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Is there a computer program that simulates biology on a molecular level? Software that has rules that simulates the rules of molecular-biology?

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What do you mean by "simulates biology on a molecular level"? There are definitely 3D molecule viewers, as well as programs for organic chemistry mechanisms, but not something that encompasses every detail of all living processes ever. – LanceLafontaine Aug 10 '12 at 1:36
    
I am currently working on a numerical model that simulates an evolving population by simulating the molecular interaction regulating gene expression. – Remi.b Dec 24 '15 at 18:26
up vote 19 down vote accepted

There is a recent paper that introduced the first molecular-level whole-cell simulation.

Karr, J.R., Sanghvi, J.C., Macklin, D.N., Gutschow, M.V., Jacobs, J.M., Bolival, B., Assad-Garcia, N., Glass, J.I., & Covert, M.W. (2012). A whole-cell computational model predicts phenotype from genotype. Cell 150:389-401 DOI: 10.1016/j.cell.2012.05.044

The authors combined 28 different sub-modules of various biological processes from the literature. Each one operates at the level of macromolecules, although models them in different ways: some by ODEs, some by logic; some by agent-based approaches. If you want to fool around their code is available online and I wrote a basic introduction/summary of the paper.

Here are some related bio.SE questions motivated by that model:

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Just a very important note, seen what the OP is asking. Simulating one cell is great, but it does not in any way mean that we can currently simulate an entire organism with that same level of detail. – nico Oct 16 '12 at 17:41
    
You might want to check out agent based modeling if you're up to programming your own model. NetLog might be able to help you. – Richard Erickson Dec 24 '15 at 17:02
    
@RichardErickson I am not sure who your comment is directed at, but I think people would struggle to implement models like Karr, Sanghvi et al. in NetLogo. I think it is also a bit misleading to suggest that a completely novice modeler (of the sort that will be just starting with NetLogo) will be in a position to program their own model at the level of detail of Karr & Sanghvi. – Artem Kaznatcheev Jan 7 at 12:13

NAMD is a molecular simulation software system with an extensive, active community of researchers

https://www-s.ks.uiuc.edu/Research/namd/

it has a slick visualization package called VMD

https://www-s.ks.uiuc.edu/Research/vmd/

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I think this is a good answer, more useful than mine. But could you make it a bit more self-contained by saying a bit more about NAMD and maybe including an example reference where it is used in the literature? And why you think it's visualization package is particularly slick. – Artem Kaznatcheev Jan 7 at 12:16

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