GPUPeP: Parallel Enzymatic Numerical P System simulator with a Python-based interface.
ENPS simulator
Enzymatic Numerical P System
GPUPeP
Graphical Processing Unit (GPU)
Membrane computing
Python-based interface
Journal
Bio Systems
ISSN: 1872-8324
Titre abrégé: Biosystems
Pays: Ireland
ID NLM: 0430773
Informations de publication
Date de publication:
Oct 2020
Oct 2020
Historique:
received:
31
10
2019
revised:
07
06
2020
accepted:
08
06
2020
pubmed:
15
6
2020
medline:
2
7
2021
entrez:
15
6
2020
Statut:
ppublish
Résumé
Membrane computing is a computational paradigm inspired by the structure and behavior of a living cell. P Systems are the computing devices that are used to realize membrane computing models. Numerous theoretical studies on many variants of P Systems have shown them to be computationally universal. There is a wide range of applications of P Systems from modeling of biological processes to image processing. Among many variants of P Systems, one of the most important is Enzymatic Numerical P System (ENPS). ENPS is a class of P System in which membranes operate on numerical values. To realize the power of ENPS there are a few simulators developed. Each and every simulator has some advantages as well as some disadvantages. Here, a GPU based simulator using Python as a user interaction language is developed. This tool is a completely parallel variant, compatible with a Python based sequential simulator (PeP) which was the first Python based work for ENPS. The developed simulator uses CUDA to interact with GPU and gives the desired speed up, while processing the membranes. There are two important case studies which show the performance of the developed tool to be far better than the other serial simulators.
Identifiants
pubmed: 32535178
pii: S0303-2647(20)30082-4
doi: 10.1016/j.biosystems.2020.104186
pii:
doi:
Types de publication
Journal Article
Review
Langues
eng
Sous-ensembles de citation
IM
Pagination
104186Informations de copyright
Copyright © 2020 Elsevier B.V. All rights reserved.