The FLAME-accelerated signalling tool (FaST) for facile parallelisation of flexible agent-based models of cell signalling

Version 1.0

Fullstone, Gavin, 2021, "The FLAME-accelerated signalling tool (FaST) for facile parallelisation of flexible agent-based models of cell signalling", https://doi.org/10.18419/darus-1327, DaRUS, V1

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Subject	Medicine, Health and Life Sciences
Related Publication	The FLAME-accelerated signalling tool (FaST) for facile parallelisation of flexible agent-based models of cell signalling. npj Systems Biology and Applications (2020)6:10 doi: 10.1038/s41540-020-0128-x
Notes	This study used the following software to generate data: FLAME LIBMBOARD 0.3.1, FLAME Xparser 0.17.0, FLAME GPU 1.4, Visual Studio Community 2015, GCC 4.2.1, OpenMPI 2.0.2, NVIDIA CUDA 9.0, MATLAB 2016b, MCell 3.4, Cellblender 1.1. All data analysis and statistics were performed using Graphad Prism 6.0h.

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	1 to 5 of 5 Files	Download
	FaST_Software.tar.gz Gzip Archive - 22.4 MB - Feb 8, 2021 - 2 Downloads MD5: d376ee3832fd7f69aa5df64b1a92d8ed FaST Software	Download
	Iteration_Data.tar.gz Gzip Archive - 176.8 MB - Feb 8, 2021 - 2 Downloads MD5: 07af6f8fd541cff76eba7a76b831407d Example iteration data from model	Download
	MCell_Model.tar.gz Gzip Archive - 6.2 MB - Feb 8, 2021 - 2 Downloads MD5: 26f67bc5fe080a35de8c0998f7722b48 MCell model used as a comparison in manuscript	Download
	Paper_Data.pzfx application/x-graphpad-prism-pzfx - 6.3 MB - Feb 8, 2021 - 1 Download MD5: 36090e76082a4433d3aa6f13d01fbc2b All processed data from manuscript	Download
	Visualiser_Config.xml XML - 38.0 KB - Feb 8, 2021 - 4 Downloads MD5: adb80a8703013c41106515b7038891c0 Visualiser configurations file to be used with FLAME Visualiser Software	Download

Citation Metadata

Dataset Persistent ID	doi:10.18419/darus-1327
Publication Date	2021-02-08
Title	The FLAME-accelerated signalling tool (FaST) for facile parallelisation of flexible agent-based models of cell signalling
Author	Fullstone, Gavin (Universität Stuttgart) - ORCID: 0000-0001-5246-3443
Contact	Use email button above to contact. Fullstone, Gavin (Universität Stuttgart)
Description	This folder contains the FaST software, as well as all the raw data and tools to replicate this study. Paper_Data.pzfx: All raw and processed data in the main figures MCell_Model.tar.gz: The MCell model used in Figure 5 FaST_Software.tar.gz: The FaST software tool. Scripts to replicate the findings of the study are enclosed in the /example folder. Documentation and a tutorial for building the simulations is included in the /doc folder Visualiser_Config.xml: A configuration file for visualising model simulations, for use with the FLAME Visualiser Software Iteration_Data.tar.gz: Contains an example of raw outputs from a single ApoptoCell simulation
Subject	Medicine, Health and Life Sciences
Related Publication	The FLAME-accelerated signalling tool (FaST) for facile parallelisation of flexible agent-based models of cell signalling. npj Systems Biology and Applications (2020)6:10 doi: 10.1038/s41540-020-0128-x https://doi.org/10.1038/s41540-020-0128-x
Notes	This study used the following software to generate data: FLAME LIBMBOARD 0.3.1, FLAME Xparser 0.17.0, FLAME GPU 1.4, Visual Studio Community 2015, GCC 4.2.1, OpenMPI 2.0.2, NVIDIA CUDA 9.0, MATLAB 2016b, MCell 3.4, Cellblender 1.1. All data analysis and statistics were performed using Graphad Prism 6.0h.
Depositor	Fullstone, Gavin
Deposit Date	2021-02-04

Metadata for Research Software

Software version	v.1.3
Development Status	inactive
Code Repository	https://zenodo.org/record/3757764#.YCDrdS2ZOX0
Programming Language	Matlab (to run FaST itself); C (to run FaST Simulations); CUDA (to run FaST Simulations on GPUs)
Operating Systems	Windows; OS X; Unix
Application Category	Systems Biology
Application Subcategory	Particle-based Modelling
Software Requirements	Matlab Matlab Runtime FLAME CPU http://flame.ac.uk FLAME GPU http://www.flamegpu.com

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