@@ -47,9 +47,9 @@ Rq: The distinction between pivp_string and pivp_list is not always obvious.
:-use_module(reaction_rules).
:-use_module(util).
:-doc('Biocham can also compile mathematical expressions and solutions of polynomial differential equations into biochemical reaction networks using only positive concentration values.').
:-doc('The Turing completeness of continuous CRNs \\cite{FLBP17cmsb} states that any computable function over the reals can be computed by a CRN over a finite set of molecular species. Biocham uses the proof of that result to compile any computable real function presented as the solution of a polynomial differential equation system into a finite CRN. The restriction to reactions with at most two reactants is an option.').
:-devdoc('\\begin{todo} Implement the decomposition into at most binary reactions as an option.\\end{todo}').
:-doc('BIOCHAM models can also be defined by influence systems with forces, possibly mixed to reactions with rates.').
:-doc('In the syntax described by the grammar below, one influence rule (either positive "->" or negative "-<") expresses that a conjunction of sources (or their negation after the separator "/" for inhibitors) has an influence on a target molecular species. This syntax necessitates to write the Boolean activation (resp. deactivation) functions of the molecular species in Disjunctive Normal Form, i.e. with several positive (resp. negative) influences in which the sources are interpreted by a conjunction \\cite{FMRS16cmsb}.').
:-doc('In the syntax described by the grammar below, one influence rule (either positive "->" or negative "-<") expresses that a conjunction of sources (or their negation after the separator "/" for inhibitors) has an influence on a target molecular species. This syntax necessitates to write the Boolean activation (resp. deactivation) functions of the molecular species in Disjunctive Normal Form, i.e. with several positive (resp. negative) influences in which the sources are interpreted by a conjunction \\cite{FMRS18tcbb}.').
%%%%% Generate the influence graph with the reactions as labels
multistability_graph:-
biocham_command,
doc("Creates the influence graph of the current model (same as \\command{influence_graph/1}) with the arcs labelled with the reactions they originate from"),
doc("Creates the influence graph of the current model (same as \\command{influence_graph/1}) with the arcs labelled with the reactions they originate from \\cite{BFS18jtb}"),
option(force_graph,yesno,ForceMultistabilityGraph,'Force the creation of the graph'),
all_items([kind:graph],AllGraphs),
(
...
...
@@ -931,8 +931,8 @@ check_acyclicity :-
check_multistability:-
biocham_command,
doc('Check the multistability of the current model by reducing the multistability graph and finding positive feedback loops that can lead to multistability.
Graphs that do not contain any positve feedback loop cannot exhibit multiple steady states.
doc('Check the multistationarity of the current model by reducing the multistability graph and searching positive feedback loops that can lead to multistability.
Models that do not contain any positive feedback loop cannot exhibit multiple steady states \\cite{BFS18jtb}.
\\item reaction networks (i.e. Feinberg's Chemical Reaction Networks, CRNs, compatible with SBML)
\\item influence networks (variant of Thomas's regulatory networks, compatible with qualSBML).
\\end{itemize}
Both types of models can be combined and interpreted in a hierarchy of semantics, including the differential semantics (Ordinary Differential Equations), stochastic semantics (Continuous-time Markov Chain), Petri net semantics, and Boolean semantics including several variants defined by options \\cite{FMRS16cmsb}.").
Both types of models can be combined and interpreted in a hierarchy of semantics, including the differential semantics (Ordinary Differential Equations), stochastic semantics (Continuous-time Markov Chain), Petri net semantics, and Boolean semantics including several variants defined by options \\cite{FMRS18tcbb}.").
:-doc('Biocham can compile a GPAC circuit (Shannon\'sGeneralPurposeAnalogComputer)intoanabstractreactionnetworkusingpositiveaswellasnegativeconcentrationvalues.OnlyweakGPACs,inwhichtheintegrationgateiswithrespecttotimeandnotavariable,areconsidered.Thevariablesassociatedtothedifferentpointsofthecircuitscanbenamedwiththe"::"operator.Dydefaulttheyarenamedx0,x1,...ThesyntaxofweakGPACcircuitsisasfollows:').
:-doc('Biocham can compile a GPAC circuit (Shannon\'sGeneralPurposeAnalogComputer)intoanabstractCRNusingpositiveaswellasnegativeconcentrationvalues.OnlyweakGPACs,inwhichtheintegrationgateiswithrespecttotimeandnotavariable,areconsidered.Thevariablesassociatedtothedifferentpointsofthecircuitscanbenamedwiththe"::"operator.Dydefaulttheyarenamedx0,x1,...ThesyntaxofweakGPACcircuitsisasfollows:').