SynBioSS: the synthetic biology modeling suite

Hill, Arthur V.; Tomshine, Jonathan R.; Weeding, Emma; Sotiropoulos, Vassilios; Kaznessis, Yiannis N.

doi:10.1093/bioinformatics/btn468

Cited by 83 publications

(58 citation statements)

References 16 publications

(14 reference statements)

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“…-coke formation (Moustafa and Froment, 2003;QuintanaSolórzano et al, 2005), -biomass conversion (Rangarajan et al, 2010), -oxidative coupling of methane (Simon et al, 2007), -silicon hydride clustering (Wong et al, 2004), -hydrocarboxylation , -carbonylation (Bruk et al, 1998), -organic synthesis (Fontain and Reitsam, 1991), -biological processes (Valdes-Perez, 1992b;Klein et al, 2002;Faeder et al, 2003Faeder et al, , 2005Li et al, 2004;Hatzimanikatis et al, 2004Hatzimanikatis et al, , 2005Blinov et al, 2005a, b;Mayeno et al, 2005;Henry et al, 2007Henry et al, , 2010Hill et al, 2008;Finley et al, 2009), -and many more.…”

Section: Simulation Of Large Complex Reaction Network 421 Network mentioning

confidence: 99%

A Review of Kinetic Modeling Methodologies for Complex Processes

Oliveira

Hudebine

Denis

et al. 2016

Oil Gas Sci. Technol. – Rev. IFP Energies nouvelles

125

113

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-In this paper, kinetic modeling techniques for complex chemical processes are reviewed. After a brief historical overview of chemical kinetics, an overview is given of the theoretical background of kinetic modeling of elementary steps and of multistep reactions. Classic lumping techniques are introduced and analyzed. Two examples of lumped kinetic models (atmospheric gasoil hydrotreating and residue hydroprocessing) developed at IFP Energies nouvelles (IFPEN) are presented. The largest part of this review describes advanced kinetic modeling strategies, in which the molecular detail is retained, i.e. the reactions are represented between molecules or even subdivided into elementary steps. To be able to retain this molecular level throughout the kinetic model and the reactor simulations, several hurdles have to be cleared first: (i) the feedstock needs to be described in terms of molecules, (ii) large reaction networks need to be automatically generated, and (iii) a large number of rate equations with their rate parameters need to be derived. For these three obstacles, molecular reconstruction techniques, deterministic or stochastic network generation programs, and single-event micro-kinetics and/or linear free energy relationships have been applied at IFPEN, as illustrated by several examples of kinetic models for industrial refining processes.Résumé -Une revue de méthodes de modélisation cinétique pour des procédés complexesDans cet article, les techniques de modélisation cinétique des processus chimiques complexes sont examinées. Après un bref aperçu historique de la cinétique chimique, un aperçu des bases théoriques de la modélisation cinétique d'étapes élémentaires et de réactions globales est présenté. Les techniques classiques de regroupement (lumping) sont ensuite présentées et analysées. Deux exemples de modèles cinétiques regroupés (pour l'hydrotraitement de gazole atmosphérique et pour l'hydrotraitement de résidus) développés à IFP Energies nouvelles (IFPEN) sont présentés. La plus grande partie de cette revue décrit des stratégies avancées de modélisation cinétique, dans lesquelles le détail moléculaire est retenu : les réactions entre les molécules sont représentées ou même subdivisées en étapes élémentaires. Pour être en mesure de conserver ce niveau moléculaire à la fois dans le modèle cinétique et dans les simulations de réacteurs, plusieurs obstacles doivent d'abord être éliminés : (i) la charge doit être décrite en termes de molécules, (ii) les grands réseaux réactionnels doivent être générés automatiquement et (iii) un grand nombre d'équations de vitesse avec leurs paramètres de vitesse doit être dérivé. Pour ces trois obstacles, des techniques de reconstruction moléculaire, des programmes de génération de réseaux déterministes ou stochastiques, et des modèles microcinétiques basés sur des événements constitutifs (single events) et/ou des

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Section: Simulation Of Large Complex Reaction Network 421 Network mentioning

confidence: 99%

A Review of Kinetic Modeling Methodologies for Complex Processes

Oliveira

Hudebine

Denis

et al. 2016

Oil Gas Sci. Technol. – Rev. IFP Energies nouvelles

125

113

View full text Add to dashboard Cite

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“…This makes the tools strongly dependent on the information manually provided by the user. For instance, BioJADE [Goler 2004] and the Synthetic Biology Software Suite (SynBioSS) [Hill et al 2008;Weeding et al 2010] seemed promising by allowing connection to the Registry, but both tools are now outdated. While TinkerCell is regularly updated, it lacks presently a proper connection with public available libraries of biological parts [Chandran et al 2009].…”

Section: Drag and Drop Toolsmentioning

confidence: 99%

Synthetic Biology and Microdevices

Venken

Marchal

Vanderleyden

2013

J. Emerg. Technol. Comput. Syst.

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Recent developments demonstrate that the combination of microbiology with micro-and nanoelectronics is a successful approach to develop new miniaturized sensing devices and other technologies. In the last decade, there is a shift from the optimization of the abiotic components, e.g. the chip, to the improvement of the processing capabilities of cells through genetic engineering. The synthetic biology approach will not only give rise to systems with new functionalities, but will also improve the robustness and speed of their response towards applied signals. To this end, the development of new genetic circuits has to be guided by computational design methods that enable to tune and optimize the circuit response. As the successful design of genetic circuits is highly dependent on the quality and reliability of its composing elements, intense characterization of standard biological parts will be crucial for an efficient rational design process in the development of new genetic circuits. Microengineered devices can thereby offer a new analytical approach for the study of complex biological parts and systems. By summarizing the recent techniques in creating new synthetic circuits and in integrating biology with microdevices, this review aims at emphasizing the power of combining synthetic biology with microfluidics and microelectronics.

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“…Further advance in computational synthetic biology will result from tools that combine and integrate most of the tasks discussed, starting with the choice and assembly of biological parts to the compilation and modification of the corresponding DNA sequences. Examples of such tools comprise SynBioSS (Hill et al, 2008); Clotho and Biskit (Grunberg et al, 2007). Critical elements are still lacking, such as tools for automatic information integration (literature and databases), and tools that re-use standardized model entities for optimal circuit design.…”

Section: Computational Tools For Synthetic Biologymentioning

confidence: 99%