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Instead of the currently used IzhikevichCell model.

Include RateML in the list of related tools/standards also.

The right hand TOC does not scroll, goes out of the page, and covers the right nav button on long pages, like the schemas.

https://github.com/NeuralEnsemble/NeuroinformaticsTutorial/blob/master/Exercises/Exercise1_NeuroMorpho_to_OSB.md needs to be imported to the docs. At the moment, we link to it.

The page needs to be checked for correctness also. For example, does the Java applet run? Does CVapp still work or is there a replacement?

Finally, what's the long term plan here (post OSBv1?)

This is primarily for OSBv1 where the file type is detected by the name of the file.

• cell files should be named *.cell.nml
• network files should be named *.net.nml
• ?

What should we do with the main slider and its images? 🤔

Worth looking into whether better sized logos are available for the funding bodies.

It's set up already but needs completing.

The text has been migrated but needs to be checked for correctness.

@pgleeson : you'll have to do this, assigning to you 😄

Copy over the how-to guides from here which cover conversion of models to NeuroML.

It'll be good to somehow link the definitions in the schemas to examples (XML or Python?) so users can quickly see how they are to be used.

For example: https://github.com/NeuroML/NeuroML2/blob/master/examples/NML2_FullNeuroML.nml#L46

Most are to be referred in the /../.../... form following the document hierarchy. Some components where a size is provided are to be referenced using the [..] index notation. It'll be good to document this somewhere so it is clear to users.

These need to be checked to see if they have changed.

Keywords aren't in different colours in Python snippets etc., so perhaps we need to choose a different Pygments theme.

We need to check if the images on the landing page here are up to date or if we want to tweak/update them:

https://neuroml.github.io/Documentation/Landing.html

(This will be the first thing people will see, so these images need to be right.)

At the moment, we show some XML examples, but since we want users to use Python, we need to link to the Python libNeuroML api documentation also.

Since NeuroML is about re-use, a page listing how people can share NeuroML models would be nice:

• neuroml-db.org
• OSB
• modeldb
• ...?

Or perhaps we add this all to the "finding NeuroML models" page?

https://docs.neuroml.org/Userdocs/FindingNeuroMLModels.html

@pgleeson : what do you think?

This will help users learn that they can interact with NeuroML using Python, and that they do not have to work with XML files directly.

The sources are included here, but the page needs more information and introductory/explanatory text.

@pgleeson : I'm afraid I don't know enough about the full eco-system to complete this. Assigning to you for the moment.

See: NeuroML/NeuroML2#136

They should work out of the box, but it is possible that they don't work in all HTML tags or something of the sort.

This always seems to fail for some reason, and since we don't have access to all the logs, this is particularly hard to debug. For the time being, I've disabled the execution of the books on GitHub actions. We'll look into this later.

This needs to be right at the front so that it's the first thing visible to anyone that comes to the NeuroML web-space. It could either go in the docs, or the new landing page that we're planning to add.

It's sort of an elevator speech that tells the reader the advantages of using NeuroML.

• modular
• standardised
• structured
• which makes validation, visualisation etc. in-built features of the system
• simulator independence: write in NeuroML and simulate in whatever simulator backend.

We had a few questions about writing new mechanisms etc. in LEMS, so a page on this would be useful.

https://docs.neuroml.org/Userdocs/NeuroMLv2.html needs review.

A CoC needs to be drafted and added to the docs.

Some coretypes do have example snippets but these aren't picked up by the generator script. This needs to be investigated.

For example, there are lines using spike in the example for spikeArray, but they're not picked up as examples for spike itself.

https://docs.neuroml.org/Userdocs/Schemas/Inputs.html?highlight=spikes#spikearray

Thought: this maybe because I pick bits from the start tag to the end tag, so single lined tags that do not have start and end tags may not be picked.

It isn't obvious or intuitive how one should record information from simulations, such as spike times or membrane potentials (or other quantities). So a page that gives an overview of how to refer to different things would be useful.

The recording bit also should be explained in each example so people can use them as reference.

Are these usable/stable/maintained? They haven't seen commits in the last few years from the looks of it.

If these are not actively maintained, we shouldn't put them in the same place as the other supported tools since we don't want users using these (and then opening issues/asking questions that we won't be able to help with). A separate page for "other tools" or "tools under development" would work best perhaps?

Follow these steps: https://jupyterbook.org/publish/gh-pages.html

Search terms aren't highlighted on the page.

This includes the different LEMS bits that are required to simulate the NeuroML model. It'll go under NeuroMLv2.

We should be able to use generateast.py for this too, but it'll have to go in a different location so a few tweaks may be needed.

Add a table here that summarises what the different simulators support.

Then go into more details for each simulator.

This page:

https://neuroml.github.io/Documentation/NeuroMLOrg/Funding.html

Source: https://github.com/NeuroML/Documentation/edit/master/source/NeuroMLOrg/Funding.md

A section that details how one can export models developed in the NEURON simulator into NeuroML is required.

https://neuroml.org/neuron_tools

See also: https://github.com/NeuroML/pyNeuroML/tree/master/pyneuroml/neuron

Synapses has a few of these:
https://github.com/NeuroML/NeuroML2/blob/master/NeuroML2CoreTypes/Synapses.xml#L86

Perhaps useful for new users?

What are we to use?

• pyNeuroML or PyNeuroML (git repo uses pyNeuroML)
• pyLEMS or PyLEMS (git repo is called pylems but the read me uses PyLEMS)

Ideally, these should be consistent in the docs, and on PyPi etc.

Since it's jLEMS etc., perhaps we settle on pyNeuroML and pyLEMS? I'll use these for the time being.

A page that details the different ways in which NeuroML models may be created is required.

Linked issues:

• exporting from Neuron (#27 )
• converting conductance based models (#31 ), which is about copying over the howto section from the Google doc here.

It'll be good to wrap the XML/Python code snippets so that users don't have to scroll horizontally.

Should hopefully be doable in jupyter-book.

Copy over the contents.

We'll use the OLM cell from here for this example:

https://github.com/mbezaire/ca1/blob/master/NeuroML2/

The hoc file is here: https://github.com/mbezaire/ca1/blob/master/cells/class_olmcell.hoc

Before visualising and simulating, models need to be validated to check them for correctness.

For commonly asked questions, that we mark using the "question" tag, it'll be good to collect them in the docs in a FAQ page.

I've added one here now with an example FAQ page:

https://github.com/NeuroML/Documentation/blob/master/source/Userdocs/FAQ.md

The generated schema pages need to be tweaked.

See: NeuroML/NeuroML2#138

https://www.neuroml.org/tool_support has been slightly updated recently, but there are a number of new NeuroML compliant sw applications/libraries/databases that could be added!

Source of page: https://github.com/NeuroML/NeuroMLWebsite/blob/master/app/views/welcome/tool_support.html.erb

Add to retitled heading Core NeuroML libraries

• https://github.com/NeuroML/NeuroMLlite

Add subheading Supporting Databases/Neuroinformatics Resources and add

• Open Source Brain
• NeuroML-DB
• Move Neuromorpho here
• https://github.com/OpenSourceBrain/BlueBrainProjectShowcase
• https://github.com/OpenSourceBrain/AllenInstituteNeuroML
• MouseLight? https://github.com/OpenSourceBrain/MouseLightShowcase

Add to Other applications with NeuroML support

• NetPyNE
• Brian (PyNN & pointer to https://github.com/OpenSourceBrain/BrianShowcase)
• Sonata NeuralEnsemble/Networks_SIG#1
• NineML (!) NeuralEnsemble/Networks_SIG#6
• SpineML (see above)
• NEST (PyNN & pointer to https://github.com/OpenSourceBrain/NESTShowcase)
• XPP
• SEDML

Add heading Legacy software

• Add paragraph stating "The following software has previously had NeuroML support, but may no longer be maintained"
• Move any applications with broken links here...

This will discuss the OMV bits

• neurolex bits
• more bits like this: https://github.com/OpenSourceBrain/OSB_API/blob/master/python/examples/granulecell.xml

We need Java on the platforms to run jnml.