Meta-stochastic simulation of biochemical models for systems and synthetic biology. 2015

Daven Sanassy, and Paweł Widera, and Natalio Krasnogor
Interdisciplinary Computing and Complex BioSystems (ICOS) Research Group, School of Computing Science, Newcastle University , Newcastle upon Tyne, Tyne and Wear, NE1 7RU, United Kingdom.

Stochastic simulation algorithms (SSAs) are used to trace realistic trajectories of biochemical systems at low species concentrations. As the complexity of modeled biosystems increases, it is important to select the best performing SSA. Numerous improvements to SSAs have been introduced but they each only tend to apply to a certain class of models. This makes it difficult for a systems or synthetic biologist to decide which algorithm to employ when confronted with a new model that requires simulation. In this paper, we demonstrate that it is possible to determine which algorithm is best suited to simulate a particular model and that this can be predicted a priori to algorithm execution. We present a Web based tool ssapredict that allows scientists to upload a biochemical model and obtain a prediction of the best performing SSA. Furthermore, ssapredict gives the user the option to download our high performance simulator ngss preconfigured to perform the simulation of the queried biochemical model with the predicted fastest algorithm as the simulation engine. The ssapredict Web application is available at http://ssapredict.ico2s.org. It is free software and its source code is distributed under the terms of the GNU Affero General Public License.

UI MeSH Term Description Entries
D008954 Models, Biological Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment. Biological Model,Biological Models,Model, Biological,Models, Biologic,Biologic Model,Biologic Models,Model, Biologic
D003198 Computer Simulation Computer-based representation of physical systems and phenomena such as chemical processes. Computational Modeling,Computational Modelling,Computer Models,In silico Modeling,In silico Models,In silico Simulation,Models, Computer,Computerized Models,Computer Model,Computer Simulations,Computerized Model,In silico Model,Model, Computer,Model, Computerized,Model, In silico,Modeling, Computational,Modeling, In silico,Modelling, Computational,Simulation, Computer,Simulation, In silico,Simulations, Computer
D000465 Algorithms A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task. Algorithm
D001669 Biochemical Phenomena The chemical processes, enzymatic activities, and pathways of living things and related temporal, dimensional, qualitative, and quantitative concepts. Biochemical Processes,Biochemical Concepts,Biochemical Phenomenon,Biochemical Process,Phenomena, Biochemical,Biochemical Concept,Concept, Biochemical,Concepts, Biochemical,Phenomenon, Biochemical,Process, Biochemical,Processes, Biochemical
D013269 Stochastic Processes Processes that incorporate some element of randomness, used particularly to refer to a time series of random variables. Process, Stochastic,Stochastic Process,Processes, Stochastic
D016014 Linear Models Statistical models in which the value of a parameter for a given value of a factor is assumed to be equal to a + bx, where a and b are constants. The models predict a linear regression. Linear Regression,Log-Linear Models,Models, Linear,Linear Model,Linear Regressions,Log Linear Models,Log-Linear Model,Model, Linear,Model, Log-Linear,Models, Log-Linear,Regression, Linear,Regressions, Linear
D049490 Systems Biology Comprehensive, methodical analysis of complex biological systems by monitoring responses to perturbations of biological processes. Large scale, computerized collection and analysis of the data are used to develop and test models of biological systems. Biology, Systems
D058615 Synthetic Biology A field of biological research combining engineering in the formulation, design, and building (synthesis) of novel biological structures, functions, and systems. Biologies, Synthetic,Biology, Synthetic,Synthetic Biologies
D020407 Internet A loose confederation of computer communication networks around the world. The networks that make up the Internet are connected through several backbone networks. The Internet grew out of the US Government ARPAnet project and was designed to facilitate information exchange. World Wide Web,Cyber Space,Cyberspace,Web, World Wide,Wide Web, World

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