| 1 | (define-variable |
|---|
| 2 | :class "var-help" |
|---|
| 3 | :super-classes ("variable") |
|---|
| 4 | :system-theoretic "help") |
|---|
| 5 | |
|---|
| 6 | (define-variable |
|---|
| 7 | :class "var-real-parameter" |
|---|
| 8 | :super-classes ("variable") |
|---|
| 9 | :system-theoretic "real-parameter") |
|---|
| 10 | |
|---|
| 11 | (define-variable |
|---|
| 12 | :class "var-integer-parameter" |
|---|
| 13 | :super-classes ("variable") |
|---|
| 14 | :system-theoretic "integer-parameter") |
|---|
| 15 | |
|---|
| 16 | (define-variable |
|---|
| 17 | :class "var-input" |
|---|
| 18 | :super-classes ("variable") |
|---|
| 19 | :system-theoretic "input") |
|---|
| 20 | |
|---|
| 21 | (define-variable |
|---|
| 22 | :class "concentration" |
|---|
| 23 | :super-classes ("variable") |
|---|
| 24 | :unit "mol/l") |
|---|
| 25 | |
|---|
| 26 | (define-variable |
|---|
| 27 | :class "var-output" |
|---|
| 28 | :super-classes ("variable") |
|---|
| 29 | :system-theoretic "output") |
|---|
| 30 | |
|---|
| 31 | (define-module |
|---|
| 32 | :class "library" |
|---|
| 33 | :super-classes ("module") |
|---|
| 34 | :documentation "Library") |
|---|
| 35 | |
|---|
| 36 | (define-variable |
|---|
| 37 | :class "var-rate" |
|---|
| 38 | :super-classes ("variable") |
|---|
| 39 | :value "100.0d0" |
|---|
| 40 | :minimum "0.0d0" |
|---|
| 41 | :maximum "100000.0d0" |
|---|
| 42 | :unit "1/h") |
|---|
| 43 | |
|---|
| 44 | (define-variable |
|---|
| 45 | :class "scaling-parameter" |
|---|
| 46 | :super-classes ("variable") |
|---|
| 47 | :documentation "parameter to perform manual numeric scaling of rate-laws |
|---|
| 48 | etc. for optimization. It is marked as a help-variable to eventually |
|---|
| 49 | remove it by the equation-optimizer in Promot." |
|---|
| 50 | :system-theoretic "help" |
|---|
| 51 | :value "1.0d0") |
|---|
| 52 | |
|---|
| 53 | (define-variable |
|---|
| 54 | :class "molar-flux" |
|---|
| 55 | :super-classes ("variable") |
|---|
| 56 | :minimum "0.0d0" |
|---|
| 57 | :maximum "1000.0d0" |
|---|
| 58 | :unit "mol/s") |
|---|
| 59 | |
|---|
| 60 | (define-module |
|---|
| 61 | :class "predefined" |
|---|
| 62 | :super-classes ("library")) |
|---|
| 63 | |
|---|
| 64 | (define-module |
|---|
| 65 | :class "c2" |
|---|
| 66 | :super-classes ("predefined")) |
|---|
| 67 | |
|---|
| 68 | (define-module |
|---|
| 69 | :class "c2a" |
|---|
| 70 | :super-classes ("c2") |
|---|
| 71 | :icon "../../../../../home/saezr/ProMoT_models/SignalTransd/TCR/predefined/icons/C2a.gif") |
|---|
| 72 | |
|---|
| 73 | (define-module |
|---|
| 74 | :class "reaction" |
|---|
| 75 | :super-classes ("library")) |
|---|
| 76 | |
|---|
| 77 | (define-module |
|---|
| 78 | :class "special-reaction" |
|---|
| 79 | :super-classes ("reaction")) |
|---|
| 80 | |
|---|
| 81 | (define-variable |
|---|
| 82 | :class "var-activity" |
|---|
| 83 | :super-classes ("var-real-parameter")) |
|---|
| 84 | |
|---|
| 85 | (define-variable |
|---|
| 86 | :class "reaction-rate" |
|---|
| 87 | :super-classes ("molar-flux") |
|---|
| 88 | :unit "mol/s") |
|---|
| 89 | |
|---|
| 90 | (define-module |
|---|
| 91 | :class "kinetics" |
|---|
| 92 | :super-classes ("reaction") |
|---|
| 93 | :variables |
|---|
| 94 | (("r" |
|---|
| 95 | :is-a "reaction-rate" |
|---|
| 96 | :documentation "reaction-rate" |
|---|
| 97 | :system-theoretic "help" |
|---|
| 98 | :report "lumped" |
|---|
| 99 | :unit "umol/g_dw/h") |
|---|
| 100 | ("skal" |
|---|
| 101 | :is-a "scaling-parameter"))) |
|---|
| 102 | |
|---|
| 103 | (define-module |
|---|
| 104 | :class "catalytic" |
|---|
| 105 | :super-classes ("kinetics")) |
|---|
| 106 | |
|---|
| 107 | (define-module |
|---|
| 108 | :class "structure" |
|---|
| 109 | :super-classes ("reaction") |
|---|
| 110 | :variables |
|---|
| 111 | (("r"))) |
|---|
| 112 | |
|---|
| 113 | (define-variable |
|---|
| 114 | :class "var-concentration" |
|---|
| 115 | :super-classes ("concentration") |
|---|
| 116 | :value "1.0d-4" |
|---|
| 117 | :minimum "0.0d0" |
|---|
| 118 | :maximum "10.0d0") |
|---|
| 119 | |
|---|
| 120 | (define-variable |
|---|
| 121 | :class "var-concentration-in" |
|---|
| 122 | :super-classes ("var-concentration" "var-input") |
|---|
| 123 | :absolute-error "1.0d-8") |
|---|
| 124 | |
|---|
| 125 | (define-terminal |
|---|
| 126 | :class "term-concentration-in" |
|---|
| 127 | :super-classes ("terminal") |
|---|
| 128 | :icon "icons/term_concentration_in.gif" |
|---|
| 129 | :link-color "green" |
|---|
| 130 | :variables |
|---|
| 131 | (("c" |
|---|
| 132 | :is-a "var-concentration-in" |
|---|
| 133 | :unit "umol/g_dw"))) |
|---|
| 134 | |
|---|
| 135 | (define-module |
|---|
| 136 | :class "enz-0eff" |
|---|
| 137 | :super-classes ("structure") |
|---|
| 138 | :terminals |
|---|
| 139 | (("t_enz" |
|---|
| 140 | :is-a "term-concentration-in" |
|---|
| 141 | :geometry-side "top" |
|---|
| 142 | :geometry-position "0.5"))) |
|---|
| 143 | |
|---|
| 144 | (define-module |
|---|
| 145 | :class "en1" |
|---|
| 146 | :super-classes ("catalytic" "enz-0eff") |
|---|
| 147 | :documentation "enzimatic reaction with 1st order kinetics" |
|---|
| 148 | :parameters |
|---|
| 149 | (("r" |
|---|
| 150 | :value "t_enz.c*sa*a.c")) |
|---|
| 151 | :variables |
|---|
| 152 | (("sa" |
|---|
| 153 | :is-a "var-activity"))) |
|---|
| 154 | |
|---|
| 155 | (define-variable |
|---|
| 156 | :class "var-rate-out" |
|---|
| 157 | :super-classes ("var-rate" "var-output") |
|---|
| 158 | :absolute-error "1.0d-8") |
|---|
| 159 | |
|---|
| 160 | (define-terminal |
|---|
| 161 | :class "term-reaction-flux" |
|---|
| 162 | :super-classes ("terminal") |
|---|
| 163 | :icon "icons/term_react_blue.gif" |
|---|
| 164 | :link-color "blue" |
|---|
| 165 | :variables |
|---|
| 166 | (("c" |
|---|
| 167 | :is-a "var-concentration-in" |
|---|
| 168 | :unit "umol/g_dw") |
|---|
| 169 | ("r" |
|---|
| 170 | :is-a "var-rate-out" |
|---|
| 171 | :positive-vector-direction "out" |
|---|
| 172 | :unit "umol/g_dw/h"))) |
|---|
| 173 | |
|---|
| 174 | (define-module |
|---|
| 175 | :class "s-a-b" |
|---|
| 176 | :super-classes ("structure") |
|---|
| 177 | :terminals |
|---|
| 178 | (("a" |
|---|
| 179 | :is-a "term-reaction-flux") |
|---|
| 180 | ("b" |
|---|
| 181 | :is-a "term-reaction-flux")) |
|---|
| 182 | :equations |
|---|
| 183 | (("stoech_a" |
|---|
| 184 | :relation "a.r == -r") |
|---|
| 185 | ("stoech_b" |
|---|
| 186 | :relation "b.r == r"))) |
|---|
| 187 | |
|---|
| 188 | (define-module |
|---|
| 189 | :class "s-a-b_l" |
|---|
| 190 | :super-classes ("s-a-b") |
|---|
| 191 | :terminals |
|---|
| 192 | (("a" |
|---|
| 193 | :geometry-side "right" |
|---|
| 194 | :geometry-position "0.5") |
|---|
| 195 | ("b" |
|---|
| 196 | :geometry-side "left" |
|---|
| 197 | :geometry-position "0.5"))) |
|---|
| 198 | |
|---|
| 199 | (define-module |
|---|
| 200 | :class "trans2a-en1_l" |
|---|
| 201 | :super-classes ("en1" "s-a-b_l") |
|---|
| 202 | :properties |
|---|
| 203 | (("abstract" |
|---|
| 204 | :value "no")) |
|---|
| 205 | :icon "icons/irrev_l") |
|---|
| 206 | |
|---|
| 207 | (define-module |
|---|
| 208 | :class "s-a-b_r" |
|---|
| 209 | :super-classes ("s-a-b") |
|---|
| 210 | :terminals |
|---|
| 211 | (("a" |
|---|
| 212 | :geometry-side "left" |
|---|
| 213 | :geometry-position "0.5") |
|---|
| 214 | ("b" |
|---|
| 215 | :geometry-side "right" |
|---|
| 216 | :geometry-position "0.5"))) |
|---|
| 217 | |
|---|
| 218 | (define-module |
|---|
| 219 | :class "trans2a-en1_r" |
|---|
| 220 | :super-classes ("en1" "s-a-b_r") |
|---|
| 221 | :properties |
|---|
| 222 | (("abstract" |
|---|
| 223 | :value "no")) |
|---|
| 224 | :icon "icons/irrev_r") |
|---|
| 225 | |
|---|
| 226 | (define-module |
|---|
| 227 | :class "help" |
|---|
| 228 | :super-classes ("library")) |
|---|
| 229 | |
|---|
| 230 | (define-module |
|---|
| 231 | :class "adapter" |
|---|
| 232 | :super-classes ("help")) |
|---|
| 233 | |
|---|
| 234 | (define-variable |
|---|
| 235 | :class "var-concentration-out" |
|---|
| 236 | :super-classes ("var-concentration" "var-output") |
|---|
| 237 | :absolute-error "1.0d-8") |
|---|
| 238 | |
|---|
| 239 | (define-variable |
|---|
| 240 | :class "var-state-concentration-out" |
|---|
| 241 | :super-classes ("var-concentration-out") |
|---|
| 242 | :system-theoretic "output") |
|---|
| 243 | |
|---|
| 244 | (define-variable |
|---|
| 245 | :class "var-rate-in" |
|---|
| 246 | :super-classes ("var-rate" "var-input") |
|---|
| 247 | :absolute-error "1.0d-8") |
|---|
| 248 | |
|---|
| 249 | (define-terminal |
|---|
| 250 | :class "term-storage-flux" |
|---|
| 251 | :super-classes ("terminal") |
|---|
| 252 | :icon "icons/term_stor_blue.gif" |
|---|
| 253 | :link-color "blue" |
|---|
| 254 | :variables |
|---|
| 255 | (("c" |
|---|
| 256 | :is-a "var-concentration-out") |
|---|
| 257 | ("r" |
|---|
| 258 | :is-a "var-rate-in" |
|---|
| 259 | :positive-vector-direction "in" |
|---|
| 260 | :unit "umol/g_dw/h"))) |
|---|
| 261 | |
|---|
| 262 | (define-module |
|---|
| 263 | :class "adapter-flux" |
|---|
| 264 | :super-classes ("adapter") |
|---|
| 265 | :documentation "splits a flux-terminal into 2" |
|---|
| 266 | :properties |
|---|
| 267 | (("abstract" |
|---|
| 268 | :value "no")) |
|---|
| 269 | :icon "icons/adapter.gif" |
|---|
| 270 | :terminals |
|---|
| 271 | (("in" |
|---|
| 272 | :is-a "term-reaction-flux" |
|---|
| 273 | :geometry-side "LEFT" |
|---|
| 274 | :geometry-position "0.47333333" |
|---|
| 275 | :variables |
|---|
| 276 | (("r" |
|---|
| 277 | :is-eq-to "parent.r"))) |
|---|
| 278 | ("out" |
|---|
| 279 | :is-a "term-storage-flux" |
|---|
| 280 | :geometry-side "RIGHT" |
|---|
| 281 | :geometry-position "0.47333333" |
|---|
| 282 | :variables |
|---|
| 283 | (("c" |
|---|
| 284 | :is-eq-to "parent.c")))) |
|---|
| 285 | :variables |
|---|
| 286 | (("c" |
|---|
| 287 | :is-a "var-state-concentration-out") |
|---|
| 288 | ("r" |
|---|
| 289 | :is-a "var-rate-out" |
|---|
| 290 | :positive-vector-direction "out" |
|---|
| 291 | :value "0.0d0")) |
|---|
| 292 | :equations |
|---|
| 293 | (("hurg" |
|---|
| 294 | :relation "c == in.c") |
|---|
| 295 | ("rate" |
|---|
| 296 | :relation "r == out.r"))) |
|---|
| 297 | |
|---|
| 298 | (define-module |
|---|
| 299 | :class "cyclic_en1" |
|---|
| 300 | :super-classes ("special-reaction") |
|---|
| 301 | :documentation "two 1st-order reactions in a cycle" |
|---|
| 302 | :properties |
|---|
| 303 | (("abstract" |
|---|
| 304 | :value "no")) |
|---|
| 305 | :icon "icons/cyclic.gif" |
|---|
| 306 | :geometry-width "273" |
|---|
| 307 | :geometry-height "252" |
|---|
| 308 | :terminals |
|---|
| 309 | (("a" |
|---|
| 310 | :is-eq-to "aa.in" |
|---|
| 311 | :geometry-side "LEFT" |
|---|
| 312 | :geometry-position "0.47619048") |
|---|
| 313 | ("b" |
|---|
| 314 | :is-eq-to "ab.in" |
|---|
| 315 | :geometry-side "RIGHT" |
|---|
| 316 | :geometry-position "0.50396824") |
|---|
| 317 | ("enz1" |
|---|
| 318 | :is-eq-to "reaction1.t_enz" |
|---|
| 319 | :geometry-side "TOP" |
|---|
| 320 | :geometry-position "0.45421246") |
|---|
| 321 | ("enz2" |
|---|
| 322 | :is-eq-to "reaction2.t_enz" |
|---|
| 323 | :geometry-side "BOTTOM" |
|---|
| 324 | :geometry-position "0.46153846")) |
|---|
| 325 | :modules |
|---|
| 326 | (("aa" |
|---|
| 327 | :is-a "adapter-flux" |
|---|
| 328 | :geometry-x "42" |
|---|
| 329 | :geometry-y "120") |
|---|
| 330 | ("ab" |
|---|
| 331 | :is-a "adapter-flux" |
|---|
| 332 | :geometry-x "204" |
|---|
| 333 | :geometry-y "127") |
|---|
| 334 | ("reaction1" |
|---|
| 335 | :is-a "trans2a-en1_r" |
|---|
| 336 | :geometry-x "124" |
|---|
| 337 | :geometry-y "89" |
|---|
| 338 | :variables |
|---|
| 339 | (("sa" |
|---|
| 340 | :is-eq-to "parent.r1_sa"))) |
|---|
| 341 | ("reaction2" |
|---|
| 342 | :is-a "trans2a-en1_l" |
|---|
| 343 | :geometry-x "127" |
|---|
| 344 | :geometry-y "154" |
|---|
| 345 | :variables |
|---|
| 346 | (("sa" |
|---|
| 347 | :is-eq-to "parent.r2_sa")))) |
|---|
| 348 | :links |
|---|
| 349 | (("aaout_reaction1a_467359" |
|---|
| 350 | :terminals ("aa.out" "reaction1.a" "reaction2.b") |
|---|
| 351 | :nodes (("57" "121")) |
|---|
| 352 | :edges (("0" "-1" (("48" "120"))) ("1" "-1" nil) ("2" "-1" nil))) |
|---|
| 353 | ("reaction1b_abin_467365" |
|---|
| 354 | :terminals ("reaction1.b" "ab.out" "reaction2.a") |
|---|
| 355 | :nodes (("190" "124")) |
|---|
| 356 | :edges (("0" "-1" (("174" "108"))) ("1" "-1" nil) ("2" "-1" nil)))) |
|---|
| 357 | :variables |
|---|
| 358 | (("r1_sa" |
|---|
| 359 | :is-a "var-activity" |
|---|
| 360 | :system-theoretic "real-parameter") |
|---|
| 361 | ("r2_sa" |
|---|
| 362 | :is-a "var-activity" |
|---|
| 363 | :system-theoretic "real-parameter"))) |
|---|
| 364 | |
|---|
| 365 | (define-module |
|---|
| 366 | :class "storage" |
|---|
| 367 | :super-classes ("library")) |
|---|
| 368 | |
|---|
| 369 | (define-terminal |
|---|
| 370 | :class "term-concentration-out" |
|---|
| 371 | :super-classes ("terminal") |
|---|
| 372 | :icon "icons/term_concentration_out.gif" |
|---|
| 373 | :link-color "green" |
|---|
| 374 | :variables |
|---|
| 375 | (("c" |
|---|
| 376 | :is-a "var-concentration-out" |
|---|
| 377 | :unit "umol/g_dw"))) |
|---|
| 378 | |
|---|
| 379 | (define-module |
|---|
| 380 | :class "storage-intra-const_c" |
|---|
| 381 | :super-classes ("storage") |
|---|
| 382 | :documentation "Constant concentration with concentration-terminals" |
|---|
| 383 | :properties |
|---|
| 384 | (("abstract" |
|---|
| 385 | :value "no")) |
|---|
| 386 | :icon "icons/storage_small" |
|---|
| 387 | :terminals |
|---|
| 388 | (("co" |
|---|
| 389 | :is-a "term-concentration-out" |
|---|
| 390 | :geometry-side "bottom" |
|---|
| 391 | :geometry-position "0.5")) |
|---|
| 392 | :variables |
|---|
| 393 | (("c0" |
|---|
| 394 | :is-a "var-real-parameter" |
|---|
| 395 | :documentation "Constant concentration value" |
|---|
| 396 | :report "lumped" |
|---|
| 397 | :value "1.0d0")) |
|---|
| 398 | :equations |
|---|
| 399 | (("hurg" |
|---|
| 400 | :relation "co.c == c0"))) |
|---|
| 401 | |
|---|
| 402 | (define-module |
|---|
| 403 | :class "multistage-storage" |
|---|
| 404 | :super-classes ("storage")) |
|---|
| 405 | |
|---|
| 406 | (define-module |
|---|
| 407 | :class "storage-intra" |
|---|
| 408 | :super-classes ("storage") |
|---|
| 409 | :documentation "intracellular storage without mue with flux-terminals" |
|---|
| 410 | :properties |
|---|
| 411 | (("abstract" |
|---|
| 412 | :value "no")) |
|---|
| 413 | :icon "icons/storage" |
|---|
| 414 | :terminals |
|---|
| 415 | (("cf" |
|---|
| 416 | :is-a "term-storage-flux" |
|---|
| 417 | :geometry-side "right" |
|---|
| 418 | :geometry-position "0.5" |
|---|
| 419 | :variables |
|---|
| 420 | (("c" |
|---|
| 421 | :is-eq-to "parent.c0")))) |
|---|
| 422 | :variables |
|---|
| 423 | (("c0" |
|---|
| 424 | :is-a "var-state-concentration-out" |
|---|
| 425 | :documentation "Initial concentration" |
|---|
| 426 | :report "lumped")) |
|---|
| 427 | :equations |
|---|
| 428 | (("bal" |
|---|
| 429 | :relation ":diff<t> c0 == cf.r"))) |
|---|
| 430 | |
|---|
| 431 | (define-module |
|---|
| 432 | :class "storage-mult-2st" |
|---|
| 433 | :super-classes ("multistage-storage") |
|---|
| 434 | :properties |
|---|
| 435 | (("abstract" |
|---|
| 436 | :value "no")) |
|---|
| 437 | :icon "icons/1bs-2st" |
|---|
| 438 | :geometry-width "406" |
|---|
| 439 | :geometry-height "401" |
|---|
| 440 | :parameters |
|---|
| 441 | (("st1.c0" |
|---|
| 442 | :value "parent.totalconc")) |
|---|
| 443 | :terminals |
|---|
| 444 | (("cf1" |
|---|
| 445 | :is-eq-to "st1.cf" |
|---|
| 446 | :geometry-side "RIGHT" |
|---|
| 447 | :geometry-position "0.3") |
|---|
| 448 | ("cf2" |
|---|
| 449 | :is-eq-to "st2.cf" |
|---|
| 450 | :geometry-side "RIGHT" |
|---|
| 451 | :geometry-position "0.7") |
|---|
| 452 | ("cot" |
|---|
| 453 | :is-a "term-concentration-in" |
|---|
| 454 | :documentation "terminal for the reactions where the total molecule is involved" |
|---|
| 455 | :geometry-side "top" |
|---|
| 456 | :geometry-position "0.5")) |
|---|
| 457 | :modules |
|---|
| 458 | (("st1" |
|---|
| 459 | :is-a "storage-intra" |
|---|
| 460 | :geometry-x "78" |
|---|
| 461 | :geometry-y "125") |
|---|
| 462 | ("st2" |
|---|
| 463 | :is-a "storage-intra" |
|---|
| 464 | :geometry-x "77" |
|---|
| 465 | :geometry-y "218")) |
|---|
| 466 | :variables |
|---|
| 467 | (("totalconc" |
|---|
| 468 | :is-eq-to "cot.c"))) |
|---|
| 469 | |
|---|
| 470 | (define-module |
|---|
| 471 | :class "term-conv" |
|---|
| 472 | :super-classes ("help") |
|---|
| 473 | :documentation "converts different terminal-types") |
|---|
| 474 | |
|---|
| 475 | (define-module |
|---|
| 476 | :class "cf2co" |
|---|
| 477 | :super-classes ("term-conv") |
|---|
| 478 | :documentation "converts a cf-term to a co-term" |
|---|
| 479 | :properties |
|---|
| 480 | (("abstract" |
|---|
| 481 | :value "no")) |
|---|
| 482 | :icon "icons/adapter" |
|---|
| 483 | :terminals |
|---|
| 484 | (("cf" |
|---|
| 485 | :is-a "term-reaction-flux" |
|---|
| 486 | :geometry-side "LEFT" |
|---|
| 487 | :geometry-position "0.52666664" |
|---|
| 488 | :variables |
|---|
| 489 | (("c" |
|---|
| 490 | :is-eq-to "parent.c"))) |
|---|
| 491 | ("co" |
|---|
| 492 | :is-a "term-concentration-out" |
|---|
| 493 | :geometry-side "RIGHT" |
|---|
| 494 | :geometry-position "0.52666664")) |
|---|
| 495 | :variables |
|---|
| 496 | (("c" |
|---|
| 497 | :is-a "var-concentration-in")) |
|---|
| 498 | :equations |
|---|
| 499 | (("free" |
|---|
| 500 | :relation "co.c == c") |
|---|
| 501 | ("rate" |
|---|
| 502 | :relation "cf.r == 0.0d0"))) |
|---|
| 503 | |
|---|
| 504 | (define-module |
|---|
| 505 | :class "c2a-en1-bs" |
|---|
| 506 | :super-classes ("c2a") |
|---|
| 507 | :documentation "protein in 2 states, active-inactive, using multistage, reactiosn are 1st order" |
|---|
| 508 | :properties |
|---|
| 509 | (("abstract" |
|---|
| 510 | :value "no")) |
|---|
| 511 | :icon "../../../../../home/saezr/ProMoT_models/SignalTransd/TCR/predefined/icons/C2a.gif" |
|---|
| 512 | :geometry-width "378" |
|---|
| 513 | :geometry-height "275" |
|---|
| 514 | :terminals |
|---|
| 515 | (("input" |
|---|
| 516 | :is-eq-to "reaction.enz1" |
|---|
| 517 | :geometry-side "TOP" |
|---|
| 518 | :geometry-position "0.5") |
|---|
| 519 | ("output" |
|---|
| 520 | :is-eq-to "aco.co" |
|---|
| 521 | :geometry-side "BOTTOM" |
|---|
| 522 | :geometry-position "0.5233333")) |
|---|
| 523 | :modules |
|---|
| 524 | (("aco" |
|---|
| 525 | :is-a "cf2co" |
|---|
| 526 | :geometry-x "206" |
|---|
| 527 | :geometry-y "199") |
|---|
| 528 | ("activ" |
|---|
| 529 | :is-a "storage-mult-2st" |
|---|
| 530 | :geometry-x "266" |
|---|
| 531 | :geometry-y "167") |
|---|
| 532 | ("activtotal" |
|---|
| 533 | :is-a "storage-intra-const_c" |
|---|
| 534 | :geometry-x "271" |
|---|
| 535 | :geometry-y "77") |
|---|
| 536 | ("phosphatase" |
|---|
| 537 | :is-a "storage-intra-const_c" |
|---|
| 538 | :geometry-x "84" |
|---|
| 539 | :geometry-y "215") |
|---|
| 540 | ("reaction" |
|---|
| 541 | :is-a "cyclic_en1" |
|---|
| 542 | :geometry-x "153" |
|---|
| 543 | :geometry-y "126" |
|---|
| 544 | :variables |
|---|
| 545 | (("r1_sa" |
|---|
| 546 | :is-eq-to "parent.r1_sa") |
|---|
| 547 | ("r2_sa" |
|---|
| 548 | :is-eq-to "parent.r2_sa")))) |
|---|
| 549 | :links |
|---|
| 550 | (("activcot_activtotalco" |
|---|
| 551 | :terminals ("activ.cot" "activtotal.co")) |
|---|
| 552 | ("deact204" |
|---|
| 553 | :terminals ("activ.cf1" "reaction.a")) |
|---|
| 554 | ("phos7953" |
|---|
| 555 | :terminals ("phosphatase.co" "reaction.enz2")) |
|---|
| 556 | ("reactionb_acocf_473370" |
|---|
| 557 | :terminals ("reaction.b" "aco.cf" "activ.cf2") |
|---|
| 558 | :nodes (("201" "127")) |
|---|
| 559 | :edges (("0" "-1" (("176" "128"))) ("1" "-1" nil) ("2" "-1" nil)))) |
|---|
| 560 | :variables |
|---|
| 561 | (("r1_sa" |
|---|
| 562 | :is-a "var-real-parameter") |
|---|
| 563 | ("r2_sa" |
|---|
| 564 | :is-a "var-real-parameter"))) |
|---|
| 565 | |
|---|
| 566 | (define-module |
|---|
| 567 | :class "hill_mod" |
|---|
| 568 | :super-classes ("catalytic" "enz-0eff") |
|---|
| 569 | :documentation "Hill Kinetics modified to allow 1st order for kmm=0" |
|---|
| 570 | :parameters |
|---|
| 571 | (("r" |
|---|
| 572 | :value "t_enz.c*sa*a.c ^ h/(1+kmm ^ h*a.c ^ h)")) |
|---|
| 573 | :variables |
|---|
| 574 | (("h" |
|---|
| 575 | :is-a "var-real-parameter") |
|---|
| 576 | ("kmm" |
|---|
| 577 | :is-a "var-real-parameter") |
|---|
| 578 | ("sa" |
|---|
| 579 | :is-a "var-activity"))) |
|---|
| 580 | |
|---|
| 581 | (define-module |
|---|
| 582 | :class "trans2a-hill_mod_r" |
|---|
| 583 | :super-classes ("hill_mod" "s-a-b_r") |
|---|
| 584 | :properties |
|---|
| 585 | (("abstract" |
|---|
| 586 | :value "no")) |
|---|
| 587 | :icon "icons/irrev_r.gif") |
|---|
| 588 | |
|---|
| 589 | (define-module |
|---|
| 590 | :class "cyclic_hill_mod" |
|---|
| 591 | :super-classes ("cyclic_en1") |
|---|
| 592 | :documentation "cycle of reactions with hill_mod kinetics" |
|---|
| 593 | :parameters |
|---|
| 594 | (("r1_sa" |
|---|
| 595 | :system-theoretic "real-parameter") |
|---|
| 596 | ("r2_sa" |
|---|
| 597 | :system-theoretic "real-parameter")) |
|---|
| 598 | :modules |
|---|
| 599 | (("reaction1" |
|---|
| 600 | :is-a "trans2a-hill_mod_r" |
|---|
| 601 | :variables |
|---|
| 602 | (("h" |
|---|
| 603 | :is-eq-to "parent.r1_h") |
|---|
| 604 | ("kmm" |
|---|
| 605 | :is-eq-to "parent.r1_kmm") |
|---|
| 606 | ("sa" |
|---|
| 607 | :is-eq-to "parent.r1_sa"))) |
|---|
| 608 | ("reaction2" |
|---|
| 609 | :is-a "trans2a-hill_mod_r" |
|---|
| 610 | :variables |
|---|
| 611 | (("h" |
|---|
| 612 | :is-eq-to "parent.r2_h") |
|---|
| 613 | ("kmm" |
|---|
| 614 | :is-eq-to "parent.r2_kmm") |
|---|
| 615 | ("sa" |
|---|
| 616 | :is-eq-to "parent.r2_sa")))) |
|---|
| 617 | :variables |
|---|
| 618 | (("r1_h" |
|---|
| 619 | :is-a "var-real-parameter" |
|---|
| 620 | :system-theoretic "real-parameter") |
|---|
| 621 | ("r1_kmm" |
|---|
| 622 | :is-a "var-real-parameter" |
|---|
| 623 | :system-theoretic "real-parameter") |
|---|
| 624 | ("r2_h" |
|---|
| 625 | :is-a "var-activity" |
|---|
| 626 | :system-theoretic "real-parameter") |
|---|
| 627 | ("r2_kmm" |
|---|
| 628 | :is-a "var-activity" |
|---|
| 629 | :system-theoretic "real-parameter"))) |
|---|
| 630 | |
|---|
| 631 | (define-module |
|---|
| 632 | :class "c2a-hill-mod-bs" |
|---|
| 633 | :super-classes ("c2a-en1-bs") |
|---|
| 634 | :modules |
|---|
| 635 | (("reaction" |
|---|
| 636 | :is-a "cyclic_hill_mod" |
|---|
| 637 | :variables |
|---|
| 638 | (("r1_h" |
|---|
| 639 | :is-eq-to "parent.r1_h") |
|---|
| 640 | ("r1_kmm" |
|---|
| 641 | :is-eq-to "parent.r1_kmm") |
|---|
| 642 | ("r1_sa" |
|---|
| 643 | :is-eq-to "parent.r1_sa") |
|---|
| 644 | ("r2_h" |
|---|
| 645 | :is-eq-to "parent.r2_h") |
|---|
| 646 | ("r2_kmm" |
|---|
| 647 | :is-eq-to "parent.r2_kmm") |
|---|
| 648 | ("r2_sa" |
|---|
| 649 | :is-eq-to "parent.r2_sa")))) |
|---|
| 650 | :variables |
|---|
| 651 | (("r1_h" |
|---|
| 652 | :is-a "var-real-parameter") |
|---|
| 653 | ("r1_kmm" |
|---|
| 654 | :is-a "var-real-parameter") |
|---|
| 655 | ("r2_h" |
|---|
| 656 | :is-a "var-real-parameter") |
|---|
| 657 | ("r2_kmm" |
|---|
| 658 | :is-a "var-real-parameter"))) |
|---|
| 659 | |
|---|
| 660 | (define-module |
|---|
| 661 | :class "c2a-hill-mod-bs-prep" |
|---|
| 662 | :super-classes ("c2a-hill-mod-bs") |
|---|
| 663 | :documentation "just give values to the parameters of the class c2a-en1-bs" |
|---|
| 664 | :parameters |
|---|
| 665 | (("r1_h" |
|---|
| 666 | :value "1.0d0") |
|---|
| 667 | ("r1_kmm" |
|---|
| 668 | :value "1.0d-8") |
|---|
| 669 | ("r1_sa" |
|---|
| 670 | :value "1.0d0") |
|---|
| 671 | ("r2_h" |
|---|
| 672 | :value "1.0d0") |
|---|
| 673 | ("r2_kmm" |
|---|
| 674 | :value "1.0d-8") |
|---|
| 675 | ("r2_sa" |
|---|
| 676 | :value "1.0d0"))) |
|---|
| 677 | |
|---|
| 678 | (define-module |
|---|
| 679 | :class "signal2hill" |
|---|
| 680 | :super-classes ("help") |
|---|
| 681 | :documentation "converts into hill eq" |
|---|
| 682 | :properties |
|---|
| 683 | (("abstract" |
|---|
| 684 | :value "no")) |
|---|
| 685 | :icon "icons/prodsignals.gif" |
|---|
| 686 | :terminals |
|---|
| 687 | (("in1" |
|---|
| 688 | :is-a "term-concentration-in" |
|---|
| 689 | :geometry-side "TOP" |
|---|
| 690 | :geometry-position "0.5") |
|---|
| 691 | ("out" |
|---|
| 692 | :is-a "term-concentration-out" |
|---|
| 693 | :geometry-side "BOTTOM" |
|---|
| 694 | :geometry-position "0.5" |
|---|
| 695 | :variables |
|---|
| 696 | (("c" |
|---|
| 697 | :is-eq-to "parent.c")))) |
|---|
| 698 | :variables |
|---|
| 699 | (("c" |
|---|
| 700 | :is-a "var-state-concentration-out" |
|---|
| 701 | :report "lumped") |
|---|
| 702 | ("h" |
|---|
| 703 | :is-a "var-real-parameter" |
|---|
| 704 | :value "1.0d0") |
|---|
| 705 | ("kmm" |
|---|
| 706 | :is-a "var-real-parameter" |
|---|
| 707 | :value "0.0d0") |
|---|
| 708 | ("sa" |
|---|
| 709 | :is-a "var-real-parameter" |
|---|
| 710 | :value "1.0d0")) |
|---|
| 711 | :equations |
|---|
| 712 | (("hurg" |
|---|
| 713 | :relation "c == in1.c ^ h*sa/(kmm ^ h+in1.c ^ h)"))) |
|---|
| 714 | |
|---|
| 715 | (define-module |
|---|
| 716 | :class "sum" |
|---|
| 717 | :super-classes ("help") |
|---|
| 718 | :documentation "These classes are needed for add signals, eg enz_tot=enz1+enz2") |
|---|
| 719 | |
|---|
| 720 | (define-module |
|---|
| 721 | :class "prod-2-signal" |
|---|
| 722 | :super-classes ("sum") |
|---|
| 723 | :documentation "multiplies 2 concentrations" |
|---|
| 724 | :properties |
|---|
| 725 | (("abstract" |
|---|
| 726 | :value "no")) |
|---|
| 727 | :icon "icons/prodsignals.gif" |
|---|
| 728 | :terminals |
|---|
| 729 | (("in1" |
|---|
| 730 | :is-a "term-concentration-in" |
|---|
| 731 | :geometry-side "TOP" |
|---|
| 732 | :geometry-position "0.1") |
|---|
| 733 | ("in2" |
|---|
| 734 | :is-a "term-concentration-in" |
|---|
| 735 | :geometry-side "TOP" |
|---|
| 736 | :geometry-position "0.9") |
|---|
| 737 | ("out" |
|---|
| 738 | :is-a "term-concentration-out" |
|---|
| 739 | :geometry-side "BOTTOM" |
|---|
| 740 | :geometry-position "0.5" |
|---|
| 741 | :variables |
|---|
| 742 | (("c" |
|---|
| 743 | :is-eq-to "parent.c")))) |
|---|
| 744 | :variables |
|---|
| 745 | (("c" |
|---|
| 746 | :is-a "var-state-concentration-out" |
|---|
| 747 | :documentation "sum of both concentrations" |
|---|
| 748 | :report "lumped") |
|---|
| 749 | ("k1" |
|---|
| 750 | :is-a "var-real-parameter" |
|---|
| 751 | :value "1.0d0")) |
|---|
| 752 | :equations |
|---|
| 753 | (("hurg" |
|---|
| 754 | :relation "c == k1*in1.c*in2.c"))) |
|---|
| 755 | |
|---|
| 756 | (define-module |
|---|
| 757 | :class "div-2-signal" |
|---|
| 758 | :super-classes ("prod-2-signal") |
|---|
| 759 | :documentation "one positive and one negative ( in a multiplicative manner) input" |
|---|
| 760 | :parameters |
|---|
| 761 | (("hurg" |
|---|
| 762 | :relation "c == in1.c/(1+k1*in2.c)"))) |
|---|
| 763 | |
|---|
| 764 | (define-module |
|---|
| 765 | :class "feedbjefe" |
|---|
| 766 | :super-classes ("module") |
|---|
| 767 | :diva-directory "/afs/mpi-magdeburg.mpg.de/home/saezr/tmp/" |
|---|
| 768 | :diva-cg-file-name "feedb.cg" |
|---|
| 769 | :diva-fortran-files-subname "daa01" |
|---|
| 770 | :diva-data-file-name "feedb.dat" |
|---|
| 771 | :diva-latex-file-name "feedb.tex" |
|---|
| 772 | :diva-anl-file-name "feedb.anl" |
|---|
| 773 | :geometry-width "388" |
|---|
| 774 | :geometry-height "434" |
|---|
| 775 | :parameters |
|---|
| 776 | (("x1.activ" |
|---|
| 777 | :model-name "mod1") |
|---|
| 778 | ("x1.activ.c_2" |
|---|
| 779 | :report "lumped" |
|---|
| 780 | :dont-optimize "yes" |
|---|
| 781 | :model-name "x1") |
|---|
| 782 | ("x1.activtotal.c0" |
|---|
| 783 | :model-name "x10") |
|---|
| 784 | ("x1.r1_h" |
|---|
| 785 | :model-name "h1") |
|---|
| 786 | ("x1.r1_kmm" |
|---|
| 787 | :model-name "km1") |
|---|
| 788 | ("x1.r1_sa" |
|---|
| 789 | :model-name "k1") |
|---|
| 790 | ("x1.r2_h" |
|---|
| 791 | :model-name "h1r") |
|---|
| 792 | ("x1.r2_kmm" |
|---|
| 793 | :model-name "km1r") |
|---|
| 794 | ("x1.r2_sa" |
|---|
| 795 | :model-name "k1r") |
|---|
| 796 | ("x1.reaction" |
|---|
| 797 | :model-name "r1") |
|---|
| 798 | ("x2.activ" |
|---|
| 799 | :model-name "mod2") |
|---|
| 800 | ("x2.activ.st_2" |
|---|
| 801 | :report "lumped" |
|---|
| 802 | :model-name "x2") |
|---|
| 803 | ("x2.activtotal.c0" |
|---|
| 804 | :model-name "x20") |
|---|
| 805 | ("x2.r1_h" |
|---|
| 806 | :model-name "h2") |
|---|
| 807 | ("x2.r1_kmm" |
|---|
| 808 | :model-name "km2") |
|---|
| 809 | ("x2.r1_sa" |
|---|
| 810 | :model-name "k2") |
|---|
| 811 | ("x2.r2_h" |
|---|
| 812 | :model-name "h2r") |
|---|
| 813 | ("x2.r2_kmm" |
|---|
| 814 | :model-name "km2r") |
|---|
| 815 | ("x2.r2_sa" |
|---|
| 816 | :model-name "k2r") |
|---|
| 817 | ("x2.reaction" |
|---|
| 818 | :model-name "r2")) |
|---|
| 819 | :modules |
|---|
| 820 | (("div" |
|---|
| 821 | :is-a "div-2-signal" |
|---|
| 822 | :geometry-x "123" |
|---|
| 823 | :geometry-y "154") |
|---|
| 824 | ("input" |
|---|
| 825 | :is-a "storage-intra-const_c" |
|---|
| 826 | :geometry-x "92" |
|---|
| 827 | :geometry-y "85" |
|---|
| 828 | :variables |
|---|
| 829 | (("c0" |
|---|
| 830 | :is-eq-to "parent.inputgen"))) |
|---|
| 831 | ("signal2hill" |
|---|
| 832 | :is-a "signal2hill" |
|---|
| 833 | :geometry-x "280" |
|---|
| 834 | :geometry-y "151") |
|---|
| 835 | ("x1" |
|---|
| 836 | :is-a "c2a-hill-mod-bs-prep" |
|---|
| 837 | :geometry-x "123" |
|---|
| 838 | :geometry-y "215") |
|---|
| 839 | ("x2" |
|---|
| 840 | :is-a "c2a-hill-mod-bs-prep" |
|---|
| 841 | :geometry-x "277" |
|---|
| 842 | :geometry-y "214")) |
|---|
| 843 | :links |
|---|
| 844 | (("divin1_inputco" |
|---|
| 845 | :terminals ("div.in1" "input.co") |
|---|
| 846 | :edges (("0" "1" nil))) |
|---|
| 847 | ("x1input_divout" |
|---|
| 848 | :terminals ("x1.input" "div.out") |
|---|
| 849 | :edges (("0" "1" nil))) |
|---|
| 850 | ("x1output_signal2hillin1" |
|---|
| 851 | :terminals ("x1.output" "signal2hill.in1") |
|---|
| 852 | :edges (("0" "1" (("128" "272") ("200" "272") ("200" "120") ("280" "120"))))) |
|---|
| 853 | ("x2input_signal2hillout" |
|---|
| 854 | :terminals ("x2.input" "signal2hill.out") |
|---|
| 855 | :edges (("0" "1" nil))) |
|---|
| 856 | ("x2output_divin2" |
|---|
| 857 | :terminals ("x2.output" "div.in2") |
|---|
| 858 | :edges (("0" "1" (("280" "272") ("216" "272") ("216" "144")))))) |
|---|
| 859 | :variables |
|---|
| 860 | (("inputgen" |
|---|
| 861 | :is-a "var-help" |
|---|
| 862 | :value ":cond(switcher == 2,inputstr,switcher == 0,0,1)") |
|---|
| 863 | ("inputstr" |
|---|
| 864 | :is-a "var-real-parameter" |
|---|
| 865 | :value "10.0d0") |
|---|
| 866 | ("switcher" |
|---|
| 867 | :is-a "var-integer-parameter" |
|---|
| 868 | :documentation "switch=1 tetramer stimulation, switch=2 antibody |
|---|
| 869 | stimulation, switcher=0,no stimulus " |
|---|
| 870 | :value "1"))) |
|---|
| 871 | |
|---|
