R Packages: Combinitorially Complex Equilibrium Model Selection (ccems) performs model selections of equilibriums in general and quasi-equilibriums of enzyme complexes in particular. Estimates of dissociation constants K that best describe a dataset are found by systematically scanning through all possibilities of K being infinity and/or plausibly equal to other K. The automatically generated models are then fitted to data. Automation enables searches of spaces too large to be specified by hand, e.g. spaces generated by combinatorially complex equilibriums. Current limitations are to 2-reactant systems, average protein mass data or enzyme reaction rate data, and systems where total reactant concentrations are approximately known exactly (i.e. reconstituted from purified reactants).
SBMLR includes an SBML-like R model object and functions to share, edit, test, view and analyze models. These functions include saveSBML which exports SBML model objects to SBML level 2 model files; readSBML which imports a limited range of SBML level 2 model files back to SBMLR; saveSBMLR and readSBMLR which exchange SBML objects with SBMLR model definition files used for model editing; simulate which uses lsoda of R’s odesolve package to simulate SBML models; summary which summarizes models, including species and reaction dataframes which contain initial concentrations, initial fluxes, and reaction rate laws; and == which tests the equality of models with respect to these dataframes.
These two packages form a pipeline: data -> enzyme models -> enzyme network models. Latest versions are available here.
Teaching: I will teach a course in Advanced R Programming in the spring of 2010, see EPBI415. Materials created for a course in Integrative Cancer Biology taught in 2005 are available as are May 2008 updates.
Other Links: cv, my departmental webpage, my papers, slides, the case cran mirror, microarray data packages and family photos.
Website maintained by Tom Radivoyevitch .