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A python library for simulating small networks of multicompartmental neurons
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morphforge is a high level, simulator independent, Python library for building simulations of small populations of multi-compartmental neurons, in which membrane voltage is calculated from the sum of individual ionic currents flowing across a membrane. It was built as part of Mike Hull’s Ph.D thesis; investigating the role of electrical coupling in small populations of interneurons in Xenopus laevis tadpoles. The use-case of the API is to allows the user to quickly construct simulations of small populations of neurons and synaptic connections, with particular focus on: * allowing simulation specification, with visualisation and analysis in a minimal, clean, human readable language; * reduction of complex simulation tool chains to a single python script; * promoting reproducible research through automatic self-documentation; * encourage the re-use of components such like morphologies, neurons and channels such so that specific and stochastic variation in parameters is simple; * transparent handling of different units; * allowing the use of established formats, (e.g. NEURON nmodl files), but also simplify the definition and sharing of new channel types easily, including the possibility to support other libraries and standards easily (e.g. PyNN, 9ML, NeuroML, CSA) Morphforge is not a simulator; it is a high layer interface to simulators (currently NEURON), providing a set of high-level primitives for specifying morphologies, channel distributions, synapses, in python. It was designed to remove a lot of tedious code currently needed to specify such simulations and what to record from them and provides an API to make visualising results simpler. For more information, please visit the documentation: morphforge.rtfd.org