BioPhysical Modeling

Uhhm hello i have a huge question i am very interested in well cellular or even multi cellular simulations and i have


*cell blender


  • NeuronML

and i am wondering if i could simulate these functions in bge.
some scripts would help maybe if thats not possible a guide to the source code of blender game engine
would surely help

__forgive me for the spelling errors my keyboard is missing keys

Don’t try it, those tools are not meant to be used together.

No one in biophysics uses BioBlender, it is not a serious tool. You can use Gromacs to simulate one protein for one microsecond, at fulll atomic detail, and PyMol or VMD to look at the results. Those are serious tools for working at the atomic level.
Alternatively, you can use NeuroML to model your neurons at the cellular and sub-cellular level. It is quite well-established in the community, but don’t try to derive any atomic details, they will be fantasy.
MCell is not a serious tool, it has had only one success story in the last decade, when it was combined with a large cryo-EM dataset.

I am a scientist working in biophysics (molecular modeling and cryo-EM), and my girlfriend is a neuroscientist, so I know what I am talking about.

thanks i guess but is their a way for someone a mere mortal to do these simulations who are not in a university
like this one seems pretty promising open worm

C. Elegens

the open worm by the way is attempt at a digital organism seems to be pretty promising
please dont condescend to me cause i am not a scientist ive had nothing but snobbery on this site

Wait a second… if you want to use these tools to create art (not science) this is of course perfectly possible :slight_smile: You don’t need to be in a university, just download the stuff and play around.
Just don’t expect to find a cure for cancer or something, people will be very snobbish and condescending if they think you are trying that.

C. elegans is just the Latin name for a roundworm, it is “model organism” because it is widely studied… it isn’t a digital organism! The worm is real and has even been sent into space

oh really their is a complete project on the internet i frequent quite often its on
use google i have no time to post links and yes i know that its round worm and art is a science

is their a way for someone a mere mortal to do these simulations

Can I ask what level of simulation you’re considering? For example, Mcell is built to simulate very fine level phenomena (eg movement of individual glutamate molecules across a synapse), while OpenWorm want to include the fluid dynamics of an intact worm moving through water. Then there’s everything in between: cells, cell-cell interactions, the 302 neurons of its nervous system… If you’re proposing to include all these levels in a BGE simulation, you’d be writing so much code you’d be better off building your own system anyway. Which is what OpenWorm is trying to do.

glad you asked cd38 i have an idea of a semi realistic biological chemical simulation of video game characters i would make the simulated structure of of organs that can effect the character in many ways at the chemical level all the way up to the macroscopic level eg health of the players avatar like eating drinking getting shot or whatever i am also well aware of this game called creatures by steve grand and
his later project grandroids i just want to take it a massive step further to 3d chemical simulations that make up the body im just so used to blender game engine and python :wink:

i guess i should of named this thread how to chemicaly simulate 3d organs in 3d for game characters. ive done a variety of
a bge experiments like a cube that turns toward a cube which pulses values higher than the other cubes i also have breve so am pretty committed to this

Nice project, this OpenWorm, I hadn’t heard of it before. It is something that could work if you simulate at the cellular level, C. Elegans only has ~1000 cells.

Two things that you can’t do:

  • Go down to the molecular level. A cell contains ~ 1 billion protein molecules
  • Scale this up to human. The human body has ~ 100 000 billion cells.

CD38 is right: choose your level of simulation.

oh ive chosen cellular level but… my laptop wont load it the gepeto simulation or even python
and yes no way am i going to make it a human i just intend to make simplified cellular models organs more hearts and lungs less neurons
and decisions. Again at the cellular level not molecular level to resource intensive

^^^Excuse me, but why? Realistically simulating a beating heart by modeling every single cell in it (about 2 billion) requires a massive supercomputer. Even with 1.5 million cores in an IBM Blue/Gene machine, they can barely get to 8-10 beats/minute.

i just intend to simulate 50 cells in organs that are inspired by biology semi accurate cell models in semi accurate or at least biologicaly inspired cells and organs not entirely realistic or not at all look i didnt come here start arguements and stop linking to me articles im well aware of
i think no what i ask or say someone like you bullies are going to shoot me down no matter what so in conclusion this discussion is over
this was a complete waste of my time

Man I hate this keyboard.

My friend, we’ve tried to understand your questions and help you. But if you keep the unteachable attitude you won’t get anywhere on this project, and you’re constantly going to end up on your own. I’m sorry I wasted my time too.

I recommend you use the BGE to visualize whatever you work out rather than to use the bge to run the simulation. This way you cna even decide to use another form of presentation (e.g. VRML …)

Hang on I have a hard to time discerning text from attacks or help I can’t seem to read people’s intentions well on text
But thanks for trying to deal with me though I’m not used to forums

This was kind of a last resort google didn’t help much though books helped a little

No one is attacking you dude. People just trying to help.

While I can’t help you with any of the issues you’ve posted, I just wanted to say that this whole molecular modeling thing is very interesting. I didn’t realise bioblender was a thing. I’ve always wondered how scientists create these wonderful visuals of cells and molecules interacting and creating lovely animations that help normal people (us who don’t have any education in molecular studies) understand what goes on with molecules.

Well, since most of us are horrible artists, we usually rely on resources like . PyMol is an excellent program, unfortunately its author died. I hope that one day there will be a Blender addon that will be a replacement. BioBlender was a huge disappointment for me.