Abstract
The GENESIS simulation platform was one of the first broad-scale modeling systems in computational biology to encourage modelers to develop and share model features and components. Supported by a large developer community, it participated in innovative simulator technologies such as benchmarking, parallelization, and declarative model specification and was the first neural simulator to define bindings for the Python scripting language. An important feature of the latest version of GENESIS is that it decomposes into self-contained software components complying with the Computational Biology Initiative federated software architecture. This architecture allows separate scripting bindings to be defined for different necessary components of the simulator, e.g., the mathematical solvers and graphical user interface. Python is a scripting language that provides rich sets of freely available open source libraries. With clean dynamic object-oriented designs, they produce highly readable code and are widely employed in specialized areas of software component integration. We employ a simplified wrapper and interface generator to examine an application programming interface and make it available to a given scripting language. This allows independent software components to be ‘glued’ together and connected to external libraries and applications from user-defined Python or Perl scripts. We illustrate our approach with three examples of Python scripting. (1) Generate and run a simple single-compartment model neuron connected to a stand-alone mathematical solver. (2) Interface a mathematical solver with GENESIS 3.0 to explore a neuron morphology from either an interactive command-line or graphical user interface. (3) Apply scripting bindings to connect the GENESIS 3.0 simulator to external graphical libraries and an open source three dimensional content creation suite that supports visualization of models based on electron microscopy and their conversion to computational models. Employed in this way, the stand-alone software components of the GENESIS 3.0 simulator provide a framework for progressive federated software development in computational neuroscience.
Highlights
The GEneral NEural SImulation System (GENESIS, http:// genesis-sim.org/) is a general purpose simulation platform originally developed to support the simulation of neural systems ranging from sub-cellular components and biochemical reactions to complex models of single neurons, simulations of large networks, and systems-level models.GENESIS was one of the first broad scale modeling systems in computational biology to encourage modelers to develop and share model features and components
We introduce two scripting languages employed by GENESIS 3.0 (G-3) (Python and Perl) and a simplified wrapper and interface generator (SWIG)
With the increased sophistication of the Python platform and reconfiguration of GENESIS to comply with the CBI architecture, Python interfaces have been developed for several of G-3’s core simulator components
Summary
GENESIS was one of the first broad scale modeling systems in computational biology to encourage modelers to develop and share model features and components For these people, it was the object-oriented approach taken by the simulator along with its high-level simulation language and Script Language Interpreter (SLI), that allowed the exchange, modification, and reuse of models or model components. It was the object-oriented approach taken by the simulator along with its high-level simulation language and Script Language Interpreter (SLI), that allowed the exchange, modification, and reuse of models or model components It was this community of developers and users that drove the development of the GENESIS platform. The unitary nature and density of the source code has created a‘monolithic’ application This marginalizes user contributions to simulator functionality, updates and releases have become less frequent, and the software life cycle is moved from extension to maintenance
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