Design tools for the engineering of biological systems

Created by W.Langdon from gp-bibliography.bib Revision:1.7630

@PhdThesis{rosati_elise_2018_ED269,

• author = "Elise Rosati",
• title = "Design tools for the engineering of biological systems",
• titletranslation = "Outils d'aide {\`a} la conception pour l'ing{\'e}nierie de syst{\`e}mes biologiques",
• school = "University of Strasbourg",
• year = "2018",
• month = "5 " # apr,
• address = "France",
• keywords = "genetic algorithms, genetic programming, synthetic biology, design automation, computer-aided design, modelling and simulations, gene regulatory networks, microelectronics",
• mot_clef = "Biologie synth{\'e}tique, Automatisation de la conception, Conception assist{\'e}e par ordinateur, Mod{\'e}lisation et simulations, R{\'e}seaux de r{\'e}gulation g{\'e}n{\'e}tiques, Micro{\'e}lectronique",
• publisher = "HAL CCSD",
• hal_id = "tel-01829464",
• hal_version = "v1",
• number = "2018STRAD008",
• bibsource = "OAI-PMH server at api.archives-ouvertes.fr",
• contributor = "de l'informatique et de l'imagerie Laboratoire des sciences de l'ing{\'e}nieur and Christophe Lallement",
• identifier = "NNT : 2018STRAD008; tel-01829464",
• language = "en",
• oai = "oai:HAL:tel-01829464v1",
• rights = "info:eu-repo/semantics/OpenAccess",
• URL = "https://tel.archives-ouvertes.fr/tel-01829464",
• URL = "https://tel.archives-ouvertes.fr/tel-01829464/file/rosati_elise_2018_ED269.pdf",
• URL = "https://tel.archives-ouvertes.fr/tel-01829464/document",
• size = "262 pages",
• abstract = "In synthetic biology, Gene Regulatory Networks (GRN) are one of the main ways to create new biological functions to solve problems in various areas (therapeutics, biofuels, biomaterials, biosensing). However, the complexity of the designed networks has reached a limit, thereby restraining the variety of problems they can address. How can biologists overcome this limit and further increase the complexity of their systems? The goal of this thesis is to provide the biologists with tools to assist them in the design and simulation of complex GRNs. To this aim, the current state of the art was examined and it was decided to adapt tools from the micro-electronic field to biology, as well as to create a Genetic Programming algorithm for GRN design. On the one hand, models of diffusion and of other various systems (band-pass, prey-predator, repressilator, XOR) were created and written in Verilog A. They are already implemented and well-functioning on the Spectre solver as well as a free solver, namely NgSpice. On the other hand, the first steps of automatic GRN design were achieved. Indeed, an algorithm able to optimise the parameters of a given GRN according to a specification was developed. Moreover, Genetic Programming was applied to GRN design, allowing the optimisation of both the topology and the parameters of a GRN. These tools proved their usefulness for the biologists community by efficiently answering relevant biological questions arising in the development of a system. With this work, we were able to show that adapting microelectronics and Genetic Programming tools to biology is doable and useful. By assisting design and simulation, such tools should promote the emergence of more complex systems.",
• abstract = "En biologie synth{\'e}tique, il existe plusieurs mani{\`e}res d{'}adresser les probl{\`e}mes soulev{\'e}s dans plusieurs domaines comme la th{\'e}rapeutique, les biofuels, les biomat{\'e}riaux ou encore les biocapteurs. Nous avons choisi de nous concentrer sur l{'}une d{'}entre elles : les r{\'e}seaux de r{\'e}gulation g{\'e}n{\'e}tique (RRG). Un constat peut {\^e}tre fait : la diversit{\'e} des probl{\`e}mes r{\'e}solus gr{\^a}ce aux RRGs est brid{\'e}e par la complexit{\'e} de ces RRGs, qui a atteint une limite. Quelles solutions s{'}offrent aux biologistes, pour repousser cette limite et continuer d{'}augmenter la complexit{\'e} de leur syst{\`e}me ? Cette th{\`e}se a pour but de fournir aux biologistes les outils n{\'e}cessaires {\`a} la conception et {\`a} la simulation de RRGs complexes. Un examen de l{'}{\'e}tat de l{'}art en la mati{\`e}re nous a men{\'e} {\`a} adapter les outils de la micro-{\'e}lectronique {\`a} la biologie ainsi qu{'}{\`a} cr{\'e}er un algorithme de programmation g{\'e}n{\'e}tique pour la conception des RRGs. D{'}une part, nous avons {\'e}labor{\'e} les mod{\`e}les Verilog A de diff{\'e}rents syst{\`e}mes biologiques (passe-bande, proie-pr{\'e}dateur, repressilator, XOR) ainsi que de la diffusion spatiotemporelle d{'}une mol{\'e}cule. Ces mod{\`e}les fonctionnent tr{\`e}s bien avec plusieurs simulateurs {\'e}lectroniques (Spectre et NgSpice). D{'}autre part, les premi{\`e}res marches vers l{'}automatisation de la conception de RRGs ont {\'e}t{\'e} gravies. En effet, nous avons d{\'e}velopp{\'e} un algorithme capable d{'}optimiser les param{\`e}tres d{'}un RRG pour remplir un cahier des charges donn{\'e}. De plus, la programmation g{\'e}n{\'e}tique a {\'e}t{\'e} utilis{\'e}e pour optimiser non seulement les param{\`e}tres d{'}un RRG mais aussi sa topologie. Ces outils ont su prouver leur utilit{\'e} en apportant des r{\'e}ponses pertinentes {\`a} des probl{\`e}mes soulev{\'e}s lors du d{\'e}veloppement de syst{\`e}mes biologiques. Ce travail a permis de montrer que notre approche, {\`a} savoir adapter les outils de la micro-{\'e}lectronique et utiliser des algorithmes de programmation g{\'e}n{\'e}tique, est valide dans le contexte de la biologie synth{\'e}tique. L{'}assistance que notre environnement de d{\'e}veloppement fournit au biologiste devrait encourager l{'}{\'e}mergence de syst{\`e}mes plus complexes.",
• annote = "Laboratoire des sciences de l'ing{\'e}nieur, de l'informatique et de l'imagerie ( ICube ) ; {\'E}cole Nationale du G{\'e}nie de l'Eau et de l'Environnement de Strasbourg ( ENGEES ) -Universit{\'e} de Strasbourg ( UNISTRA ) -Institut National des Sciences Appliqu{\'e}es - Strasbourg ( INSA Strasbourg ) ; Institut National des Sciences Appliqu{\'e}es ( INSA ) -Institut National des Sciences Appliqu{\'e}es ( INSA ) -Centre National de la Recherche Scientifique ( CNRS ) -Mat{\'e}riaux et nanosciences d'Alsace ; Universit{\'e} de Strasbourg ( UNISTRA ) -Universit{\'e} de Haute-Alsace (UHA) Mulhouse - Colmar ( Universit{\'e} de Haute-Alsace (UHA) ) -Institut National de la Sant{\'e} et de la Recherche M{\'e}dicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ) -Universit{\'e} de Strasbourg ( UNISTRA ) -Universit{\'e} de Haute-Alsace (UHA) Mulhouse - Colmar ( Universit{\'e} de Haute-Alsace (UHA) ) -Institut National de la Sant{\'e} et de la Recherche M{\'e}dicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ) -R{\'e}seau nanophotonique et optique ; Universit{\'e} de Strasbourg ( UNISTRA ) -Universit{\'e} de Haute-Alsace (UHA) Mulhouse - Colmar ( Universit{\'e} de Haute-Alsace (UHA) ) -Centre National de la Recherche Scientifique ( CNRS ) -Universit{\'e} de Strasbourg ( UNISTRA ) ; Universit{\'e} de Strasbourg",
• notes = "Supervisor: Christophe LALLEMENT

  ICube, UMR 7357

  also known as \cite{rosati:tel-01829464}",

}

Genetic Programming entries for Elise Rosati

Citations