                                    (CaP  ;; ion name: exported variables will be of the form {ion}_{id}
-                                     (initial-m  (CaP_inf Vrest))
-                                     (m-power    1)
-                                     (h-power    0)
-                                     (m-inf      (CaP_inf v))
-                                     (m-tau      (/ (CaP_tau v) temp_adj))))
-                                   
-                                   )
-
-                        (component (type pore)
-                                   (const gmax_CaP  = 0.01667)
-                                   (gbar_CaP = (* gmax_CaP (ghk v celsius cai cao)))
-                                   (output gbar_CaP ))
-                        
-                        (component (type accumulating-substance) (name ca) )
-                        
-                        
-                        ) ;; end CaP current
+;;           (component (type ion-channel) (name CaP)
+                        
+;;                      (component (type gate)
+                                   
+;;                                 ;; rate functions
+;;                                 (defun CaP_inf (v)  
+;;                                   (let ((cv  19)
+;;                                         (ck  5.5))
+;;                                     (/ 1.0 (+ 1.0 (exp (neg (/ (+ v cv) ck)))))))
+                                   
+;;                                 (defun CaP_tau (v)  
+;;                                   (if (> v -50) 
+;;                                       (* 1e3 (+ 0.000191 (* 0.00376 (pow (exp (neg (/ (+ v 41.9) 27.8)))  2))))
+;;                                       (* 1e3 (+ 0.00026367 (* 0.1278 (exp (* 0.10327 v)))))))
+
+;;                                 (hh-ionic-conductance 
+;;                                  (CaP  ;; ion name: exported variables will be of the form {ion}_{id}
+;;                                   (initial-m  (CaP_inf Vrest))
+;;                                   (m-power    1)
+;;                                   (h-power    0)
+;;                                   (m-inf      (CaP_inf v))
+;;                                   (m-tau      (/ (CaP_tau v) temp_adj))))
+                                   
+;;                                 )
+
+;;                      (component (type pore)
+;;                                 (const gmax_CaP  = 0.01667)
+;;                                 (gbar_CaP = (* gmax_CaP (ghk v celsius cai cao)))
+;;                                 (output gbar_CaP ))
+                        
+;;                      (component (type accumulating-substance) (name ca) )
+                        
+                        
+;;                      ) ;; end CaP current
 
              
@@ -268 +269 @@
              
              
-             )) ;; end model
+             )) ;; end model

release/3/nemo/trunk/examples/AKP06/morphology_mechanisms.hoc

@@ -16 +16 @@
 //insert CaBK
 insert Caint
-//insert CaP
+insert CaP
 //insert Ih
 insert leak
+insert PotIhCa
 
-insert PotIhCa
 soma.ena = 60   // (mV)
 soma.ek = -88   // (mV)
+//soma.eh_Ih = -30
+soma.e_Ih_PotIhCa = -30
 soma.e_leak = -61
 soma.cao = 2   // (mM)
-soma.e_Ih_PotIhCa = -30
-//soma.e_Ih = -30
-
+     
 soma.gmax_Narsg = 0.016     // (mho/cm2)
 soma.gmax_Na = 0.014
+//soma.gbar_Kv1 = 0.011
+soma.gbar_Kv1_PotIhCa = 0.011
+//soma.gbar_Kv4 = 0.0039
+soma.gbar_Kv4_PotIhCa = 0.0039
 soma.gmax_Kbin = 0.0016
+//soma.gkbar_CaBK = 0.014
+soma.gbar_CaBK_PotIhCa = 0.014
+soma.pcabar_CaP = 0.00006
+//soma.gmax_CaP_PotIhCa = 0.06
+//soma.ghbar_Ih = 0.0002
+soma.gbar_Ih_PotIhCa = 0.0002
 soma.gbar_leak = 9e-5
-
-soma.gbar_Kv1_PotIhCa = 0.011
-soma.gbar_Kv4_PotIhCa = 0.0039
-//soma.gmax_Kv4 = 0.0039
-soma.gbar_Ih_PotIhCa  = 0.0002
-//soma.gmax_Ih  = 0.0002
-soma.gmax_CaP_PotIhCa = 0.06
-//soma.gmax_CaP = 0.06
-
-soma.gbar_CaBK_PotIhCa = 0.014
-//soma.gmax_CaBK = 0.014

release/3/nemo/trunk/extensions/nemo-hh.scm

@@ -95 +95 @@
                    (m-inf      (lookup-field 'm-inf alst))
                    (m-tau      (lookup-field 'm-tau alst))
-                   (m-alpha    (or (lookup-field 'm-alpha alst)  `(/ ,m-inf ,m-tau)))
-                   (m-beta     (or (lookup-field 'm-beta alst)   `(/ (- 1 ,m-inf) ,m-tau)))
+                   (m-inf-sym  (p$ ion 'm-inf))
+                   (m-tau-sym  (p$ ion 'm-tau))
+                   (m-alpha    (or (lookup-field 'm-alpha alst)  `(/ ,m-inf-sym ,m-tau-sym)))
+                   (m-beta     (or (lookup-field 'm-beta alst)   `(/ (- 1 ,m-inf-sym) ,m-tau-sym)))
                    (open       (p$ ion 'mO))
                    (closed     (p$ ion 'mC))
@@ -102 +104 @@
                                  (transitions (-> ,closed ,open ,m-alpha) 
                                               (-> ,open ,closed ,m-beta)))))
+              (if m-inf (env-extend! m-inf-sym '(asgn) 'none `(rhs ,m-inf)))
+              (if m-tau (env-extend! m-tau-sym '(asgn) 'none `(rhs ,m-tau)))
               (apply env-extend! (cons* (p$ ion 'm) '(tscomp) initial-m mst))
               (add-external! (p$ ion 'm) 'output)

release/3/nemo/trunk/nemo.scm

@@ -168 +168 @@
 
 (define (model->nmodl options model)
-  (nemo:nmodl-translator model (lookup-def 'nmodl-method options) (lookup-def 'table options) -150 150 1))
+  (nemo:nmodl-translator model (lookup-def 'method options) (lookup-def 'table options) -150 150 1))
 
 

release/3/nemo/trunk/nmodl.scm

@@ -178 +178 @@
 (define (bind ks vs e) `(let ,(zip ks vs) ,e))
 
+(define (name-normalize expr)
+  (match expr 
+         (('if c t e)  `(if ,(name-normalize c) ,(name-normalize t) ,(name-normalize e)))
+         (('let bs e)
+          `(let ,(map (lambda (b) `(,(car b) ,(name-normalize (cadr b)))) bs) ,(name-normalize e)))
+         ((f . es) 
+          (cons f (map name-normalize es)))
+         ((? symbol? ) (nmodl-name expr))
+         ((? atom? ) expr)))
 
 (define (if-convert expr)
@@ -230 +239 @@
     (let* ((expr1 (if-convert expr))
            (expr2 (subst-convert expr1 subst-empty))
-           (expr3 (let-lift expr2)))
-      expr3)))
+           (expr3 (let-lift expr2))
+           (expr4 (name-normalize expr3)))
+      expr4)))
 
 (define (format-expr/NMODL indent expr . rest)  
@@ -607 +617 @@
                                   (map second acc-ions) (map fourth acc-ions)))
                   (asgns1 (delete-duplicates asgns0)))
-             (for-each (lambda (x) (pp indent+ ,x)) asgns1)
+             (for-each (lambda (x) (pp indent+ ,(nmodl-name x))) asgns1)
              (pp indent "}")
              
@@ -616 +626 @@
                      (if (not (null? locals)) (pp indent+ (LOCAL ,(sl\ ", " locals)))))
                    (for-each (lambda (def)
-                               (let ((n (first def)) 
+                               (let ((n (nmodl-name (first def)) )
                                      (b (second def)))
                                  (pp indent+ ,(expr->string/NMODL b n)))) asgn-eq-defs)