Composing, execution and sharing of multiscale applications

Rycerz, Katarzyna; Bubak, Marian; Ciepiela, Eryk; Harężlak, Daniel; Gubała, Tomasz; Meizner, Jan; Pawlik, Maciej; Wilk, Bartosz

doi:10.1016/j.future.2015.06.002

Cited by 9 publications

(10 citation statements)

References 26 publications

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“…The goal of this section is therefore to present the platform's conceptual view. The vision of the MEE also follows from our research related to methods, techniques and environments for programming and execution of complex scientific applications on clusters, grids, cloud and container infrastructures [24][25][26], as well as the elaboration of environments for multi-scale, multi-infrastructure and multi-programming applications [27]. Figure 3 presents the architecture of the MEE as implemented during the EurValve project to facilitate the execution of the above-mentioned HPC computations.…”

Section: The Model Execution Environment 41 Architecture and Usagementioning

confidence: 99%

The EurValve model execution environment

et al. 2020

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The goal of this paper is to present a dedicated high-performance computing (HPC) infrastructure which is used in the development of a so-called reduced-order model (ROM) for simulating the outcomes of interventional procedures which are contemplated in the treatment of valvular heart conditions. Following a brief introduction to the problem, the paper presents the design of a model execution environment, in which representative cases can be simulated and the parameters of the ROM fine-tuned to enable subsequent deployment of a decision support system without further need for HPC. The presentation of the system is followed by information concerning its use in processing specific patient cases in the context of the EurValve international collaboration.

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Section: The Model Execution Environment 41 Architecture and Usagementioning

confidence: 99%

The EurValve model execution environment

et al. 2020

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“…To address some of the challenges and requirements in modeling and simulation of GRNs, we have developed a tool called MultiGrain/MAPPER. MultiGrain/MAPPER has been developed as part of a more comprehensive project called Multiscale Applications on European e-Infrastructures (MAP-PER) [2,3,5]. Efficient execution of coupled multiscale simulations is a major challenge in multiscale modeling and simulation.…”

Section: Tools Of the Tradementioning

confidence: 99%

“…MultiGrain/MAPPER is a software that implements the multi-swarm PSO algorithm described in Section 3.2. MultiGrain/MAPPER is an applicationspecific component of a distributed multiscale computing architecture called MAPPER [2,6,30,1]. The MAPPER architecture has been designed to meet the large-scale computing requirements of multiscale modeling and simulation applications across a variety of domains.…”

Section: Multigrain/mapper Softwarementioning

confidence: 99%

“…This approach has been designed for modeling and simulation of large gene-regulatory networks. The tool was developed as part of the European FP7 project Multiscale Applications on European e-Infrastructures (MAPPER) [2,3,4,5]. The goal of MAPPER was to develop a general framework and technology facilitating the development, deployment and execution of distributed multiscale modeling and simulation applications [1,6].…”

Section: Introductionmentioning

confidence: 99%

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MultiGrain/MAPPER: A distributed multiscale computing approach to modeling and simulating gene regulation networks

Mizeranschi

Swain

Scona

et al. 2016

Future Generation Computer Systems

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Modeling and simulation of gene-regulatory networks (GRNs) has become an important aspect of modern systems biology investigations into mechanisms underlying gene regulation. A key task in this area is the automated inference or reverse-engineering of dynamic mechanistic GRN models from gene expression time-course data. Besides a lack of suitable data (in particular multi-condition data from the same system), one of the key challenges of this task is the computational complexity involved. The more genes in the GRN system and the more parameters a GRN model has, the higher the computational load. The computational challenge is likely to increase substantially in the near future when we tackle larger GRN systems. The goal of this study was to develop a distributed computing framework and system for reverse-engineering of GRN models. We present the resulting software called MultiGrain/MAPPER. This software is based on a new architecture and tools supporting multiscale computing in a distributed computing environment. A key feature of MultiGrain/MAPPER is the realization of GRN reverse-engineering based on the underlying distributed computing framework and multi-swarm particle swarm optimization. We demonstrate some of the features of MultiGrain/MAPPER and evaluate its performance using

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“…A tool [15,23] is available to compose new applications by a drag and drop operation, using previously defined components. This is illustrated in figure 11.…”

Section: Multiscale Modelling Languagementioning

confidence: 99%

A framework for multi-scale modelling

Chopard

Borgdorff

Hoekstra

2014

Phil. Trans. R. Soc. A.

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One contribution of 13 to a Theme Issue 'Multi-scale systems in fluids and soft matter: approaches, numerics and applications' . We review a methodology to design, implement and execute multi-scale and multi-science numerical simulations. We identify important ingredients of multi-scale modelling and give a precise definition of them. Our framework assumes that a multi-scale model can be formulated in terms of a collection of coupled single-scale submodels. With concepts such as the scale separation map, the generic submodel execution loop (SEL) and the coupling templates, one can define a multi-scale modelling language which is a bridge between the application design and the computer implementation. Our approach has been successfully applied to an increasing number of applications from different fields of science and technology.

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Composing, execution and sharing of multiscale applications

Cited by 9 publications

References 26 publications

The EurValve model execution environment

The EurValve model execution environment

MultiGrain/MAPPER: A distributed multiscale computing approach to modeling and simulating gene regulation networks

A framework for multi-scale modelling

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