Literature DB >> 24927840

Modeling and simulation using CellDesigner.

Yukiko Matsuoka1, Akira Funahashi, Samik Ghosh, Hiroaki Kitano.   

Abstract

In silico modeling and simulation are effective means to understand how the regulatory systems function in life. In this chapter, we explain how to build a model and run the simulation using CellDesigner, adopting the standards such as SBML and SBGN.

Mesh：

Year:  2014        PMID： 24927840     DOI： 10.1007/978-1-4939-0805-9_11

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  28 in total

Review 1.  Systems Biology for Smart Crops and Agricultural Innovation: Filling the Gaps between Genotype and Phenotype for Complex Traits Linked with Robust Agricultural Productivity and Sustainability.

Authors:  Anil Kumar; Rajesh Kumar Pathak; Sanjay Mohan Gupta; Vikram Singh Gaur; Dinesh Pandey
Journal:  OMICS       Date:  2015-10

2.  Oscillation of cAMP and Ca(2+) in cardiac myocytes: a systems biology approach.

Authors:  Takehisa Kamide; Satoshi Okumura; Samik Ghosh; Yoko Shinoda; Yasumasa Mototani; Yoshiki Ohnuki; Huiling Jin; Wenqian Cai; Kenji Suita; Itaru Sato; Masanari Umemura; Takayuki Fujita; Utako Yokoyama; Motohiko Sato; Kazuharu Furutani; Hiroaki Kitano; Yoshihiro Ishikawa
Journal:  J Physiol Sci       Date:  2015-01-14       Impact factor: 2.781

3.  A graphical and computational modeling platform for biological pathways.

Authors:  Alessandra Livigni; Laura O'Hara; Marta E Polak; Tim Angus; Derek W Wright; Lee B Smith; Tom C Freeman
Journal:  Nat Protoc       Date:  2018-03-15       Impact factor: 13.491

4.  O-Glycologue: A Formal-Language-Based Generator of O-Glycosylation Networks.

Authors:  Andrew G McDonald; Gavin P Davey
Journal:  Methods Mol Biol       Date:  2022

Review 5.  Machine Learning and Hybrid Methods for Metabolic Pathway Modeling.

Authors:  Miroslava Cuperlovic-Culf; Thao Nguyen-Tran; Steffany A L Bennett
Journal:  Methods Mol Biol       Date:  2023

6.  Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology.

Authors:  Anna Niarakis; Dagmar Waltemath; James Glazier; Falk Schreiber; Sarah M Keating; David Nickerson; Claudine Chaouiya; Anne Siegel; Vincent Noël; Henning Hermjakob; Tomáš Helikar; Sylvain Soliman; Laurence Calzone
Journal:  Brief Bioinform       Date:  2022-07-18       Impact factor: 13.994

7.  Relationship Between Dimensionality and Convergence of Optimization Algorithms: A Comparison Between Data-Driven Normalization and Scaling Factor-Based Methods Using PEPSSBI.

Authors:  Andrea Degasperi; Lan K Nguyen; Dirk Fey; Boris N Kholodenko
Journal:  Methods Mol Biol       Date:  2022

8.  Using RegulonDB, the Escherichia coli K-12 Gene Regulatory Transcriptional Network Database.

Authors:  Heladia Salgado; Irma Martínez-Flores; Víctor H Bustamante; Kevin Alquicira-Hernández; Jair S García-Sotelo; Delfino García-Alonso; Julio Collado-Vides
Journal:  Curr Protoc Bioinformatics       Date:  2018-03

9.  NetworkPainter: dynamic intracellular pathway animation in Cytobank.

Authors:  Jonathan R Karr; Harendra Guturu; Edward Y Chen; Stuart L Blair; Jonathan M Irish; Nikesh Kotecha; Markus W Covert
Journal:  BMC Bioinformatics       Date:  2015-05-25       Impact factor: 3.169

Review 10.  Mathematical modelling of metabolic regulation in aging.

Authors:  Mark T Mc Auley; Kathleen M Mooney; Peter J Angell; Stephen J Wilkinson
Journal:  Metabolites       Date:  2015-04-27
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