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BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology

Alejandro F Villaverde, David Henriques, Kieran Smallbone, Sophia Bongard, Joachim Schmid, Damjan Cicin-Sain, Anton Crombach, Julio Saez-Rodriguez, Klaus Mauch, Eva Balsa-Canto, Pedro Mendes, Johannes Jaeger (+1 others)
<span title="">2015</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;
A description of these formats is given below: • SBML [1] is a model representation format designed for systems biology applications.  ...  Implementations and files The benchmarks in the BioPreDyn-bench collection are implemented in the following formats: 1. ready-to-run implementations in Matlab, AMIGO (a Matlab toolbox), and COPASI. 2.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12918-015-0144-4">doi:10.1186/s12918-015-0144-4</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25880925">pmid:25880925</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4342829/">pmcid:PMC4342829</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kpionivsk5h2rnuc7vcczo6wy4">fatcat:kpionivsk5h2rnuc7vcczo6wy4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170808224058/http://www.iim.csic.es/~gingproc/biopredynbench/BioPreDynBench_Suppl_Info_v21072014.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/d0/22/d022914840a53c1542e560b36ca1fa9cf71d87b5.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12918-015-0144-4"> <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/PMC4342829" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

BioPreDyn-bench: benchmark problems for kinetic modelling in systems biology [article]

Alejandro F Villaverde, David Henriques, Kieran Smallbone, Sophia Bongard, Joachim Schmid, Damjan Cicin-Sain, Anton Crombach, Julio Saez-Rodriguez, Klaus Mauch, Eva Balsa-Canto, Pedro Mendes, Johannes Jaeger, (+1 others)
<span title="2014-07-22">2014</span> <span class="release-stage" >pre-print</span>
Dynamic modelling is one of the cornerstones of systems biology. Many research efforts are currently being invested in the development and exploitation of large-scale kinetic models.  ...  Here we present BioPreDyn-bench, a set of challenging parameter estimation problems which aspire to serve as reference test cases in this area.  ...  for providing the SBML qual file of model B5.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12918-015-0144-">doi:10.1186/s12918-015-0144-</a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1407.5856v1">arXiv:1407.5856v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/d5onob2t6rgmfbizqunlu2j3ea">fatcat:d5onob2t6rgmfbizqunlu2j3ea</a> </span>
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Benchmarking optimization methods for parameter estimation in large kinetic models [article]

Alejandro F. Villaverde, Fabian Froehlich, Daniel Weindl, Jan Hasenauer, Julio R Banga
<span title="2018-04-05">2018</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Results: Here, we use a collection of benchmark problems to evaluate the performance of two families of optimization methods: (i) a multi-start of deterministic local searches; and (ii) a hybrid metaheuristic  ...  While a variety of optimization methods have been suggested to surmount these issues, it is not obvious how to choose the best one for a given problem a priori , since many factors can influence their  ...  Methods and Benchmark Problems Problem definition: Parameter optimization for ODE models describing biological processes We consider deterministic dynamic systems described by nonlinear ODEs of the following  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/295006">doi:10.1101/295006</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/w3usnun4dzekhd64nd7f4ufjva">fatcat:w3usnun4dzekhd64nd7f4ufjva</a> </span>
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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.  ...  Metaheuristics are gaining increased attention as efficient solvers for hard global optimization problems arising in bioinformatics and computational systems biology.  ...  projects DPI2011-28112-C04-03, DPI2011-28112-C04-04, and TIN2013-42148-P, from the CSIC intramural project "BioREDES" (PIE-201170E018) and from the Galician Government under the Consolidation Program of  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.procs.2015.05.331">doi:10.1016/j.procs.2015.05.331</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zgyvxvgbajgcbonjs2xmomx2d4">fatcat:zgyvxvgbajgcbonjs2xmomx2d4</a> </span>
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Dynamic Optimization with Particle Swarms (DOPS): A meta-heuristic for parameter estimation in biochemical models [article]

Jeffrey Varner, Adithya Sagar, Rachel LeCover, Christine Shoemaker
<span title="2017-12-28">2017</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Conclusions: DOPS is a promising meta-heuristic approach for the estimation of biochemical model parameters in relatively few function evaluations.  ...  However, the estimation of the parameters that appear in biochemical models is a significant challenge.  ...  ., Crombach, A., Saez-Rodriguez, J., Mauch, K., Balsa-Canto, E., et al.: Biopredyn-bench: a suite of benchmark problems for dynamic modelling in systems biology.  ... 
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SBbadger: Biochemical Reaction Networks with Definable Degree Distributions [article]

Michael A. Kochen, H. Steven Wiley, Song Feng, Herbert M. Sauro
<span title="2022-02-25">2022</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
An essential step in the development of computational tools for biochemical model inference and simulation is to gauge the performance of those tools against earlier efforts and on an appropriate set of  ...  In this work we present SBbadger, a software tool for the generation of synthetic biochemical reaction or metabolic networks with user defined indegree and outdegree distributions with multiple types of  ...  The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health, the University of Washington or PNNL.  ... 
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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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