Python as a Federation Tool for GENESIS 3.0
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| Publicado en: | PLoS One vol. 7, no. 1 (Jan 2012), p. e29018 |
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| Otros Autores: | , , |
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Public Library of Science
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| Acceso en línea: | Citation/Abstract Full Text Full Text - PDF |
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| 024 | 7 | |a 10.1371/journal.pone.0029018 |2 doi | |
| 035 | |a 1323090165 | ||
| 045 | 2 | |b d20120101 |b d20120131 | |
| 084 | |a 174835 |2 nlm | ||
| 100 | 1 | |a Cornelis, Hugo | |
| 245 | 1 | |a Python as a Federation Tool for GENESIS 3.0 | |
| 260 | |b Public Library of Science |c Jan 2012 | ||
| 513 | |a Journal Article | ||
| 520 | 3 | |a 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. | |
| 610 | 4 | |a University of Texas | |
| 651 | 4 | |a Texas | |
| 651 | 4 | |a United States--US | |
| 653 | |a Language | ||
| 653 | |a Parallel processing | ||
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| 653 | |a Computational neuroscience | ||
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| 653 | |a Mathematical analysis | ||
| 653 | |a Mathematical morphology | ||
| 653 | |a Software | ||
| 653 | |a Electron microscopy | ||
| 653 | |a Solvers | ||
| 653 | |a Neurosciences | ||
| 653 | |a Graphical user interface | ||
| 653 | |a Perl | ||
| 653 | |a Computer simulation | ||
| 653 | |a Linux | ||
| 653 | |a Neurons | ||
| 653 | |a Computer programs | ||
| 653 | |a Economic | ||
| 653 | |a Architectural engineering | ||
| 653 | |a Programming languages | ||
| 653 | |a Three dimensional models | ||
| 653 | |a Community participation | ||
| 653 | |a Mathematical models | ||
| 653 | |a Connectivity | ||
| 653 | |a Nervous system | ||
| 653 | |a Software engineering | ||
| 653 | |a Biology | ||
| 653 | |a Computer architecture | ||
| 653 | |a Python | ||
| 653 | |a Community involvement | ||
| 700 | 1 | |a Rodriguez, Armando L | |
| 700 | 1 | |a Coop, Allan D | |
| 700 | 1 | |a Bower, James M | |
| 773 | 0 | |t PLoS One |g vol. 7, no. 1 (Jan 2012), p. e29018 | |
| 786 | 0 | |d ProQuest |t Health & Medical Collection | |
| 856 | 4 | 1 | |3 Citation/Abstract |u https://www.proquest.com/docview/1323090165/abstract/embedded/L8HZQI7Z43R0LA5T?source=fedsrch |
| 856 | 4 | 0 | |3 Full Text |u https://www.proquest.com/docview/1323090165/fulltext/embedded/L8HZQI7Z43R0LA5T?source=fedsrch |
| 856 | 4 | 0 | |3 Full Text - PDF |u https://www.proquest.com/docview/1323090165/fulltextPDF/embedded/L8HZQI7Z43R0LA5T?source=fedsrch |