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This project is huge. I'm glad to see it has come this far. It's the first ever simulation of a multi-cellular organism at a really useful detail, presented and

This project is huge. I'm glad to see it has come this far. It's the first ever simulation of a multi-cellular organism at a really useful detail, presented and made available to the masses. It's work like this that is going to help explode the use of citizen scientist work. Imagine being able to run your own experiments on a simulation first without having to buy and breed your own worms. So many more experiments can be carried out, and in parallel too. It's not an exact model yet, but it's getting closer. The end goal is to get the model to the point where if you run an experiment on the virtual worm, you can be certain you'll get the same results on the real worm.

goldfeld 13y ago
I completely agree, while at the same time I wonder if they're not being too ambitious--are there simulations like this but for simpler organisms, preferably that is open source as well? I would love to be able to just inspect and toy around with a cell and its organelles, protein production, etc, in a visual as well as programmatic way. I think that's what's missing (as in I haven't come across it) in getting me into "diy biology" as a hobbyist.
- ohblahitsme 13y ago
  There's this project by Stanford to simulate Mycoplasma genitalium: http://wholecellviz.stanford.edu http://wholecellviz.stanford.edu There's also this, which is part of the project above: http://www.cell.com/abstract/S0092-8674(12)00776-3 http://www.cell.com/abstract/S0092-8674(12)00776-3 The problem is you need to know about tons of stuff before doing anything useful with it. For example, you need to know the biology of M. genitalium (or even what the hell it is) and you need to know at least a little bit about how the biology works (i.e. what is the metabolome? etc.). Then you need to know enough about software to be able to install and get everything running (often with poor documentation). Sometimes you need access to expensive software like Matlab. So I guess that means it's coming, but very slowly and only for people who are in the field, not DIY biologists. This is actually something I'm interested in working in (once I get to grad school).
wdewind 13y ago
> Imagine being able to run your own experiments on a simulation first without having to buy and breed your own worms. So many more experiments can be carried out, and in parallel too. I'm trying to better understand the significance of the project. Can you explain this more? Wouldn't running experiments require similar level detail simulators for whatever you are trying to test?
- ohblahitsme 13y ago
  Usually when you do a genetic experiment, you have a model of how things work in your head, then you do the experiment and test that model on living organisms. It's entirely possible that your model is way off and you get results that don't mean anything. With computational models, we can test hypotheses (the models in our heads) much faster (don't have to wait for the worms to grow up) and much cheaper (we can do it on the computers all of us already own).
  - wdewind 13y ago
    Gotcha, makes sense. Very cool, thanks.
scottfr 13y ago
I'm sorry, but this sounds like a fantasy land. I am extremely skeptical that you could get a detailed and accurate enough simulation to reveal any useful novel results. The list of "unknown unknowns" that we don't even know about, yet alone are able to attempt to simulate, is impossibly large. This reminds me of the old Star Trek episodes where they would simulate the effect of the new-fangled quantum-slipstream-tachion-whatever-warp-drives in their Holodeck and then obtain meaningful results. Of course, that was nonsensical fiction. I don't see how this could be different. Simulations and models need to be incredibly focused. The art of modeling is figuring out what to exclude from the model, not what to include. Any attempt to make a really general purpose model/simulation is almost bound to overreach and fail.
- Lambdanaut 13y ago
  This model is definitely excluding a lot of details. For instance, the cells are modeled on an abstract functional basis. There isn't any cellular division occuring and it's going to take a lot more work to ever get to that level. For purely simulating behavior and understanding how the insides of the worm "function together", this model is a fantastic breakthrough. I perhaps was being hyperbolic with my original description of the worm being a catch-all for any experimentation whatsoever, but you have to admit that it has vast implications. (You also don't deserve the downvote you got. We always need somebody anchoring us to reality. )
  - eaevans99 13y ago
    Outside of the germline, C. elegans does not undergo cellular division in the adult stage. There is a fixed developmental pattern, with exactly 959 cells in the adult hermaphrodite. Also, the connectivity map of the entire nervous system is known.
    - Lambdanaut 13y ago
      Thanks for clearing that up! I do believe that this is a permanent showstopper for modeling C. Elegans reproduction, correct? I would be very curious to hear if there have been any plans to one day re-visit the model to allow reproduction, and if any thought has gone into how that process could be allowed!
zavi 13y ago
Is it fair to say that such project would have difficulty raising funds from traditional academic sources like NSF?

goldfeld 13y ago

I completely agree, while at the same time I wonder if they're not being too ambitious--are there simulations like this but for simpler organisms, preferably that is open source as well? I would love to be able to just inspect and toy around with a cell and its organelles, protein production, etc, in a visual as well as programmatic way. I think that's what's missing (as in I haven't come across it) in getting me into "diy biology" as a hobbyist.

ohblahitsme 13y ago
There's this project by Stanford to simulate Mycoplasma genitalium: http://wholecellviz.stanford.edu http://wholecellviz.stanford.edu There's also this, which is part of the project above: http://www.cell.com/abstract/S0092-8674(12)00776-3 http://www.cell.com/abstract/S0092-8674(12)00776-3 The problem is you need to know about tons of stuff before doing anything useful with it. For example, you need to know the biology of M. genitalium (or even what the hell it is) and you need to know at least a little bit about how the biology works (i.e. what is the metabolome? etc.). Then you need to know enough about software to be able to install and get everything running (often with poor documentation). Sometimes you need access to expensive software like Matlab. So I guess that means it's coming, but very slowly and only for people who are in the field, not DIY biologists. This is actually something I'm interested in working in (once I get to grad school).

wdewind 13y ago

> Imagine being able to run your own experiments on a simulation first without having to buy and breed your own worms. So many more experiments can be carried out, and in parallel too. I'm trying to better understand the significance of the project. Can you explain this more? Wouldn't running experiments require similar level detail simulators for whatever you are trying to test?

ohblahitsme 13y ago
Usually when you do a genetic experiment, you have a model of how things work in your head, then you do the experiment and test that model on living organisms. It's entirely possible that your model is way off and you get results that don't mean anything. With computational models, we can test hypotheses (the models in our heads) much faster (don't have to wait for the worms to grow up) and much cheaper (we can do it on the computers all of us already own).
- wdewind 13y ago
  Gotcha, makes sense. Very cool, thanks.

scottfr 13y ago

I'm sorry, but this sounds like a fantasy land. I am extremely skeptical that you could get a detailed and accurate enough simulation to reveal any useful novel results. The list of "unknown unknowns" that we don't even know about, yet alone are able to attempt to simulate, is impossibly large. This reminds me of the old Star Trek episodes where they would simulate the effect of the new-fangled quantum-slipstream-tachion-whatever-warp-drives in their Holodeck and then obtain meaningful results. Of course, that was nonsensical fiction. I don't see how this could be different. Simulations and models need to be incredibly focused. The art of modeling is figuring out what to exclude from the model, not what to include. Any attempt to make a really general purpose model/simulation is almost bound to overreach and fail.

Lambdanaut 13y ago
This model is definitely excluding a lot of details. For instance, the cells are modeled on an abstract functional basis. There isn't any cellular division occuring and it's going to take a lot more work to ever get to that level. For purely simulating behavior and understanding how the insides of the worm "function together", this model is a fantastic breakthrough. I perhaps was being hyperbolic with my original description of the worm being a catch-all for any experimentation whatsoever, but you have to admit that it has vast implications. (You also don't deserve the downvote you got. We always need somebody anchoring us to reality. )
- eaevans99 13y ago
  Outside of the germline, C. elegans does not undergo cellular division in the adult stage. There is a fixed developmental pattern, with exactly 959 cells in the adult hermaphrodite. Also, the connectivity map of the entire nervous system is known.
  - Lambdanaut 13y ago
    Thanks for clearing that up! I do believe that this is a permanent showstopper for modeling C. Elegans reproduction, correct? I would be very curious to hear if there have been any plans to one day re-visit the model to allow reproduction, and if any thought has gone into how that process could be allowed!

zavi 13y ago

Is it fair to say that such project would have difficulty raising funds from traditional academic sources like NSF?