Arbor is a multi-compartment neuron simulation library; compatible with next-generation accelerators; best-practices applied to research software; focussed on community-driven development.


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DSL for higher level network specifications

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We aim to design a high-level, declarative specification of network connectivity for use in simulations of morphologically detailed neurons [1]. Many simulators and network data formats use lists of 1:1 connections to describe and instantiate networks. Sometimes features exist to describe randomized connections and parameters in these connectivity descriptions. We seek to formulate and implement a domain-specific language (DSL), informed by prior art [2,3,4], that can describe such higher level connectivity. The project includes a study of the design space simulators and the requirements of neuroscientists. From this a model should be developed that captures practical users’ needs while building upon a composable structure. The end result is inclusion of this network DSL in Arbor [1], and and perhaps eventual (partial) inclusion in other formats [4].

  1. https://github.com/arbor-sim/arbor/issues/418
  2. https://www.ncbi.nlm.nih.gov/pubmed/22437992
  3. https://www.neuroml.org/
  4. https://github.com/NeuroML/NeuroMLlite/
  5. https://github.com/arbor-sim/arbor

We are estimating this to be a 6-12 month project, suitable for a Master student looking for a thesis-project, or with a optionally increased scope suitable as a side-project for a PhD student or Postdoc with some prior experience. Depending on the candidate and available time we could change the scope as needed. A background in neuroscience, especially in modeling, and experience with other simulation tools is helpful. We require a working knowledge of C++.

If you are interested, please get in touch.