Features¶
Arbor is fully featured, ready for real world modelling, and the user community is busy collaborating with us to build complex models. Best practices, tips, tricks and howtos will be documented here as the community gains experience.
Features include:
Arbor GUI: a fully featured GUI for single cell construction.
Support for a range of fileformats, including NMODL and NeuroML by way of NMLCC, a fully featured NeuroML converter for Arbor targets.
Nascent SONATA format support. The Allen mechanism database is already included in Arbor, so currently, with some manual work executing Allen models is already possible, see A single cell model from the Allen Brain Atlas.
Voltage Processes in the form of a mechanism kind. Useful for e.g. implementing voltage clamps.
Stochastic Differential Equations: both point and density mechanisms may now use white noise as part of the state updates, turning the ODEs effectively into SDEs.
Mutable connection table: the connection table can be redefined between successive phases of simulation.
Edit morphologies using Arbor API, useful for e.g. merging segment trees.
BluePyOpt integration. Parameter optimization using BluePyOpt can be done through an Arbor backend and exported to an Arbor cable cell, see this tutorial.
Inhomogeneous parameters: enables painting of scaled density mechanisms, e.g. scale with the distance from the root. (nmodl:
iexpr.)LFPyKit integration: extract extracellular signals from an Arbor cable cell.
Axial Diffusion: ions can now propagate along the dendrite by diffusion and be received by other synapses, modifying their weight upon reception.Xd can be read from and written to by NMODL density and point mechanisms. See this LaTeX file for a mathematical description of Arbor’s implementation.
Mechanism ABI, allowing for users to package their mechanism catalogues.
Built-in profiler, which enables users to quickly understand where their experiment is spending most of its time.
Faster NMODL programming guide: helps users write NMODL with performance and fewer bugs in mind.
Modelling¶
Most of the Arbor community lives in our Gitter channel, and modellers convene weekly to discuss how to use or identify missing features in a vide chat. Please join!
Under the arbor-contrib organisation, some users have shared their models. You can peruse these at your leisure, and of course add yours if you like to share! Please contact us to have your model added to our list.