Introduction and request for suggestions
Posted: Fri Feb 13, 2009 7:58 am
We are planning to augment NEURON to implement biochemical reaction-diffusion (RD) as well as facilitated cytoplasmic transport in NEURON. This would involve complementing the present integration of the one-dimensional cable equation with a meshed integration of diffusing reactants in multiple 3D (cytosolic, intranuclear, intravacuolar) and 2D (intramembranous) compartments. For this first iteration of the tool we will not address extracellular diffusion.
We plan to work with the VCELL simulator group (http://www.vcell.org). VCell utilizes some of the same integrators as NEURON (e.g. CVODE) and will provide immediate access to a set of VCML models as well as models specified in the SBML modeling metalanguage. A key difference between VCML and SBML is that VCML supports arbitrary geometries, while SBML has utilized stylized geometries and is only now being extended to full geometries.
Because tool development proceeds most efficiently in the context of real problems and user input, we are very interested in hearing how you might use such a tool in your own research. Do you have modeling projects that involve reaction-diffusion, which you were unable to pursue with NEURON? Or are you aware of important neurobiological problems that are ready to be pursued once such a tool is in place? In either case, we would like to hear from you, and we welcome the opportunity to see how your research questions might help guide the development of NEURON_RD.
Your contribution is invited, if only to vote as in "great idea" or "not needed." To help stimulate discussion, here are some questions that have arisen in our own deliberations:
o How important is it to handle arbitrary geometries?
o How much effort should be put into modeling spines?
o How important is simulation of gene expression? Of microtubule transport?
o Are there other features that may be particularly relevant to neural cells, that may not have been addressed in general cellular modeling?
We plan to work with the VCELL simulator group (http://www.vcell.org). VCell utilizes some of the same integrators as NEURON (e.g. CVODE) and will provide immediate access to a set of VCML models as well as models specified in the SBML modeling metalanguage. A key difference between VCML and SBML is that VCML supports arbitrary geometries, while SBML has utilized stylized geometries and is only now being extended to full geometries.
Because tool development proceeds most efficiently in the context of real problems and user input, we are very interested in hearing how you might use such a tool in your own research. Do you have modeling projects that involve reaction-diffusion, which you were unable to pursue with NEURON? Or are you aware of important neurobiological problems that are ready to be pursued once such a tool is in place? In either case, we would like to hear from you, and we welcome the opportunity to see how your research questions might help guide the development of NEURON_RD.
Your contribution is invited, if only to vote as in "great idea" or "not needed." To help stimulate discussion, here are some questions that have arisen in our own deliberations:
o How important is it to handle arbitrary geometries?
o How much effort should be put into modeling spines?
o How important is simulation of gene expression? Of microtubule transport?
o Are there other features that may be particularly relevant to neural cells, that may not have been addressed in general cellular modeling?