Literature DB >> 21303862

SBML-PET-MPI: a parallel parameter estimation tool for Systems Biology Markup Language based models.

Zhike Zi1.   

Abstract

UNLABELLED: Parameter estimation is crucial for the modeling and dynamic analysis of biological systems. However, implementing parameter estimation is time consuming and computationally demanding. Here, we introduced a parallel parameter estimation tool for Systems Biology Markup Language (SBML)-based models (SBML-PET-MPI). SBML-PET-MPI allows the user to perform parameter estimation and parameter uncertainty analysis by collectively fitting multiple experimental datasets. The tool is developed and parallelized using the message passing interface (MPI) protocol, which provides good scalability with the number of processors. AVAILABILITY: SBML-PET-MPI is freely available for non-commercial use at http://www.bioss.uni-freiburg.de/cms/sbml-pet-mpi.html or http://sites.google.com/site/sbmlpetmpi/.

Mesh：

Year:  2011        PMID： 21303862     DOI： 10.1093/bioinformatics/btr038

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  7 in total

1.  Spatiotemporal Control of TGF-β Signaling with Light.

Authors:  Yuchao Li; Minji Lee; Nury Kim; Guoyu Wu; Difan Deng; Jin Man Kim; Xuedong Liu; Won Do Heo; Zhike Zi
Journal:  ACS Synth Biol       Date:  2018-01-12       Impact factor: 5.110

2.  Bistability of a coupled Aurora B kinase-phosphatase system in cell division.

Authors:  Anatoly V Zaytsev; Dario Segura-Peña; Maxim Godzi; Abram Calderon; Edward R Ballister; Rumen Stamatov; Alyssa M Mayo; Laura Peterson; Ben E Black; Fazly I Ataullakhanov; Michael A Lampson; Ekaterina L Grishchuk
Journal:  Elife       Date:  2016-01-14       Impact factor: 8.140

3.  Quantitative analysis of transient and sustained transforming growth factor-β signaling dynamics.

Authors:  Zhike Zi; Zipei Feng; Douglas A Chapnick; Markus Dahl; Difan Deng; Edda Klipp; Aristidis Moustakas; Xuedong Liu
Journal:  Mol Syst Biol       Date:  2011-05-24       Impact factor: 11.429

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

Authors:  David R Penas; Patricia González; Jose A Egea; Ramón Doallo; Julio R Banga
Journal:  BMC Bioinformatics       Date:  2017-01-21       Impact factor: 3.169

Review 5.  Mathematical and Computational Modeling in Complex Biological Systems.

Authors:  Zhiwei Ji; Ke Yan; Wenyang Li; Haigen Hu; Xiaoliang Zhu
Journal:  Biomed Res Int       Date:  2017-03-13       Impact factor: 3.411

Review 6.  Dynamics of TGF-β/Smad signaling.

Authors:  Zhike Zi; Douglas A Chapnick; Xuedong Liu
Journal:  FEBS Lett       Date:  2012-04-09       Impact factor: 4.124

7.  SBSI: an extensible distributed software infrastructure for parameter estimation in systems biology.

Authors:  Richard Adams; Allan Clark; Azusa Yamaguchi; Neil Hanlon; Nikos Tsorman; Shakir Ali; Galina Lebedeva; Alexey Goltsov; Anatoly Sorokin; Ozgur E Akman; Carl Troein; Andrew J Millar; Igor Goryanin; Stephen Gilmore
Journal:  Bioinformatics       Date:  2013-01-17       Impact factor: 6.937
  7 in total

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