Metabolomics in Humans, Mice, and Rats

Led by Dr. David Wishart

This subproject, led by Dr. Wishart at the University of Alberta, is building on the existing Genome Canada-funded Metabolomics Toolbox project that is geared to the human metabolome, with in vivo and in vitro metabolomic maps of mice and rats developed through advanced visualization tools using the 4D system. It is developing software to identify and quantify metabolites in tissues and fluids using Nuclear Magnetic Resonance (NMR) or Fourier-Transform Mass Spectrometry (FT-MS) data. These data will be integrated with anatomical models in the CAVE.

This subproject also involves the development of multi-scale simulation tools that allow detailed spatio-temporal visualization of metabolic, proteomic and genomic events at the sub-cellular, supra-cellular and tissue level scale. We are currently adding to the capabilities of two simulation software packages: 1) the Pharmacokinetic Modeling Toolkit (PKMT) and the SimCell system biology simulation environment. The PKMT allows the modeling of drug (and metabolite) kinetics, diffusion and distribution at the organ-scale level, while SimCell allows the modeling of metabolic/proteomic processes at the cellular and sub-cellular level. These software multi-scale visualization/simulation systems will also be integrated into the CaveMan visualization system to permit real-time visualization/simulation of events on the CaveMan platform. Spatio-temporal data on drugs, drug distribution, metabolites and metabolite distributions will continue to be acquired from literature sources and (where necessary) from metabolomic studies conducted on real samples. The literature surveys will be aided by several locally developed text mining tools (PolySearch, BioSpider). These data will serve as the initial or boundary parameters for the simulation studies and they will also form the basis from which to compare our simulations with real data measured from fMRI, PET and other experimental visualization systems.