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For: Keller R, Dörr A, Tabira A, Funahashi A, Ziller MJ, Adams R, Rodriguez N, Novère NL, Hiroi N, Planatscher H, Zell A, Dräger A. The systems biology simulation core algorithm. BMC Syst Biol 2013;7:55. [PMID: 23826941 PMCID: PMC3707837 DOI: 10.1186/1752-0509-7-55] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 06/18/2013] [Indexed: 11/30/2022]
Number Cited by Other Article(s)
1
Bhandari G, Sharma M, Negi S, Gangola S, Bhatt P, Chen S. System biology analysis of endosulfan biodegradation in bacteria and its effect in other living systems: modeling and simulation studies. J Biomol Struct Dyn 2022;40:13171-13183. [PMID: 34622744 DOI: 10.1080/07391102.2021.1982773] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
2
Shahidi N, Pan M, Tran K, Crampin EJ, Nickerson DP. SBML to bond graphs: From conversion to composition. Math Biosci 2022;352:108901. [PMID: 36096376 DOI: 10.1016/j.mbs.2022.108901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 08/15/2022] [Accepted: 09/05/2022] [Indexed: 11/29/2022]
3
SBMLWebApp: Web-Based Simulation, Steady-State Analysis, and Parameter Estimation of Systems Biology Models. Processes (Basel) 2021. [DOI: 10.3390/pr9101830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]  Open
4
Panchiwala H, Shah S, Planatscher H, Zakharchuk M, König M, Dräger A. The systems biology simulation core library. Bioinformatics 2021;38:864-865. [PMID: 34554191 PMCID: PMC8756180 DOI: 10.1093/bioinformatics/btab669] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 08/08/2021] [Accepted: 09/20/2021] [Indexed: 02/03/2023]  Open
5
Porubsky V, Smith L, Sauro HM. Publishing reproducible dynamic kinetic models. Brief Bioinform 2021;22:bbaa152. [PMID: 32793969 PMCID: PMC8138891 DOI: 10.1093/bib/bbaa152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 05/19/2020] [Accepted: 06/17/2020] [Indexed: 11/14/2022]  Open
6
Bhatt P, Sethi K, Gangola S, Bhandari G, Verma A, Adnan M, Singh Y, Chaube S. Modeling and simulation of atrazine biodegradation in bacteria and its effect in other living systems. J Biomol Struct Dyn 2020;40:3285-3295. [PMID: 33179575 DOI: 10.1080/07391102.2020.1846623] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
7
Maggioli F, Mancini T, Tronci E. SBML2Modelica: integrating biochemical models within open-standard simulation ecosystems. Bioinformatics 2020;36:2165-2172. [PMID: 31738386 DOI: 10.1093/bioinformatics/btz860] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 10/15/2019] [Accepted: 11/15/2019] [Indexed: 11/13/2022]  Open
8
Bhatt K, Maheshwari DK. Insights into zinc-sensing metalloregulator 'Zur' deciphering mechanism of zinc transportation in Bacillus spp. by modeling, simulation and molecular docking. J Biomol Struct Dyn 2020;40:764-779. [PMID: 32924811 DOI: 10.1080/07391102.2020.1818625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
9
Pathak RK, Baunthiyal M, Pandey N, Pandey D, Kumar A. Modeling of the jasmonate signaling pathway in Arabidopsis thaliana with respect to pathophysiology of Alternaria blight in Brassica. Sci Rep 2017;7:16790. [PMID: 29196636 PMCID: PMC5711873 DOI: 10.1038/s41598-017-16884-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 11/08/2017] [Indexed: 01/01/2023]  Open
10
Choi K, Smith LP, Medley JK, Sauro HM. phraSED-ML: A paraphrased, human-readable adaptation of SED-ML. J Bioinform Comput Biol 2016;14:1650035. [PMID: 27774871 DOI: 10.1142/s0219720016500359] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
11
Funahashi A, Hiroi N. Simulation technology and its application in Systems Biology. Nihon Yakurigaku Zasshi 2016;147:101-6. [PMID: 26860650 DOI: 10.1254/fpj.147.101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
12
Dräger A, Zielinski DC, Keller R, Rall M, Eichner J, Palsson BO, Zell A. SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks. BMC SYSTEMS BIOLOGY 2015;9:68. [PMID: 26452770 PMCID: PMC4600286 DOI: 10.1186/s12918-015-0212-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 09/15/2015] [Indexed: 12/25/2022]
13
Somogyi ET, Bouteiller JM, Glazier JA, König M, Medley JK, Swat MH, Sauro HM. libRoadRunner: a high performance SBML simulation and analysis library. Bioinformatics 2015;31:3315-21. [PMID: 26085503 PMCID: PMC4607739 DOI: 10.1093/bioinformatics/btv363] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 06/05/2015] [Indexed: 11/15/2022]  Open
14
Le Novère N. Quantitative and logic modelling of molecular and gene networks. Nat Rev Genet 2015;16:146-58. [PMID: 25645874 PMCID: PMC4604653 DOI: 10.1038/nrg3885] [Citation(s) in RCA: 242] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
15
Juty N, Ali R, Glont M, Keating S, Rodriguez N, Swat MJ, Wimalaratne SM, Hermjakob H, Le Novère N, Laibe C, Chelliah V. BioModels: Content, Features, Functionality, and Use. CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY 2015. [PMID: 26225232 PMCID: PMC4360671 DOI: 10.1002/psp4.3] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
16
SBMLSimulator: A Java Tool for Model Simulation and Parameter Estimation in Systems Biology. COMPUTATION 2014;2:246-257. [PMID: 32211200 PMCID: PMC7093077 DOI: 10.3390/computation2040246] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
17
Dräger A, Palsson BØ. Improving collaboration by standardization efforts in systems biology. Front Bioeng Biotechnol 2014;2:61. [PMID: 25538939 PMCID: PMC4259112 DOI: 10.3389/fbioe.2014.00061] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 11/14/2014] [Indexed: 11/17/2022]  Open
18
Waltemath D, Bergmann FT, Chaouiya C, Czauderna T, Gleeson P, Goble C, Golebiewski M, Hucka M, Juty N, Krebs O, Le Novère N, Mi H, Moraru II, Myers CJ, Nickerson D, Olivier BG, Rodriguez N, Schreiber F, Smith L, Zhang F, Bonnet E. Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE). Stand Genomic Sci 2014. [PMCID: PMC4149000 DOI: 10.4056/sigs.5279417] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]  Open
19
Matsuoka Y, Funahashi A, Ghosh S, Kitano H. Modeling and simulation using CellDesigner. Methods Mol Biol 2014;1164:121-45. [PMID: 24927840 DOI: 10.1007/978-1-4939-0805-9_11] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
20
Vlaic S, Hoffmann B, Kupfer P, Weber M, Dräger A. GRN2SBML: automated encoding and annotation of inferred gene regulatory networks complying with SBML. Bioinformatics 2013;29:2216-7. [PMID: 23803467 DOI: 10.1093/bioinformatics/btt370] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
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