3757764
doi
10.5281/zenodo.3757764
oai:zenodo.org:3757764
user-abm
The FLAME-accelerated Signalling Tool (FaST)
Gavin Fullstone
University of Stuutgart
doi:10.1038/s41540-020-0128-x
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Agent-based modelling
Signalling
Parallelisation
Systems Biology
<p>The FLAME-accelerated signalling tool (FaST) is GUI-fronted software that produces agent-based models of signalling pathways. It particularly addresses the computational limitations in agent-based modelling by employing parallelisation on both CPU and GPU-based architecture, without the necessary prerequisite of specialist knowledge of MPI or CUDA coding. FaST takes input files containing species concentrations, diffusion coefficients and reaction kinetics to produce code for an agent-based model, then employs the general agent-based modelling software packages FLAME and FLAME GPU for facile parallelisation. In a related publication, we have demonstrated the methodology used by the tool and the conversion of an ODE-type simulation to agent-based with accurate kinetics and acceleration on both architectures, with a 53.9 × speedup achieved by GPU-parallelisation compared to CPU-serial simulations. This tool is particularly designed to include complex spatial and stochastic into models of cellular signalling processes. The generated code is further fully customisable, whilst retaining the ability to be parallelised.</p>
<p>The current version (1.3) fixes issues sometimes encountered with GPU-based models that include receptors and ligands.</p>
Zenodo
2019-04-02
info:eu-repo/semantics/other
2620047
user-abm
1.3
1587414020.33939
7578788
md5:25aba5928251570019b34dcf5aea2ac0
https://zenodo.org/records/3757764/files/FaST_release_V1.zip
16927717
md5:e562f6cbcd6aef033f18a461597436e8
https://zenodo.org/records/3757764/files/FaST_release_V2.zip
23615541
md5:bcb72b6063ebb94d8c92e7274cc3597e
https://zenodo.org/records/3757764/files/FaST_release_V3.zip
public
10.1038/s41540-020-0128-x
Is supplement to
doi
10.5281/zenodo.2620047
isVersionOf
doi