Python']Python-based geometry preparation and simulation visualization toolkits for STEPS

被引：4

作者：

Chen, Weiliang ^{[1
]}

De Schutter, Erik ^{[1
]}

机构：

[1] Okinawa Inst Sci & Technol, Computat Neurosci Unit, Kunigami, Okinawa 9040495, Japan

来源：

FRONTIERS IN NEUROINFORMATICS | 2014年 / 8卷

关键词：

STEPS; stochastic reaction diffusion simulation; !text type='Python']Python[!/text; geometry preparation; simulation visualization; tetrahedral mesh; Stochastic Simulation Algorithm; MECHANISMS; DIFFUSION;

D O I：

10.3389/fninf.2014.00037

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

STEPS is a stochastic reaction-diffusion simulation engine that implements a spatial extension of Gillespie's Stochastic Simulation Algorithm (SSA) in complex tetrahedral geometries. An extensive Python-based interface is provided to STEPS so that it can interact with the large number of scientific packages in Python. However, a gap existed between the interfaces of these packages and the STEPS user interface, where supporting toolkits could reduce the amount of scripting required for research projects. This paper introduces two new supporting toolkits that support geometry preparation and visualization for STEPS simulations.

引用

页数：11