[Neuroml-channels] RFC: channel gates

[Padraig G. <p.g...@uc...>]

Hi,

I suspected you weren't suggesting ditching all the lovely XML on the
website in favour of flat text files...

I agree that the structure of some of the specifications could be
altered to adhere to a consistent usage of attributes, etc. and a
concept of bindable entities would be useful to allow more complex
interactions within compartments. Such an overhaul can wait until after
some attempts to integrate with SBML, etc. to see what the best
framework for these concepts are. I'm also trying at the moment to
incorporate diffusible substances in 3D space (e.g. NO) and their
effects on synaptic mechanisms, etc.

The current form should be flexible enough for most channel files and if
there is a substantially different form for v2.0 an XSL file can be used
to update the existing ChannelML files to the new form.

Regards,
Padraig

P.S. I appreciate the specific functionality of Neurospaces, I meant "a
simulator using Neurospaces as a data container", just lazy typing...




Hugo Cornelis wrote:
> Hi Padraig,
>
>
> Thanks for your answers, read on below.
>
> On 1/15/07, Padraig Gleeson <p.g...@uc...> wrote:
>   
>>> I recently worked on the gate specification for Neurospaces and came
>>> up with something that is quite different from the current NeuroML
>>> specification.  There is a lot of emphasis on consistency and
>>> simplicity.
>>>
>>>       
>> Re the text format below, XML is still a lot easier to parse, and there
>> currently exist portable methods and examples for mappings to
>> Neuron/Genesis/HTML format. Making an XSL file to create a text file
>> like below from any ChannelML file should be relatively straightforward,
>> meaning existing channels could be incorporated into Neurospaces.
>>
>> Re the bindables concept, this should be useful when trying to link
>> interacting subcellular objects (I think it's similar to how the CellML
>> people link objects:
>> http://www.cellml.org/examples/examples/electrophysiological_models/hh_squid_axon_1952/)
>> I've to get some GENESIS3/Moose SBML generating code from Upi and I'll
>> start looking into it then. The first version of that won't be the most
>> stable, but the long term goal is to support a wide range of subcellular
>> processes which could influence channel/synaptic behaviour and which can
>> be mapped to mod/Genesis 2 or 3 and hopefully other simulators like
>> Neurospaces.
>>
>>     
>
> I think my question was not really clear here: the question is not
> about XML vs text formats, but much more about the physical data model
> used to represent a model, independent of the technology used.  In the
> neurospaces description format you just have biological and
> mathematical 'entities with parameters', and it is powerful enough to
> describe the cerebellar cortex network in all its details, including
> the Purkinje cells.  In the current neuroML, there is an extensive
> nesting of elements, and a seemingly arbitrary mix with attributes.
> Both of these two independent issues complicate the standard, and its
> use.  Most of my other questions are indirectly related to the more
> fundamental issue of the data model.
>
> PS1. neurospaces is not a simulator, but a middle-ware data container
> that translates a biological hierarchy into a flat matrix
> representation typically used by solvers.
>
> PS2. I am currently working on the PC model too.  So if that is ok
> with you, we can work together on getting it translated to NeuroML.
>
>
> Again thanks for your answers.
>
>
> Hugo
>
>
>