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Readme.md
TO DO List October 2016 * Currently: There is a ReactionRing stored in reactionNetwork hash table. It is created using createRing and it is of the form FF[cc][kk][xx], where cc are parameters used in the stoichiometric equations creation, kk are the reaction rates used in the creation of the steady-state equations, and xx are the concentrations. * We need: The parameters cc and kk to have options for user input and random. How to create this and update the ReactionRing? * This is not necessary. Let's have a unique master ring; let's also flatten the ring, i.e., have FF[cc,kk,xx] * Create an auxiliary function specialize(variables, values), which creates e.g. map(FF[cc,xx],FF[cc,kk,xx],...) that the user may then apply to anything. * (I don't understand how this is different from keeping the kk's as unknown parameters: We also want the option of grouping the parameters kk with the variables xx, thus making kk variables as well.) * Once the ReactionRing is fixed there should be no more changes that will affect the examples we use in MonodromySolver. The rest of the functions are auxiliary. * Create isInjective function * Create reactionMatrix, reactantMatrix, stoichiometricMatrix * Fix laplacian function * Create A matrix * Can we have random, user, and parameter kk's and cc's? * Can we group the kk's with the xx's, i.e. make them variables? * Create examples that demonstrate how to treat the cc's and kk's * Create several examples not within documentation but as stand-alone. * Update documentation and add new functions Summer 2016 * Basic Functions * Constructors (parsing non-HR formats) (Tim) * Print complexes with labels, i.e. 1->A+B, 2->C+2D,... (Chill) * (maybe) Higher level service functions (elimination, etc) * Accessors for Laplacian, other features (Tim) * Examples * Add WNT Shuttle Model (from Elizabeth's Talk) (Chill) * Are there other models to add? * Examples of solving CRN eqns (all) * Elimination, degeneration * High-dimensional solution varieties * Examples using monodromy technique, mixed volumes * Operations * Removing vs eliminating for rxns/comps/species? * Removing species? * Other manips? What do they mean? * Equations * Options for parameters: random values, etc * Observed variables (don't remember what this means, ask E) * Higher level * Multistationarity * Siphons * Finishing Touches? * Documentation