Imported:YPM/Modeling tags
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OverviewThe BNG statements in the wiki are bracketed by a series of defined modeling tags, which are interpreted by a custom MediaWiki extension (ModelExtension.php) and removed completely when the HTML page is rendered (so there is no trace of the modeling tags when the page is viewed in a web browser. A Python script is then able to traverse the wiki (by retrieving the 'edit' pages instead of the normal 'article' pages) and parse out the modeling statements based on these modeling tags and process these statements into a valid BNG file. There are 4 classes of tags used, corresponding to 4 modeling blocks in BNG files: reaction tags, parameter tags, molecule type tags, and seed species tags. Reaction tagsThe reaction rule statements are comprised of several parts: the reaction rule itself and any parameters that apply to that rule. Based on the type of reaction (unidirectional, reversable, degradation, Michaelis-Menten, etc), the reaction rule may have one or two relevant parameters. The ensemble of the reaction rule and the parameters is bracketed by <modelRxnFull> tags. These tags enclose a set of reaction rules, and parameters that apply to these rules. The rules are bracketed by <modelRxnRule> tags, and the parameters are bracketed with <modelRxnParam> tags. The parameters are applied to each reaction rule within the <modelRxnFull> tags. The text within the <modelRxnFull> tags that is not bracketed by the reaction rule or reaction parameter tags is ignored when the page is being traversed to build the BNG file. Parameter tagsThe parameter tags are used on parameter pages to define parameters, and assign them either a value or an expression (as a function of other parameters). <modelParameter> tags enclose the parameter assignment. Molecule type tagsMolecule type tags are used on species pages to define the binding sites and all possible modifications of molecules/proteins in the model. <modelMoleculeType> tags enclose the molecule type definitions. Seed species tagsSeed species tags are used on species pages to define the initial states and concentrations of species to be used a seed species (present at t = 0) in the model. <modelSeedSpecies> tags enclose the seed species definitions. Currently, the individual molecules/proteins are used as the seed species (with their expected concentration used as the initial concentration), rather than using complexes involving multiple proteins/molecules. Thus the starting point of a simulation does not represent the steady state in the absence of pheromone, but represents some non-steady state point that must be allowed to equilibrate. |
