Entire Cell Simulator

[Koeng]

Just wanted to know if there was any of these that are open source. I believe I read someone that Craig Venter institute made one... Anyway this would be a great project for anyone with knowledge of computers :)

Also is there any simulation programs with the potential to become entire cell simulations? thanks in advance :D

-Koeng

[Andrew Hessel]

This is the best to date that I am aware of:

http://wholecell.stanford.edu/

Sent from my neural interface.

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[Koeng]

Thanks :D I am downloading the virtual machine.

Although I was kinda wondering about cell simulation on the molecular scale... Like a program that folds proteins inside a simulated cell and all the chemicals react with each other and this stuff. I think this would take too much computing power though

[Eugen Leitl]

The best result I'm aware of is http://www.sciencedirect.com/science/article/pii/S0092867412007763

On a much higher layer there's http://www.openworm.org/ and other projects.

[Eugen Leitl]

On Mon, Mar 04, 2013 at 09:38:24PM -0800, Koeng wrote:

> Although I was kinda wondering about cell simulation on the molecular
> scale... Like a program that folds proteins inside a simulated cell and all

You don't know what you ask for. The fastest thing on Earth for
that should be currently http://en.wikipedia.org/wiki/Anton_(computer)
and it's limited to short times (17 us) and reasonably
small systems (23 kAtoms).

A nice package to play with is VMD/NAMD http://www.ks.uiuc.edu/Research/namd/
which also has GPGPU support (you're probably got to need that,
unless you've got a few kNode Beowulf in your basement).

> the chemicals react with each other and this stuff. I think this would take
> too much computing power though

You can say that again. And MD is a very high level of theory,
things turn awful fast as you reach down.

[David Murphy]

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.

 

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

 

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.

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[Eugen Leitl]

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.