Project Overview
Name of the project
IMPROVED MODEL DESCRIPTION FUNCTIONALITY IN BRIANContributions
The project was done by Vigneswaran C, as his Google Summer of Code - 2020 project, under the guidance of Marcel Stimberg (Primary mentor) and Dan Goodman (Secondary mentor). The project was selected under Brian team and INCF (parent organization)What is this project about?
The project aims to create a standard model description framework for Brian2 that involves collecting all required information from Brian script and represent them in intuitive hierarchy of information using dictionary-like format.Why it is needed?
In Computational Neuroscience, experimentation involves plethora of complex synaptic pathways, parameters and model dynamics and therefore standardizing the way to represent them becomes very important. Also, the representation should not pose software-based syntactic constraints for "general" users. So, the project creates a standard framework for model descriptions and also provide flexibility to build other exporters on top of it. Currently `markdown` export and `NeuroML` export (PR yet to be merged) use the base export to get information about Brian model.Weekly progress
| Week | Highlights | Issue(s) associated | Pull Request(s) associated |
|---|---|---|---|
| 1 | Collect function for NeuronGroup with name, size and Equations |
- | - |
| 2 | Collect function with Events and Identifiers |
brian2tools/issues/25 | brian2tools/pull/30 |
| 3 | Support PoissonGroup and SpikeGeneratorGroup |
brian2tools/issues/25 brian2tools/issues/29 |
brian2tools/pull/30 |
| 4 | Baseexport device | brian2tools/issues/26 | brian2tools/pull/31 |
| 5 | Supporting monitors and run_regularly(). Support multiple run() |
brian2tools/issues/33 | brian2tools/pull/31 brian2tools/pull/34 |
| 6 | Refactor NeuroML export | brian2tools/issues/27 | brian2tools/pull/35 |
| 7 | Refactor NeuroML export and conceptualize human readable export |
brian2tools/issues/27 brian2tools/issues/28 |
brian2tools/pull/35 |
| 8 | Exporter for human readable export using markdown |
brian2tools/issues/28 | brian2tools/pull/37 |
| 9 | Support Synapses | brian2tools/issues/38 | brian2tools/pull/39 |
| 10 | Support Synapses and implement array_cache mechanism |
brian2tools/issues/38 | brian2tools/pull/39 |
| 11 | Support PoissonInput, TimedArray, and Custom user functions |
brian2tools/issues/38 | brian2tools/pull/39 |
| 12 | Finalizing human readable export with mdexport device |
brian2tools/issues/28 | brian2tools/pull/37 |
| 13 | Final stretch: wrapping, documenting and report submission. Showcase: Brian2 examples descriptions using markdown export |
- |
- |