title: BluePyOpt: Leveraging Open Source Software and Cloud Infrastructure to Optimise Model Parameters in Neuroscience.
abstract: At many scales in neuroscience, appropriate mathematical models take the form of complex dynamical systems. Parameterizing such models to conform to the multitude of available experimental constraints is a global non-linear optimisation problem with a complex fitness landscape, requiring numerical techniques to find suitable approximate solutions. Stochastic optimisation approaches, such as evolutionary algorithms, have been shown to be effective, but often the setting up of such optimisations and the choice of a specific search algorithm and its parameters is non-trivial, requiring domain-specific expertise. Here we describe BluePyOpt, a Python package targeted at the broad neuroscience community to simplify this task. BluePyOpt is an extensible framework for data-driven model parameter optimisation that wraps and standardizes several existing open-source tools. It simplifies the task of creating and sharing these optimisations, and the associated techniques and knowledge. This is achieved by abstracting the optimisation and evaluation tasks into various reusable and flexible discrete elements according to established best-practices. Further, BluePyOpt provides methods for setting up both small- and large-scale optimisations on a variety of platforms, ranging from laptops to Linux clusters and cloud-based compute infrastructures. The versatility of the BluePyOpt framework is demonstrated by working through three representative neuroscience specific use cases.
authors.affiliation: Blue Brain Project, École Polytechnique Fédérale de Lausanne Geneva, Switzerland.
authors.forename: Werner
authors.initials: W
authors.lastname: Van Geit
authors.affiliation: Blue Brain Project, École Polytechnique Fédérale de Lausanne Geneva, Switzerland.
authors.forename: Michael
authors.initials: M
authors.lastname: Gevaert
authors.affiliation: Blue Brain Project, École Polytechnique Fédérale de Lausanne Geneva, Switzerland.
authors.forename: Giuseppe
authors.initials: G
authors.lastname: Chindemi
authors.affiliation: Blue Brain Project, École Polytechnique Fédérale de Lausanne Geneva, Switzerland.
authors.forename: Christian
authors.initials: C
authors.lastname: Rössert
authors.affiliation: Blue Brain Project, École Polytechnique Fédérale de Lausanne Geneva, Switzerland.
authors.forename: Jean-Denis
authors.initials: JD
authors.lastname: Courcol
authors.affiliation: Blue Brain Project, École Polytechnique Fédérale de Lausanne Geneva, Switzerland.
authors.forename: Eilif B
authors.initials: EB
authors.lastname: Muller
authors.affiliation: Blue Brain Project, École Polytechnique Fédérale de Lausanne Geneva, Switzerland.
authors.forename: Felix
authors.initials: F
authors.lastname: Schürmann
authors.affiliation: Department of Neurobiology, Alexander Silberman Institute of Life Sciences, The Hebrew University of JerusalemJerusalem, Israel; The Edmond and Lily Safra Centre for Brain Sciences, The Hebrew University of JerusalemJerusalem, Israel.
authors.forename: Idan
authors.initials: I
authors.lastname: Segev
authors.affiliation: Blue Brain Project, École Polytechnique Fédérale de LausanneGeneva, Switzerland; Laboratory of Neural Microcircuitry, Brain Mind Institute, École Polytechnique Fédérale de LausanneLausanne, Switzerland.
authors.forename: Henry
authors.initials: H
authors.lastname: Markram
keywords: bluepyopt; evolutionary algorithm; multi-objective; neuron models; open-source; optimisation; python; synaptic plasticity