NMODL and JAVA - Compatibilities and interactions

[bouteill]

In <b>'A NEURON Programming Tutorial - part D'</b>, it is mentioned that <i>"in the future it is planned that NMODL descriptions will be replaced by JAVA objects"</i>. Is this implemented? Is it still a project? If not, are there any ways to include Java code into a Neuron model? Thank you!

[ted]

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In 'A NEURON Programming Tutorial - part D', it is mentioned that "in the future it is planned that NMODL descriptions will be replaced by JAVA objects".

You're probably referring to the tutorial by Andrew Gillies and David Sterratt, specifically this
page http://www.anc.ed.ac.uk/school/neuron/t ... /tutD.html

Is this implemented? Is it still a project?

No and no. The chief problem with Java was that it was third-party software whose
existence on any particular computer coudn't be counted on, thanks to the squabble
between Sun and Microsoft, not to mention Sun's inept packaging and distribution--
things may have changed, but the last time I looked at their Java download WWW site,
it was practically intimidating for anyone who isn't pretty tech-savvy.

Java is still usable from NEURON--see below--and some individuals are makiing
productive use of it, but there isn't a Java substitute for NMODL. Those who prefer
not to use NMODL to specify properties of ligand- and voltage-gated channels can
instead use the Channel Builder, a GUI tool that takes advantage of the KSChan
class--see http://www.neuron.yale.edu/neuron/docs for a link to tutorials
on this tool, and also the Programmer's Reference entry on KSChan
http://www.neuron.yale.edu/neuron/stati ... schan.html

If not, are there any ways to include Java code into a Neuron model?

You'll have to get the source code for InterViews and NEURON, and compile them (the
latter with appropriate switches). See http://www.neuron.yale.edu/neuron/install/install.html

Use this Forum's search feature to look for java and you'll find a bunch of hits; whether
any of them are helpful, I cannot guarantee. Google NEURON's WWW site
http://www.neuron.yale.edu/ for Java turns up some links to old documentation. If
neither of those turns up what you need, ask again.

[bouteill]

Thank you very much for responding so fast. I will research in the directions you provided me with. In any case, it does not seem to be as straight forward as plugging C code into NMODL (our intention was to model a multitude of channels and molecular diffusion-reaction). Unfortunately, I did a search using the keyword 'Java' in the forum and did not find anything interesting. I will deepen my research and let you know. Thank you again!