This is actually something one of my thesis committee members worked on. http://www.cell.com/abstract/S0092-8674(12)00776-3 In silico whole cell models are an extremely new concept, and his study demonstrated its capabilities for one small bacterium. Needless to say, we have a long way to go before we can make top-down simulations of multicellular organisms, much less one as complex as a human. There are many people trying to generate "good enough" simulations for certain human diseases though, by modeling interactions between genes and biomolecules among a few tissues within the relevant organ system.

With regard to your second question, there are many "omics" assays that can now capture e.g. every mRNA, every protein, etc. at a given timepoint but you have to kill the cells. Fluorescence microscopy can work for "movie-like" time resolution on a live cell but you have to label the cellular elements with stains or antibodies and you can only utilize so many of those simultaneously on a single sample (1-5 is typical).