Re: [DIYbio] Entire Cell Simulator

On Tue, Mar 05, 2013 at 03:27:27PM +0000, David Murphy wrote:
> it's problematic trying to model a whole cell. some of the larger protiens
> are very complex and it can take a super computer days or weeks to
> reasonably accuratly model their behaviour.

M. genitalium work was compartmental. No coordinate tracking
was used.

http://covertlab.stanford.edu/publicationpdfs/Karr2012a.pdf

> A whole cell will have many many large protiens along with a lot of other
> large complex molecules.

The question is what level of detail you're caring about.

> most full cell simulators are just large state machines, they don't model
> the individual molecules but rather the levels of substances which promote
> or inhibit the production of others.

Blue Brain does even less. It seems to be enough.

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