#| Library for logical analysis of the network structure of signal transduction networks Authors: Julio Saez-Rodriguez, Martin Ginkel, Rebecca Hemenway $Id$ |# (add-icon-dir "promot:kb;SignalTransd;libraries;") (add-icon-dir "promot:kb;SignalTransd;structure;") (add-mdl-dir "promot:kb;SignalTransd;structure;") (define-module :class "struct-library" :super-classes ("module")) (define-terminal :class "term-struct" :super-classes ("terminal") :geometry-width "13" :geometry-height "13" :link-color "blue" :variables (("a" :system-theoretic "state" :value "1"))) #| (define-variable :class "var-real-parameter" :super-classes ("variable") :system-theoretic "real-parameter") (define-variable :class "var-integer-parameter" :super-classes ("variable") :system-theoretic "integer-parameter") |# (define-terminal :class "term-struct-compound" :super-classes ("term-struct") :properties (("abstract" :value "no")) :icon "icons/struct/term-compound") (define-terminal :class "term-struct-gate" :super-classes ("term-struct")) (define-terminal :class "term-struct-input" :super-classes ("term-struct-gate") :properties (("abstract" :value "no")) :icon "icons/struct/term-input" :parameters (("a" :system-theoretic "input" :value "1"))) (define-terminal :class "term-struct-output" :super-classes ("term-struct-gate") :properties (("abstract" :value "no")) :icon "icons/struct/term-output" :parameters (("a" :system-theoretic "output" :value "1"))) (define-module :class "struct-adapter" :super-classes ("struct-library") :icon "icons/struct/struct-adapt" :terminals (("input" :is-a "term-struct" :geometry-side "top" :geometry-position "0.5") ("output" :is-a "term-struct" :geometry-side "bottom" :geometry-position "0.5"))) (define-module :class "struct-adapter-compound" :super-classes ("struct-adapter") :properties (("abstract" :value "no")) :icon "icons/struct/struct-adapt" :terminals (("input" :is-a "term-struct-compound") ("output" :is-a "term-struct-compound"))) (define-module :class "struct-adapter-gate" :super-classes ("struct-adapter") :icon "icons/struct/struct-adapt" :properties (("abstract" :value "no")) :terminals (("input" :is-a "term-struct-input") ("output" :is-a "term-struct-output"))) (define-module :class "gate" :super-classes ("struct-library") :variables (("conf" :system-theoretic "real-parameter" :documentation "confidency level of this element: 1-most established (values between 0 and 1)" :value "1") ("defval" :system-theoretic "integer-parameter" :documentation "Default value of the logical state of the reaction. empty = undefined") ("time" :system-theoretic "real-parameter" :documentation "parameter determining the time-scale, 1 being the fastest" :value "1") ("logexcl" :system-theoretic "integer-parameter" :documentation "parameter defining the gate to be excluded from logical analysis. Allowed Values 0 (included) or 1 (excluded), default 0." :value "0") ("ignore_in_export" :system-theoretic "integer-parameter" :documentation "parameter determining whether the gate is exported to the CellNetAnalyzer. Allowed Values 0 (exported) or 1 (ignored in export), default 0." :value "0") ("monotone" :system-theoretic "real-parameter" :documentation "parameter defining the gate to be monotone. Allowed Values 0 (non monotone) or 1 (monotone), default 0." :value "0.01") ("map_number" :system-theoretic "integer-parameter" :documentation "parameter determining the map in CellNetAnalyzer. Should be a positive int, default is 1." :value "1") ("textbox_type" :system-theoretic "integer-parameter" :documentation "parameter determining if the textbox in CellNetAnalyzer is editable (1), not-editable (2) or non-visible (3). The default value is 1." :value "1") )) (define-module :class "gate-2" :super-classes ("gate") :terminals (("input1" :is-a "term-struct-input" :geometry-side "top" :geometry-position "0.1") ("input2" :is-a "term-struct-input" :geometry-side "top" :geometry-position "0.9") ("output" :is-a "term-struct-output" :geometry-side "bottom" :geometry-position "0.5"))) (define-module :class "gate-2-2" :super-classes ("gate-2") :terminals (("input1" :is-eq-to "gate_2.input1" :geometry-side "TOP" :geometry-position "0.1") ("input2" :is-eq-to "struct_adapter.input" :geometry-side "TOP" :geometry-position "0.5") ("input3" :is-eq-to "gate_2b.input2" :geometry-side "TOP" :geometry-position "0.9") ("output" :is-eq-to "struct_adapterb.output" :geometry-side "BOTTOM" :geometry-position "0.5")) :modules (("gate_2" :is-a "gate-2" :geometry-x "48" :geometry-y "147") ("gate_2b" :is-a "gate-2" :geometry-x "228" :geometry-y "147") ("struct_adapter" :is-a "struct-adapter-gate" :geometry-x "137" :geometry-y "82") ("struct_adapterb" :is-a "struct-adapter-gate" :geometry-x "138" :geometry-y "209")) :links (("struct_adapterbinput_gate_2output" :terminals ("struct_adapterb.input" "gate_2.output" "gate_2b.output") :nodes (("138" "158")) :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil))) ("struct_adapteroutput_gate_2input2" :terminals ("struct_adapter.output" "gate_2.input2" "gate_2b.input1") :nodes (("138" "136")) :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil)))) :variables (("visibility" :value "1")) :parameters( ("gate_2.ignore_in_export" :value "parent.ignore_in_export") ("gate_2b.ignore_in_export" :value "parent.ignore_in_export") ("struct_adapter.ignore_in_export" :value "parent.ignore_in_export") ("struct_adapterb.ignore_in_export" :value "parent.ignore_in_export"))) (define-module :class "gate-3" :super-classes ("gate") :terminals (("input1" :is-a "term-struct-input" :geometry-side "top" :geometry-position "0.1") ("input2" :is-a "term-struct-input" :geometry-side "top" :geometry-position "0.5") ("input3" :is-a "term-struct-input" :geometry-side "top" :geometry-position "0.9") ("output" :is-a "term-struct-output" :geometry-side "bottom" :geometry-position "0.5"))) (define-module :class "gate-4" :super-classes ("gate") :terminals (("input1" :is-a "term-struct-input" :geometry-side "left" :geometry-position "0.5") ("input2" :is-a "term-struct-input" :geometry-side "top" :geometry-position "0.25") ("input3" :is-a "term-struct-input" :geometry-side "top" :geometry-position "0.77") ("input4" :is-a "term-struct-input" :geometry-side "right" :geometry-position "0.5") ("output" :is-a "term-struct-output" :geometry-side "bottom" :geometry-position "0.5"))) (define-module :class "gate-5" :super-classes ("gate") :terminals (("input1" :is-a "term-struct-input" :geometry-side "left" :geometry-position "0.9") ("input2" :is-a "term-struct-input" :geometry-side "left" :geometry-position "0.1") ("input3" :is-a "term-struct-input" :geometry-side "top" :geometry-position "0.5") ("input4" :is-a "term-struct-input" :geometry-side "right" :geometry-position "0.1") ("input5" :is-a "term-struct-input" :geometry-side "right" :geometry-position "0.9") ("output" :is-a "term-struct-output" :geometry-side "bottom" :geometry-position "0.5"))) (define-module :class "gate-6" :super-classes ("gate") :terminals (("input1" :is-a "term-struct-input" :geometry-side "left" :geometry-position "0.9") ("input2" :is-a "term-struct-input" :geometry-side "left" :geometry-position "0.1") ("input3" :is-a "term-struct-input" :geometry-side "top" :geometry-position "0.5") ("input4" :is-a "term-struct-input" :geometry-side "right" :geometry-position "0.1") ("input5" :is-a "term-struct-input" :geometry-side "right" :geometry-position "0.5") ("input6" :is-a "term-struct-input" :geometry-side "right" :geometry-position "0.9") ("output" :is-a "term-struct-output" :geometry-side "bottom" :geometry-position "0.5"))) (define-module :class "activ" :super-classes ("gate") :properties (("abstract" :value "no")) :icon "icons/struct/activ" :terminals (("input1" :is-a "term-struct-input" :geometry-side "top" :geometry-position "0.5") ("output" :is-a "term-struct-output" :geometry-side "bottom" :geometry-position "0.5"))) (define-module :class "and" :super-classes ("gate") :icon "icons/struct/and") (define-module :class "and-2" :super-classes ("and" "gate-2") :properties (("abstract" :value "no"))) (define-module :class "and-2-2" :super-classes ("and" "gate-2-2") :properties (("abstract" :value "no")) :modules (("gate_2" :is-a "and-2") ("gate_2b" :is-a "and-2")) :parameters( ("gate_2.ignore_in_export" :value "parent.ignore_in_export") ("gate_2b.ignore_in_export" :value "parent.ignore_in_export"))) (define-module :class "and-3" :super-classes ("and" "gate-3") :properties (("abstract" :value "no"))) (define-module :class "and-4" :super-classes ("and" "gate-4") :properties (("abstract" :value "no"))) (define-module :class "and-5" :super-classes ("and" "gate-5") :properties (("abstract" :value "no"))) (define-module :class "and-6" :super-classes ("and" "gate-6") :properties (("abstract" :value "no"))) (define-module :class "compound" :super-classes ("struct-library") :icon "icons/struct/comp" :parameters (("input.a" :system-theoretic "real-parameter")) :terminals (("input" :is-a "term-struct-compound" :geometry-side "top" :geometry-position "0.5")) :variables (("defval" :system-theoretic "integer-parameter" :documentation "Default value of the logical state of the reaction. empty = undefined") ("ignore_in_export" :system-theoretic "integer-parameter" :documentation "parameter determining whether the compound is exported to the CellNetAnalyzer. Allowed Values 0 (exported) or 1 (ignored in export), default 0." :value "0") ("map_number" :system-theoretic "integer-parameter" :documentation "parameter determining the map in CellNetAnalyzer. Should be a positive int, default is 1." :value "1") ("textbox_type" :system-theoretic "integer-parameter" :documentation "parameter determining if the textbox in CellNetAnalyzer is editable (1), not-editable (2) or non-visible (3). The default value is 1." :value "1") )) (define-module :class "receptor" :super-classes ("compound") :properties (("abstract" :value "no")) :icon "icons/struct/receptor") (define-module :class "ligand" :super-classes ("compound") :properties (("abstract" :value "no")) :icon "icons/struct/ligand") (define-module :class "kinase" :super-classes ("compound") :properties (("abstract" :value "no")) :icon "icons/struct/kinase") (define-module :class "dummy" :super-classes ("compound") :properties (("abstract" :value "no")) :icon "icons/struct/dummy") (define-module :class "phosphatase" :super-classes ("compound") :properties (("abstract" :value "no")) :icon "icons/struct/phosphatase") (define-module :class "ubiquitin-ligase" :super-classes ("compound") :properties (("abstract" :value "no")) :icon "icons/struct/ubiquitinLigase") (define-module :class "adapter" :super-classes ("compound") :properties (("abstract" :value "no")) :icon "icons/struct/adapter") (define-module :class "transfactor" :super-classes ("compound") :properties (("abstract" :value "no")) :icon "icons/struct/transfactor") (define-module :class "gtpase" :super-classes ("compound") :properties (("abstract" :value "no")) :icon "icons/struct/gpro") (define-module :class "gprotein" :super-classes ("compound") :properties (("abstract" :value "no")) :icon "icons/struct/gpro") (define-module :class "gef" :super-classes ("compound") :properties (("abstract" :value "no")) :documentation "guanine nucleotide exchange factor" :icon "icons/struct/gef") (define-module :class "gap" :super-classes ("compound") :properties (("abstract" :value "no")) :documentation "gtpase activating protein" :icon "icons/struct/gap") (define-module :class "reservoir" :super-classes ("compound") :properties (("abstract" :value "no")) :icon "icons/struct/reservoir") (define-module :class "other" :super-classes ("compound") :properties (("abstract" :value "no"))) (define-module :class "drug" :super-classes ("compound") :properties (("abstract" :value "no")) :icon "icons/struct/drug") (define-module :class "external-stimulus" :super-classes ("compound") :properties (("abstract" :value "no")) :icon "icons/struct/externalStimulus") (define-module :class "phenotype" :super-classes ("compound") :properties (("abstract" :value "no")) :icon "icons/struct/phenotype") (define-module :class "boundary" :super-classes ("gate")) (define-module :class "source" :super-classes ("boundary") :properties (("abstract" :value "no")) :icon "icons/struct/input" :terminals (("output" :is-a "term-struct-output" :geometry-side "bottom" :geometry-position "0.5"))) (define-module :class "drain" :super-classes ("boundary") :properties (("abstract" :value "no")) :icon "icons/struct/output" :terminals (("input" :is-a "term-struct-input" :geometry-side "top" :geometry-position "0.5"))) (define-module :class "not" :super-classes ("struct-library") :properties (("abstract" :value "no")) :icon "icons/struct/not" :terminals (("input" :is-a "term-struct-input" :geometry-side "top" :geometry-position "0.5") ("output" :is-a "term-struct-output" :geometry-side "bottom" :geometry-position "0.5"))) (define-module :class "or" :super-classes ("gate") :icon "icons/struct/or") (define-module :class "or-2" :super-classes ("or" "gate-2") :properties (("abstract" :value "no")) :terminals (("input1" :is-eq-to "activ.input1") ("input2" :is-eq-to "activ2.input1") ("output" :is-eq-to "struct_adapter.output")) :modules (("activ" :is-a "activ" :geometry-x "71" :geometry-y "81") ("activ2" :is-a "activ" :geometry-x "202" :geometry-y "84") ("struct_adapter" :is-a "struct-adapter-gate" :geometry-x "124" :geometry-y "176")) :links (("struct_adapterinput_activ2output" :terminals ("struct_adapter.input" "activ2.output" "activ.output") :nodes (("136" "112")) :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil)))) :parameters( ("activ.ignore_in_export" :value "parent.ignore_in_export") ("activ2.ignore_in_export" :value "parent.ignore_in_export") ("struct_adapter.ignore_in_export" :value "parent.ignore_in_export"))) (define-module :class "or-3" :super-classes ("or" "gate-3") :properties (("abstract" :value "no")) :geometry-width "438" :geometry-height "300" :terminals (("input1" :is-eq-to "activ.input1") ("input2" :is-eq-to "activ2.input1") ("input3" :is-eq-to "activ0.input1") ("output" :is-eq-to "struct_adapter.output")) :modules (("activ" :is-a "activ" :geometry-x "71" :geometry-y "81") ("activ0" :is-a "activ" :geometry-x "290" :geometry-y "85") ("activ2" :is-a "activ" :geometry-x "202" :geometry-y "84") ("struct_adapter" :is-a "struct-adapter-gate" :geometry-x "124" :geometry-y "176")) :links (("struct_adapterinput_activ2output" :terminals ("struct_adapter.input" "activ2.output" "activ.output" "activ0.output") :nodes (("136" "112")) :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil) ("3" "-1" nil)))) :parameters( ("activ.ignore_in_export" :value "parent.ignore_in_export") ("activ0.ignore_in_export" :value "parent.ignore_in_export") ("activ2.ignore_in_export" :value "parent.ignore_in_export") ("struct_adapter.ignore_in_export" :value "parent.ignore_in_export"))) (define-module :class "or-4" :super-classes ("or" "gate-4") :properties (("abstract" :value "no")) :geometry-width "407" :geometry-height "300" :terminals (("input1" :is-eq-to "activ.input1") ("input2" :is-eq-to "activ2.input1") ("input3" :is-eq-to "activ0.input1") ("input4" :is-eq-to "activ1.input1") ("output" :is-eq-to "struct_adapter.output")) :modules (("activ" :is-a "activ" :geometry-x "55" :geometry-y "129") ("activ0" :is-a "activ" :geometry-x "250" :geometry-y "77") ("activ1" :is-a "activ" :geometry-x "330" :geometry-y "127") ("activ2" :is-a "activ" :geometry-x "122" :geometry-y "76") ("struct_adapter" :is-a "struct-adapter-gate" :geometry-x "172" :geometry-y "176")) :links (("struct_adapterinput_activ2output" :terminals ("struct_adapter.input" "activ2.output" "activ.output" "activ0.output" "activ1.output") :nodes (("174" "104")) :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil) ("3" "-1" nil) ("4" "-1" nil)))) :parameters( ("activ.ignore_in_export" :value "parent.ignore_in_export") ("activ0.ignore_in_export" :value "parent.ignore_in_export") ("activ1.ignore_in_export" :value "parent.ignore_in_export") ("activ2.ignore_in_export" :value "parent.ignore_in_export") ("struct_adapter.ignore_in_export" :value "parent.ignore_in_export"))) (define-module :class "or-5" :super-classes ("or" "gate-5") :properties (("abstract" :value "no")) :geometry-width "407" :geometry-height "300" :terminals (("input1" :is-eq-to "activ.input1") ("input2" :is-eq-to "activ2.input1") ("input3" :is-eq-to "activ0.input1") ("input4" :is-eq-to "activ1.input1") ("input5" :is-eq-to "activ3.input1") ("output" :is-eq-to "struct_adapter.output")) :modules (("activ" :is-a "activ" :geometry-x "55" :geometry-y "129") ("activ0" :is-a "activ" :geometry-x "250" :geometry-y "77") ("activ1" :is-a "activ" :geometry-x "330" :geometry-y "127") ("activ2" :is-a "activ" :geometry-x "122" :geometry-y "76") ("activ3" :is-a "activ" :geometry-x "165" :geometry-y "62") ("struct_adapter" :is-a "struct-adapter-gate" :geometry-x "172" :geometry-y "176")) :links (("struct_adapterinput_activ2output" :terminals ("struct_adapter.input" "activ2.output" "activ.output" "activ0.output" "activ1.output" "activ3.output") :nodes (("174" "104")) :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil) ("3" "-1" nil) ("4" "-1" nil) ("5" "-1" nil)))) :parameters( ("activ.ignore_in_export" :value "parent.ignore_in_export") ("activ0.ignore_in_export" :value "parent.ignore_in_export") ("activ1.ignore_in_export" :value "parent.ignore_in_export") ("activ2.ignore_in_export" :value "parent.ignore_in_export") ("activ3.ignore_in_export" :value "parent.ignore_in_export") ("struct_adapter.ignore_in_export" :value "parent.ignore_in_export"))) (define-module :class "somehow" :super-classes ("gate") :documentation " classes to represent incomplete truth tables") (define-module :class "somehow-2" :super-classes ("gate-2" "somehow") :properties (("abstract" :value "no")) :icon "icons/struct/somehow") (define-module :class "somehow-3" :super-classes ("gate-3" "somehow") :properties (("abstract" :value "no")) :icon "icons/struct/somehow") (define-module :class "somehow-4" :super-classes ("gate-4" "somehow") :properties (("abstract" :value "no")) :icon "icons/struct/somehow") (define-module :class "somehow-5" :super-classes ("gate-5" "somehow") :properties (("abstract" :value "no")) :icon "icons/struct/somehow") (define-module :class "struct-model" :super-classes ("module") :documentation "superclass that must be used as a marker for all structural network modules opened in the visual editor")