Imported:YPM/Brief overview of the organization of the model
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GeneralUsers should not be shy about editing the wiki, especially when adding information, correcting mistakes, and adding comments. See wiki conventions for more information on editing pages. There are four types of pages in the model: reaction pages, parameter pages, species pages, and constraint pages. Within these pages are relevant facts from the literature, including references for every fact. The pages explicitly describe assumptions made in choosing reactions and parameters to include in a model, even if there is no available evidence for the assumptions. These pages contain "machine readable" statements, which are meant to be read by BioNetGen (BNG). These BNG statements are bracketed by a series of defined modeling tags, which are visible when a user edits pages, but are removed when pages are viewed normally in a web browser. These tags can be used to parse the wiki into a BNG file, which can be edited or further processed into an SBML file. A tutorial on how to use BioNetGen can be found on the BioNetWiki. Reaction pagesReactions are grouped together such that related reactions appear on the same page (such as G protein nucleotide hydrolysis and nucleotide exchange). In some cases this grouping is very natural, but due to the complexity of the pathway, in some cases the division into pages is somewhat forced. Reaction pages specify information relevant to the particular reactions of interest. Rule-based reactions are specified based on the facts listed, as well as a series of assumptions that bridge the gap between the what's known and what the reaction rules specify. We use rule-based reactions because complex models can be represented more concisely using rules rather than enumerating all possible instantiations of that rule, especially in the face of combinatorial explosion (see Hlavacek et al. 2006 PMID 16849649). See :Category:Reactions - Yeast Pheromone Response Model or Yeast_pheromone_response_model#Reactions for a complete list of reaction pages. Parameter pagesEach parameter in the model has its own wiki page, and is assigned a value or an expression (a function of other parameters) on its page. Each parameter page also contain a brief summary of the source of the parameter value, our confidence in this value, and a few additional notes including links to the the reaction pages and parameter constraint pages that cite that particular parameter. See :Category:Parameters - Yeast Pheromone Response Model for a complete list of parameter pages. Species pagesProteins in the model each have their own species page. Each species page includes basic information about the protein, links to the reaction pages that involve that protein, and BioNetGen statements to define the protein's binding and modification sites, initial state and initial concentration. See :Category:Species - Yeast Pheromone Response Model or Yeast_pheromone_response_model#Elemental_Species for a complete list of species pages. Parameter constraint pagesThere are two types of parameter constraints in the model: thermodynamic contraints, and simplifying constraints (assumptions). Both types of constraints are detailed on the various constraint pages. Thermodynamic cycles are detailed, assumptions are listed, and we explicitly define independent and dependent (contrained) parameters. The dependent parameters are defined in terms of other independent parameters both in the parameter contraint pages, as well as in their parameter pages. See Yeast_pheromone_response_model#Parameter_Constraint_Assumption_Pages for a complete list of parameter constraint pages. |
