Changeset 28034 in project
 Timestamp:
 01/04/13 08:46:59 (7 years ago)
 Location:
 release/4/nemo/trunk
 Files:

 3 edited
Legend:
 Unmodified
 Added
 Removed

release/4/nemo/trunk/examples/Golgi/Golgi.nemo
r28024 r28034 10 10 (input v celsius) 11 11 12 (const V_t = 35)13 12 14 13 (component (type defaults) 14 (const V_t = 35) 15 15 (const celsius = 30) 16 17 (output celsius) 16 (output celsius V_t) 18 17 ) 19 18 20 (component (type membranecapacitance) 21 (const C_m = 1.0) 22 (output C_m )) 19 20 (component (type membranetau) 21 (const tau_m = 1e3) 22 (output tau_m )) 23 23 24 24 … … 102 102 (Q10 * Abeta_u * exp((v  V0beta_u) / Kbeta_u))) 103 103 104 104 (s_inf = ((alpha_s (v Q10))/(alpha_s (v Q10) + beta_s (v Q10)))) 105 (tau_s = (1 / (alpha_s (v Q10) + beta_s (v Q10)) )) 106 107 (u_inf = ((alpha_u (v Q10))/(alpha_u (v Q10) + beta_u (v Q10)) )) 108 (tau_u = (1 / (alpha_u (v Q10) + beta_u (v Q10)) )) 109 105 110 (hhionicgate 106 111 (CaHVA ;; ion name: exported variables will be of the form {ion}_{id} 107 (initialm ((alpha_s (v Q10))/(alpha_s (v Q10) + beta_s (v Q10)) ))108 (initialh ((alpha_u (v Q10))/(alpha_u (v Q10) + beta_u (v Q10)) ))112 (initialm s_inf) 113 (initialh u_inf) 109 114 (mpower 2) 110 115 (hpower 1) 111 (minf ((alpha_s (v Q10) / (alpha_s (v Q10) + beta_s (v Q10)) )))112 (mtau ((1 / (alpha_s (v Q10) + beta_s (v Q10)) )))113 (hinf ((alpha_u (v Q10) / (alpha_u (v Q10) + beta_u (v Q10)) )))114 (htau ((1 / (alpha_u (v Q10) + beta_u (v Q10)) )))116 (minf s_inf) 117 (mtau tau_s) 118 (hinf u_inf) 119 (htau tau_s) 115 120 )) 116 121 … … 532 537 (defun beta_c (v cai Q10) 533 538 (Q10 * Abeta_c / (1 + (cai / (Bbeta_c * exp (v / Kbeta_c))) ))) 534 539 540 (c_inf = ((alpha_c (v cai Q10)) / (alpha_c (v cai Q10) + beta_c (v cai Q10)) )) 541 (tau_c = (1 / (alpha_c (v cai Q10) + beta_c (v cai Q10)) )) 535 542 536 543 (hhionicgate 537 544 (KCa ;; ion name: exported variables will be of the form {ion}_{id} 538 (initialm ((alpha_c (v cai Q10)) / (alpha_c (v cai Q10) + beta_c (v cai Q10)) ))545 (initialm c_inf) 539 546 (mpower 1) 540 547 (hpower 0) 541 (malpha (alpha_c (v cai Q10))) 542 (mbeta (beta_c (v cai Q10)))548 (minf c_inf) 549 (mtau tau_c) 543 550 )) 544 551 … … 662 669 (Q10 * Abeta_n * exp((v  V0beta_n) / Kbeta_n) )) 663 670 671 (n_inf = ((alpha_n (v Q10)) / (alpha_n (v Q10) + beta_n (v Q10)) )) 672 (tau_n = (1 / (alpha_n (v Q10) + beta_n (v Q10)) )) 673 664 674 (hhionicgate 665 675 (KV ;; ion name: exported variables will be of the form {ion}_{id} 666 (initialm ((alpha_n (v Q10)) / (alpha_n (v Q10) + beta_n (v Q10)) ))676 (initialm n_inf) 667 677 (mpower 4) 668 678 (hpower 0) 669 (m alpha (alpha_n(v Q10)))670 (m beta (beta_n(v Q10)))679 (minf (n_inf)) 680 (mtau (tau_n)) 671 681 )) 672 682 ) … … 830 840 (Q10 * Abeta_v / (1 + exp((v  V0beta_v) / Kbeta_v) ))) 831 841 842 (u_inf = ((alpha_u (v Q10)) / (alpha_u (v Q10) + beta_u (v Q10)) )) 843 (tau_u = (1 / (alpha_u (v Q10) + beta_u (v Q10)))) 844 845 (v_inf = ((alpha_v (v Q10)) / (alpha_v (v Q10) + beta_v (v Q10)) )) 846 (tau_v = (1 / (alpha_v (v Q10) + beta_v (v Q10)) )) 832 847 833 848 (hhionicgate 834 849 (Na ;; ion name: exported variables will be of the form {ion}_{id} 835 (initialm ( (alpha_u (v Q10)) / (alpha_u (v Q10) + beta_u (v Q10))))836 (initialh ( (alpha_v (v Q10)) / (alpha_v (v Q10) + beta_v (v Q10))))850 (initialm (u_inf)) 851 (initialh (v_inf)) 837 852 (mpower 3) 838 853 (hpower 1) 839 (m alpha (alpha_u (v Q10)))840 (m beta (beta_u (v Q10)))841 (h alpha (alpha_v (v Q10)))842 (h beta (beta_v (v Q10)))854 (minf (u_inf)) 855 (mtau (tau_u)) 856 (hinf (v_inf)) 857 (htau (tau_v)) 843 858 )) 844 859 … … 972 987 (Q10 * Abeta_f * exp( ( v  V0beta_f ) / Kbeta_f ) )) 973 988 989 (s_inf = ((alpha_s (v Q10)) / (alpha_s (v Q10) + beta_s (v Q10)) )) 990 (tau_s = (1 / (alpha_s (v Q10) + beta_s (v Q10)) )) 991 (f_inf = ((alpha_f (v Q10)) / (alpha_f (v Q10) + beta_f (v Q10)) )) 992 (tau_f = (1 / (alpha_f (v Q10) + beta_f (v Q10)) )) 993 974 994 (hhionicgate 975 995 (NaR ;; ion name: exported variables will be of the form {ion}_{id} 976 (initialm ( (alpha_s (v Q10)) / (alpha_s (v Q10) + beta_s (v Q10))))977 (initialh ( (alpha_f (v Q10)) / (alpha_f (v Q10) + beta_f (v Q10))))996 (initialm (s_inf)) 997 (initialh (f_inf)) 978 998 (mpower 1) 979 999 (hpower 1) 980 (m alpha (alpha_s (v Q10)))981 (m beta (beta_s (v Q10)))982 (h alpha (alpha_f (v Q10)))983 (h beta (beta_f (v Q10)))1000 (minf (s_inf)) 1001 (mtau (tau_s)) 1002 (hinf (f_inf)) 1003 (htau (tau_f)) 984 1004 985 1005 )) 
release/4/nemo/trunk/nemomatlab.scm
r28033 r28034 464 464 (define (outputdy sysname method globals stateindexmap 465 465 rateeqdefs reactioneqdefs asgneqdefs externaleqdefs 466 poolions mcapieqs veq indent indent+)466 poolions ieqs veq indent indent+) 467 467 468 468 (pp indent ,nl (function ,(case method ((cvode) "[dy flag]") (else "dy")) … … 1014 1014 (outputdy sysname method globals stateindexmap 1015 1015 rateeqdefs reactioneqdefs asgneqdefs externaleqdefs 1016 poolions mcapieqs veq1016 poolions ieqs veq 1017 1017 indent indent+))) 1018 1018 (if (not output) (closeoutputport output1))) 
release/4/nemo/trunk/nemonest.scm
r28033 r28034 496 496 (define (outputdy sysname method imports constdefs stateindexmap 497 497 externaleqdefs rateeqdefs reactioneqdefs asgneqdefs 498 poolions mcapieqs veq indent indent+)498 poolions ieqs veq indent indent+) 499 499 500 500 … … 1558 1558 sysname method stateindexmap steadystateindexmap 1559 1559 constdefs asgneqdefs initeqdefs rateeqdefs 1560 reactioneqdefs ieqs poolions permions1561 synapseinfo 1560 reactioneqdefs defaults ieqs poolions permions 1561 synapseinfo 1562 1562 indent indent+) 1563 1563 … … 1706 1706 } 1707 1707 EOF 1708 (if (lookupdef 'V_t constdefs) threshold "")1708 (if (lookupdef 'V_t defaults) threshold "") 1709 1709 ))) 1710 1710 … … 2263 2263 (importssansv (filter (lambda (x) (not (equal? 'v (first x)))) imports)) 2264 2264 2265 (veq (cond ((and mcap mres marea (lookupdef 'v imports)) 2266 (list 'v (rhsexpr/C++ `(+ "(node.B_.I_stim_)" 2267 (/ (* (neg ,(sum inames)) ,marea) (* 2. ,mres ,mcap)))))) 2268 ((and marea (lookupdef 'v imports)) 2269 (list 'v (rhsexpr/C++ `(+ "(node.B_.I_stim_)" 2270 (* (neg ,(sum inames)) ,marea))))) 2271 (else (list 'v 0.0)))) 2272 2273 (veq (and (member 'v globals) (not (null? inames)) 2265 (veq (and (not (null? inames)) 2274 2266 (let ((istim "(node.B_.I_stim_)" )) 2275 2267 (cond ((and mrc marea) 2276 2268 (list 'v (rhsexpr/C++ `(/ (+ ,istim (* (neg ,(sum inames)) ,marea)) ,mrc)))) 2277 2269 (marea 2278 (list 'v (rhsexpr/C++ `(+ istim (* (neg ,(sum inames)) ,marea)))))2270 (list 'v (rhsexpr/C++ `(+ ,istim (* (neg ,(sum inames)) ,marea))))) 2279 2271 (mrc 2280 (list 'v (rhsexpr/C++ `(/ (+ istim (neg ,(sum inames))) ,mrc))))2272 (list 'v (rhsexpr/C++ `(/ (+ ,istim (neg ,(sum inames))) ,mrc)))) 2281 2273 (else 2282 (list 'v (rhsexpr/C++ `(+ istim (neg ,(sum inames))))))2274 (list 'v (rhsexpr/C++ `(+ ,istim (neg ,(sum inames)))))) 2283 2275 )))) 2284 2276 … … 2363 2355 (outputdy sysname method importssansv constdefs stateindexmap 2364 2356 externaleqdefs rateeqdefs reactioneqdefs asgneqdefs 2365 poolions mcapieqs veq2357 poolions ieqs veq 2366 2358 indent indent+) 2367 2359 )) … … 2423 2415 sysname method stateindexmap steadystateindexmap 2424 2416 constdefs asgneqdefs initeqdefs rateeqdefs 2425 reactioneqdefs ieqs poolions permions2417 reactioneqdefs defaults ieqs poolions permions 2426 2418 synapseinfo indent indent+) 2427 2419 (pp indent ,nl)
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