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A cooperative strategy for parameter estimation in large scale systems biology models

Alejandro F Villaverde, Jose A Egea, Julio R Banga
<span title="">2012</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/xua5vbjwszdirewaoqnikiu5zm" style="color: black;">BMC Systems Biology</a> </i> &nbsp;
Results: A new approach for parameter estimation of large scale models, called Cooperative Enhanced Scatter Search (CeSS), is presented.  ...  Most mathematical models in systems biology present three characteristics which make this problem very difficult to solve: they are highly non-linear, they have a large number of parameters to be estimated  ...  We thank Wolfram Liebermeister for supplying the metabolic model of E. coli ("Model 1").  ... 
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Parallel Metaheuristics in Computational Biology: An Asynchronous Cooperative Enhanced Scatter Search Method

David R. Penas, Patricia González, José A. Egea, Julio R. Banga, Ramón Doallo
<span title="">2015</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/cx3f4s3qmfe6bg4qvuy2cxezyu" style="color: black;">Procedia Computer Science</a> </i> &nbsp;
However, its application to very hard problems, like those considering parameter estimation in dynamic models of systems biology, still results in excessive computation times.  ...  Several challenging parameter estimation problems from the domain of computational systems biology are used to assess the efficiency of the proposal and evaluate its scalability in a parallel environment  ...  For cooperation to be efficient, in large-scale difficult problems, like calibration in large-scale systems biology models, each parallel process must adopt a different strategy to increase the diversification  ... 
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MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics

Jose A Egea, David Henriques, Thomas Cokelaer, Alejandro F Villaverde, Aidan MacNamara, Diana-Patricia Danciu, Julio R Banga, Julio Saez-Rodriguez
<span title="">2014</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
Additionally, the R version includes BayesFit for parameter estimation by Bayesian inference. The eSS and VNS methods can be run on a single-thread or in parallel using a cooperative strategy.  ...  Conclusions: MEIGO provides a free, open-source platform for optimization that can be applied to multiple domains of systems biology and bioinformatics.  ...  Acknowledgements The authors thank Alexandra Vatsiou for testing MEIGO.  ... 
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Global Optimization in Systems Biology: Stochastic Methods and Their Applications [chapter]

Eva Balsa-Canto, J. R. Banga, J. A. Egea, A. Fernandez-Villaverde, G. M. de Hijas-Liste
<span title="2011-11-18">2011</span> <i title="Springer New York"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/er3gzecicffxdofml2pzi2i6pa" style="color: black;">Advances in Experimental Medicine and Biology</a> </i> &nbsp;
However the nonlinear and highly constrained nature of systems biology models, together with the usually large number of decision variables, can make their solution a daunting task, therefore calling for  ...  Mathematical optimization is at the core of many problems in systems biology: i) as the underlying hypothesis for model development, ii) in model identification or iii) in the computation of optimal stimulation  ...  Parameter estimation in complex systems biology models The problem of parameter estimation in biochemical pathways, formulated as a nonlinear programming problem where the objective is to compute the model  ... 
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MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics [article]

Jose A Egea, David Henriques, Thomas Cokelaer, Alejandro F Villaverde, Julio R Banga, Julio Saez-Rodriguez
<span title="2013-11-22">2013</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Both methods can be run on a single-thread or in parallel using a cooperative strategy. The code is supplied under GPLv3 and is available at . Documentation and examples are included.  ...  MEIGO provides a free, open-source platform for optimization, that can be applied to multiple domains of systems biology and bioinformatics.  ...  Large-scale calibration of systems biology models were also presented and solved in that paper.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1311.5735v1">arXiv:1311.5735v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/k6gaabpgsve35lh6znzqa6jtqy">fatcat:k6gaabpgsve35lh6znzqa6jtqy</a> </span>
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Parameter Estimation Using Divide-and-Conquer Methods for Differential Equation Models

Seongho Kim
<span title="">2016</span> <i title="OMICS Publishing Group"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/pslllprjybgehpmmjuieptnl5u" style="color: black;">Journal of Biometrics &amp; Biostatistics</a> </i> &nbsp;
The Biostatistics Core is supported in part by NIH Cancer Center Support Grant P30 CA022453 to the Karmanos Cancer Institute at Wayne State University.  ...  [12] employed a cooperative co-evolutionary algorithm with a decomposition strategy to handle large S-system models with noisy time-series data. When there are no closed loops, Koh et al.  ...  Then we estimate parameters for each sub-system, followed by refinement of the estimates through communication among subsystems.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4172/2155-6180.1000305">doi:10.4172/2155-6180.1000305</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27489746">pmid:27489746</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4968870/">pmcid:PMC4968870</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pywkiq55xjg4bcfotyjmf3x2fe">fatcat:pywkiq55xjg4bcfotyjmf3x2fe</a> </span>
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A parallel metaheuristic for large mixed-integer dynamic optimization problems, with applications in computational biology

David R. Penas, David Henriques, Patricia González, Ramón Doallo, Julio Saez-Rodriguez, Julio R. Banga, Jordi Garcia-Ojalvo
<span title="2017-08-15">2017</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3gm7274mfe6fcs7e3jterqlri" style="color: black;">PLoS ONE</a> </i> &nbsp;
A parallel metaheuristic for large MIDO problems, with applications in computational biology PLOS ONE | https://doi.org/10.A parallel metaheuristic for large MIDO problems, with applications in computational  ...  Further, these results open up new possibilities for other MIDO-based large-scale applications in the life sciences such as metabolic engineering, synthetic biology, drug scheduling.  ...  A., Doallo R., Banga J., Parameter estimation in large-scale systems biology models: a parallel and self-adaptive cooperative strategy, BMC Bioinformatics 18 (1) (2017) 52. https://doi.org/10.1186/s12859  ... 
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Mathematical modeling of gene expression: a guide for the perplexed biologist

Ahmet Ay, David N. Arnosti
<span title="2011-03-21">2011</span> <i title="Informa UK Limited"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/jf6xzofahfdgdpjb2zn6cikmli" style="color: black;">Critical reviews in biochemistry and molecular biology</a> </i> &nbsp;
The detailed analysis of transcriptional networks holds a key for understanding central biological processes, and interest in this field has exploded due to new large-scale data acquisition techniques.  ...  for quantitative understanding of biological systems.  ...  This project was supported by a Special Projects Grant from the MSU Foundation and NIH GM 56976 to D.N.A., and fellowships from the MSU Quantitative Biology Initiative and Gene Expression in Development  ... 
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Rites of passage: requirements and standards for building kinetic models of metabolic phenotypes

Ljubisa Miskovic, Milenko Tokic, Georgios Fengos, Vassily Hatzimanikatis
<span title="">2015</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/leca7sevx5fbxol36lihhcvvce" style="color: black;">Current Opinion in Biotechnology</a> </i> &nbsp;
Villaverde AF, Egea JA, Banga JR: A cooperative strategy for parameter estimation in large scale systems biology models. BMC Syst Biol 2012, 6:75.  ...  The overarching ambition of kinetic metabolic modeling is to capture the dynamic behavior of metabolism to such an extent that systems and synthetic biology strategies can reliably be tested in silico.  ...  L.M. and V.H. were supported by the Ecole Polytechnique Fé dé rale de Lausanne (EPFL), and the RTD grants MalarX and BattleX within SystemsX.ch, the Swiss Initiative for Systems Biology evaluated by the  ... 
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Enhanced parallel Differential Evolution algorithm for problems in computational systems biology

D.R. Penas, J.R. Banga, P. González, R. Doallo
<span title="">2015</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/spnlkxfb7fevrarnlb7rv32roy" style="color: black;">Applied Soft Computing</a> </i> &nbsp;
However, for most realistic applications, like those considering parameter estimation in dynamic models, DE still requires excessive computation times.  ...  Many key problems in computational systems biology and bioinformatics can be formulated and solved using a global optimization framework.  ...  Result for parameter estimation problems in systems biology In computational systems biology, parameter estimation in models of nonlinear dynamic systems seeks to obtain a decision vector p, that optimizes  ... 
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Optimization in computational systems biology

Julio R Banga
<span title="">2008</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/xua5vbjwszdirewaoqnikiu5zm" style="color: black;">BMC Systems Biology</a> </i> &nbsp;
This commentary is focused on applications of mathematical optimization in computational systems biology.  ...  Optimization aims to make a system or design as effective or functional as possible. Mathematical optimization methods are widely used in engineering, economics and science.  ...  Acknowledgements The author would like to thank Matt Hodgkinson for his valuable comments, and acknowledges financial support from EU project BaSysBio LSHG-CT-2006-037469  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1752-0509-2-47">doi:10.1186/1752-0509-2-47</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18507829">pmid:18507829</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2435524/">pmcid:PMC2435524</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/st2yu6xte5d5hkg2ez3plk4daa">fatcat:st2yu6xte5d5hkg2ez3plk4daa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171129043027/https://core.ac.uk/download/pdf/36016853.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/7f/ed/7fed224dd7b5c4511ba5deba83ba055f52ba8d84.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1752-0509-2-47"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2435524" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Dynamic Modeling of Cell-Free Biochemical Networks Using Effective Kinetic Models

Joseph Wayman, Adithya Sagar, Jeffrey Varner
<span title="2015-03-03">2015</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/vt2hc3xcijfofb7cwnxv4hhszi" style="color: black;">Processes</a> </i> &nbsp;
Many of the challenges confronting genomescale kinetic modeling can potentially be overcome in a cell-free system.  ...  Cell-free systems offer many advantages for the study, manipulation and modeling of metabolism compared to in vivo processes.  ...  even for large systems.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/pr3010138">doi:10.3390/pr3010138</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2sqq4afca5ah7iz7dk356houdy">fatcat:2sqq4afca5ah7iz7dk356houdy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170814100523/http://static1.1.sqspcdn.com/static/f/444194/25415817/1410137111157/Paper_v1.pdf?token=IYpSSKmaNDlyHVf%2F%2BcNtM%2Bd8fe8%3D" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/f0/8b/f08b1b6cc7a40cf29e129eb8761cbafefa45e742.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/pr3010138"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> mdpi.com </button> </a>

Mathematical and Computational Modeling in Complex Biological Systems

Zhiwei Ji, Ke Yan, Wenyang Li, Haigen Hu, Xiaoliang Zhu
<span title="">2017</span> <i title="Hindawi Limited"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/icbhosh775h7bgzgot6avm3cua" style="color: black;">BioMed Research International</a> </i> &nbsp;
Recent developments in high-throughput technologies urge the systems biology to achieve more precise models for complex diseases.  ...  The use of computational models in systems biology allows us to explore the pathogenesis of complex diseases, improve our understanding of the latent molecular mechanisms, and promote treatment strategy  ...  This study was also supported by the Foundation of Talent's Startup Project in Zhejiang Gongshang University (no. 1120XJ2116016).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1155/2017/5958321">doi:10.1155/2017/5958321</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28386558">pmid:28386558</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5366773/">pmcid:PMC5366773</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/e6pyjhqdyzfllk6q2l5yjzssf4">fatcat:e6pyjhqdyzfllk6q2l5yjzssf4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190225213125/http://pdfs.semanticscholar.org/74ad/745a6af6ccbf35dda9f20551afbec8134924.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/74/ad/74ad745a6af6ccbf35dda9f20551afbec8134924.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1155/2017/5958321"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> hindawi.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5366773" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Parameter estimation in large-scale systems biology models: a parallel and self-adaptive cooperative strategy

David R. Penas, Patricia González, Jose A. Egea, Ramón Doallo, Julio R. Banga
<span title="2017-01-21">2017</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
The development of large-scale kinetic models is one of the current key issues in computational systems biology and bioinformatics.  ...  Here we consider the problem of parameter estimation in nonlinear dynamic models.  ...  They acknowledge support of the publication fee by the CSIC Open Access Publication Support Initiative through its Unit of Information Resources for Research (URICI).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-016-1452-4">doi:10.1186/s12859-016-1452-4</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28109249">pmid:28109249</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5251293/">pmcid:PMC5251293</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/swsugtre6fc6vp7x67fmimldiu">fatcat:swsugtre6fc6vp7x67fmimldiu</a> </span>
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Cascading failures and the emergence of cooperation in evolutionary-game based models of social and economical networks

Wen-Xu Wang, Ying-Cheng Lai, Dieter Armbruster
<span title="">2011</span> <i title="AIP Publishing"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/jh7idzebgzcuffjreetqux4374" style="color: black;">Chaos</a> </i> &nbsp;
For evolutionary biology, our result may provide hints to the mechanism of large-scale species extinction in a relatively short time period.  ...  Our results can be useful for understanding large-scale catastrophe in real-world systems and in particular, they may yield insights into significant social and economical phenomena such as large-scale  ...  Yang for discussions. This work was supported by AFOSR under Grant No. FA9550-10-1-0083 and by NSF under Grants Nos. BECS-1023101 and CDI-1026710.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1063/1.3621719">doi:10.1063/1.3621719</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21974647">pmid:21974647</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ztqmzhdd6zc6ngqshbp3enr4bi">fatcat:ztqmzhdd6zc6ngqshbp3enr4bi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20120712181539/http://chaos1.la.asu.edu/~yclai/papers/Chaos_2011_WLA.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/e1/37/e1370a130acfbbc3ae013fa3e55843ccc11f463d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1063/1.3621719"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>
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