NeuroML 2 checklist

What’s needed for NeuroML 2?

The following was originally a list of items required for the NeuroML v2.0 beta release. Most of these are complete, and we're gradually moving these to issues here and here for easier tracking.

It's not everything that will be needed for NML2, but will be an important milestone for encouraging developers to take up v2.0.

Essential

• Schema/LEMS definition files moved from SourceForge to GitHub: https://github.com/NeuroML/NeuroML2.

• NML2 LEMS definitions working with latest https://github.com/LEMS/jLEMS (moved from https://github.com/robertcannon/jLEMS).

• PyLEMS (https://github.com/LEMS/pylems, moved from https://github.com/lisphacker/pylems) supporting the above examples using same form of LEMS. Mostly done, see here.

• http://www.neuroml.org/NeuroML2CoreTypes/Cells.html as core documentation for NML2 types ; links to appropriate place in Schema/direct to LEMS definition files/NML examples should be added.

• ChannelML->NML2 converter taking metadata info from NeuroML v1.8.1 files & putting it in NML 2 ionChannel etc. as RDF elements (e.g. see this example). Status: started, see here.

• GHK stabilised & supported in at least 2 models (see here and here); updated in Schema doc; checked by Robert, Avrama & others. See also https://github.com/OpenSourceBrain/ghk-nernst.

• Finalise folder structure for generated NeuroML 2 models in OSB (e.g. NeuroML2 directory in top level in every project); have multiple OSB projects with NeuroML2 dirs containing valid NeuroML 2 files.

• Support mapping of channels with parameters element in v1.8.1 to NML2; allow overwriting of parameters in channelDensity element, e.g. see use of vhalfl here (this doesn’t yet work...): http://www.opensourcebrain.org/embedded/ca1pyramidalcell/cellMechanisms/hd.nml.html http://www.opensourcebrain.org/embedded/ca1pyramidalcell/cellTypes/SomaOnly_hd.nml.html In progress, see issues here and here.

• Complete support for (& examples of) instance based networks in NML2, including locations & segment specific connections; connections in population element. Related to above point. See example here. Generally complete, see here.

• Rename old Java based libNeuroML; integrate well with other Java packages here . Complete, see https://github.com/NeuroML/jNeuroML. Update info pages to explain full Python & Java libraries; see http://www.neuroml.org/neuroml2.php.

• https://github.com/NeuralEnsemble/libNeuroML updated to latest Schema; using Python preferred method names for API; updated generateDS.py generating core API directly from Schema. Completed recently by @vellamike.

Good to have

• STDP checked & implemented

• Morris Lecar finalised & incorporated

Probably not by beta release, needed for final release

Synapse centred network description.

Info on this moved to: https://github.com/NeuroML/NeuroML2/issues/18.