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

Learn about Data Citation Standards.

Dataset Metrics

9 Downloads

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.

Find

Filter by

	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 - 2 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

Waiver

Our Community Norms as well as good scientific practices expect that proper credit is given via citation. Please use the data citation above, generated by the Dataverse.

CC BY - "Attribution" Creative Commons CC BY Attribution 4.0 International icon

Guestbook

No guestbook is assigned to this dataset, you will not be prompted to provide any information on file download.

Preview Guestbook

Upon downloading files the guestbook asks for the following information.

Guestbook Name

Collected Data

Account Information

Dataset	Summary	Contributors	Published
No records found.

Share Dataset

Share this dataset on your favorite social media networks.

Dataset Citations

Citations for this dataset are retrieved from Crossref via DataCite using Make Data Count standards. For more information about dataset metrics, please refer to the User Guide.

Sorry, no citations were found.

Restricted Files Selected

The restricted file(s) selected may not be downloaded because you have not been granted access.

Restricted Files Selected

The restricted file(s) selected may not be downloaded because you have not been granted access.

Click Continue to download the files you have access to download.

Delete Dataset

Are you sure you want to delete this dataset and all of its files? You cannot undelete this dataset.

Delete Draft Version

Are you sure you want to delete this draft version? Files will be reverted to the most recently published version. You cannot undelete this draft.

Unpublished Dataset Private URL

Private URL can only be used with unpublished versions of datasets.

Unpublished Dataset Private URL

Are you sure you want to disable the Private URL? If you have shared the Private URL with others they will no longer be able to use it to access your unpublished dataset.

Delete Files

The file(s) will be deleted after you click on the Delete button.

Files will not be removed from previously published versions of the dataset.

Compute

This dataset contains restricted files you may not compute on because you have not been granted access.

Deaccession Dataset

Are you sure you want to deaccession? The selected version(s) will no longer be viewable by the public.

Deaccession Dataset

Are you sure you want to deaccession this dataset? It will no longer be viewable by the public.

Version Differences Details

Please select two versions to view the differences.

Version Differences Details

Version:
Last Updated:

Select File(s)

Please select a file or files to be downloaded.

Select File(s)

Please select a file or files for access request.

Select File(s)

Please select a file or files to be deleted.

Select File(s)

Please select unrestricted file(s) to be restricted.

Select File(s)

Please select restricted file(s) to be unrestricted.

Select File(s)

Please select a file or files to be edited.

Select File(s)

Please select a file or files to be edited.

Edit Tags

Select existing file tags or create new tags to describe your files. Each file can have more than one tag.

Request Access

You need to Log In to request access to this file.

Dataset Terms

Please confirm and/or complete the information needed below in order to continue.

Package File Download

Use the Download URL in a Wget command or a download manager to download this package file. Download via web browser is not recommended. User Guide - Downloading a Dataverse Package via URL

- -

Download URL

https://darus.uni-stuttgart.de/api/access/datafile/

Request Access

Please confirm and/or complete the information needed below in order to request access to files in this dataset.

Compute Batch

Clear Batch

Dataset	Dataset Persistent ID

Compute Batch

File Restrictions

Terms of Access

Request Access

Enable access request

Submit for Review

You will not be able to make changes to this dataset while it is in review.

Publish Dataset

Are you sure you want to publish this dataset? Once you do so it must remain published.

Please use the publication checklist for authors (english version) to check your dataset for publication readiness.

Publish Dataset

This dataset cannot be published until Software Platform is published. Would you like to publish both right now?

Please use the publication checklist for authors (english version) to check your dataset for publication readiness.

Once you publish this dataset it must remain published.

Publish Dataset

Are you sure you want to republish this dataset?

Select if this is a minor or major version update.

Minor Release (1.1)

Major Release (2.0)

Publish Dataset

This dataset cannot be published until Software Platform is published by its administrator.

Publish Dataset

This dataset cannot be published until Software Platform and Stuttgart Research Center Systems Biology are published.

Return to Author

Return this dataset to contributor for modification.