Cargando…

SBML and MathML support for the stochastic reaction-diffusion simulator STEPS

Detalles Bibliográficos
Autores principales:	Hepburn, Iain, Chen, Weiliang, De Schutter, Erik
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2011
Materias:	Poster Presentation
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3240525/ http://dx.doi.org/10.1186/1471-2202-12-S1-P57

Ejemplares similares

Implementation of parallel spatial stochastic reaction-diffusion simulation in STEPS
por: Chen, Weiliang, et al.
Publicado: (2015)

STEPS: efficient simulation of stochastic reaction–diffusion models in realistic morphologies
por: Hepburn, Iain, et al.
Publicado: (2012)

Accurate approximation to stochastic reaction diffusion on unstructured meshes in STEPS
por: Hepburn, Iain, et al.
Publicado: (2015)

Accurate approximation and MPI parallelization of spatial stochastic reaction-diffusion in STEPS
por: Hepburn, Iain, et al.
Publicado: (2014)

Dendritic Volume Mesh Reconstruction for STEPS: How Does Mesh Quality Affect Stochastic Reaction-Diffusion Simulation?
por: Chen, Weiliang, et al.
Publicado: (2013)

Tetrahedral mesh generation and visualization for stochastic reaction-diffusion simulation
por: Chen, Weiliang, et al.
Publicado: (2010)

Improving performance of the STochastic Engine for Pathway Simulation (STEPS)
por: Chen, Weiliang, et al.
Publicado: (2011)

Parallel STEPS: Large Scale Stochastic Spatial Reaction-Diffusion Simulation with High Performance Computers
por: Chen, Weiliang, et al.
Publicado: (2017)

Improving Data Caching of the STochastic Engine for Pathway Simulation (STEPS)
por: Chen, Weiliang, et al.
Publicado: (2012)

Hierarchical Stochastic Simulation Algorithm for SBML Models of Genetic Circuits
por: Watanabe, Leandro H., et al.
Publicado: (2014)

Initial state of single spines affects probability of induction of cerebellar long term depression in a stochastic model
por: Jain, Anant, et al.
Publicado: (2013)

STEPS: Modeling and Simulating Complex Reaction-Diffusion Systems with Python
por: Wils, Stefan, et al.
Publicado: (2009)

A computational study of stochastic mechanisms in dendritic calcium spike generation
por: Anwar, Haroon, et al.
Publicado: (2012)

Python-based geometry preparation and simulation visualization toolkits for STEPS
por: Chen, Weiliang, et al.
Publicado: (2014)

libAnnotationSBML: a library for exploiting SBML annotations
por: Swainston, Neil, et al.
Publicado: (2009)

MakeSBML: A tool for converting between Antimony and SBML
por: Jardine, Bartholomew E, et al.
Publicado: (2023)

Efficient calculation of the quasi-static electrical potential on a tetrahedral mesh and its implementation in STEPS
por: Hepburn, Iain, et al.
Publicado: (2013)

SBML2HYB: a Python interface for SBML compatible hybrid modeling
por: Pinto, José, et al.
Publicado: (2023)

STEPS 4.0: Fast and memory-efficient molecular simulations of neurons at the nanoscale
por: Chen, Weiliang, et al.
Publicado: (2022)

Novel Ground-Up 3D Multicellular Simulators for Synthetic Biology CAD Integrating Stochastic Gillespie Simulations Benchmarked with Topologically Variable SBML Models
por: Matzko, Richard Oliver, et al.
Publicado: (2023)

SBML-SAT: a systems biology markup language (SBML) based sensitivity analysis tool
por: Zi, Zhike, et al.
Publicado: (2008)

SBML2L(a)T(E)X: Conversion of SBML files into human-readable reports
por: Dräger, Andreas, et al.
Publicado: (2009)

LibSBMLSim: a reference implementation of fully functional SBML simulator
por: Takizawa, Hiromu, et al.
Publicado: (2013)

SBMLKinetics: a tool for annotation-independent classification of reaction kinetics for SBML models
por: Xu, Jin
Publicado: (2023)

Simulating Stochastic Reaction-Diffusion Systems on and within Moving Boundaries
por: Ghosh, Atiyo, et al.
Publicado: (2015)

Efficient stochastic simulation of reaction–diffusion processes via direct compilation
por: Lis, Mieszko, et al.
Publicado: (2009)

Stochastic modeling and simulation of reaction-diffusion system with Hill function dynamics
por: Chen, Minghan, et al.
Publicado: (2017)

The blending region hybrid framework for the simulation of stochastic reaction–diffusion processes
por: Yates, Christian A., et al.
Publicado: (2020)

MOCCASIN: converting MATLAB ODE models to SBML
por: Gómez, Harold F., et al.
Publicado: (2016)

libRoadRunner 2.0: a high performance SBML simulation and analysis library
por: Welsh, Ciaran, et al.
Publicado: (2022)

JSBML: a flexible Java library for working with SBML
por: Dräger, Andreas, et al.
Publicado: (2011)

Integrating Systems Biology Markup Language (SBML) with NEURON
por: Bulanova, Anna S, et al.
Publicado: (2014)

An automated model annotation system (AMAS) for SBML models
por: Shin, Woosub, et al.
Publicado: (2023)

An Automated Model Annotation System (AMAS) for SBML Models
por: Shin, Woosub, et al.
Publicado: (2023)

Stochastic modelling of reaction–diffusion processes
por: Erban, Radek, et al.
Publicado: (2020)

The Input Signal Step Function (ISSF), a Standard Method to Encode Input Signals in SBML Models with Software Support, Applied to Circadian Clock Models
por: Adams, R.R., et al.
Publicado: (2012)

Simulation-based mastery learning (SBML) for rapid acquisition of upper endoscopy knowledge and skills–initial observation
por: Nguyen-Vu, Tiffany, et al.
Publicado: (2020)

Payao: a community platform for SBML pathway model curation
por: Matsuoka, Yukiko, et al.
Publicado: (2010)

Qualitative translation of relations from BioPAX to SBML qual
por: Büchel, Finja, et al.
Publicado: (2012)

Annotation of SBML models through rule-based semantic integration
por: Lister, Allyson L, et al.
Publicado: (2010)

Cannot write session to /tmp/vufind_sessions/sess_dn2l9gtlvj84khh1b2l2bfci68