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For: Garny A, Nickerson DP, Cooper J, Weber dos Santos R, Miller AK, McKeever S, Nielsen PMF, Hunter PJ. CellML and associated tools and techniques. Philos Trans A Math Phys Eng Sci 2008;366:3017-3043. [PMID: 18579471 DOI: 10.1098/rsta.2008.0094] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Number Cited by Other Article(s)
1
Zaniboni M. Ventricular Repolarization and Calcium Transient Show Resonant Behavior under Oscillatory Pacing Rate. Biomolecules 2022;12:biom12070873. [PMID: 35883429 PMCID: PMC9313145 DOI: 10.3390/biom12070873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 06/10/2022] [Accepted: 06/21/2022] [Indexed: 11/24/2022]  Open
2
Hendrix M, Clerx M, Tamuri AU, Keating SM, Johnstone RH, Cooper J, Mirams GR. cellmlmanip and chaste_codegen: automatic CellML to C++ code generation with fixes for singularities and automatically generated Jacobians. Wellcome Open Res 2022;6:261. [PMID: 35299708 PMCID: PMC8902258 DOI: 10.12688/wellcomeopenres.17206.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/16/2022] [Indexed: 11/20/2022]  Open
3
Sher A, Niederer SA, Mirams GR, Kirpichnikova A, Allen R, Pathmanathan P, Gavaghan DJ, van der Graaf PH, Noble D. A Quantitative Systems Pharmacology Perspective on the Importance of Parameter Identifiability. Bull Math Biol 2022;84:39. [PMID: 35132487 PMCID: PMC8821410 DOI: 10.1007/s11538-021-00982-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 11/30/2021] [Indexed: 12/31/2022]
4
Hendrix M, Clerx M, Tamuri AU, Keating SM, Johnstone RH, Cooper J, Mirams GR. chaste codegen: automatic CellML to C++ code generation with fixes for singularities and automatically generated Jacobians. Wellcome Open Res 2021;6:261. [PMID: 35299708 PMCID: PMC8902258 DOI: 10.12688/wellcomeopenres.17206.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2021] [Indexed: 02/15/2024]  Open
5
Zaniboni M, Cacciani F. Restitution and adaptation measurements for the estimate of short-term cardiac action potential memory: comparison of five human ventricular models. Europace 2020;21:1594-1602. [PMID: 31419289 DOI: 10.1093/europace/euz205] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 07/10/2019] [Indexed: 11/14/2022]  Open
6
Zhang S, Zhang E, Ho H. Extrapolation for a pharmacokinetic model for acetaminophen from adults to neonates: A Latin Hypercube Sampling analysis. Drug Metab Pharmacokinet 2020;35:329-333. [PMID: 32307228 DOI: 10.1016/j.dmpk.2020.03.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 02/24/2020] [Accepted: 03/24/2020] [Indexed: 02/02/2023]
7
Ladd D, Tilūnaitė A, Roderick HL, Soeller C, Crampin EJ, Rajagopal V. Assessing Cardiomyocyte Excitation-Contraction Coupling Site Detection From Live Cell Imaging Using a Structurally-Realistic Computational Model of Calcium Release. Front Physiol 2019;10:1263. [PMID: 31632297 PMCID: PMC6783691 DOI: 10.3389/fphys.2019.01263] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 09/17/2019] [Indexed: 01/11/2023]  Open
8
Lei CL, Clerx M, Beattie KA, Melgari D, Hancox JC, Gavaghan DJ, Polonchuk L, Wang K, Mirams GR. Rapid Characterization of hERG Channel Kinetics II: Temperature Dependence. Biophys J 2019;117:2455-2470. [PMID: 31451180 PMCID: PMC6990152 DOI: 10.1016/j.bpj.2019.07.030] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/20/2019] [Accepted: 07/17/2019] [Indexed: 11/29/2022]  Open
9
Mapping Tyrosine Kinase Receptor Dimerization to Receptor Expression and Ligand Affinities. Processes (Basel) 2019. [DOI: 10.3390/pr7050288] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]  Open
10
Hoekstra AG, Chopard B, Coster D, Portegies Zwart S, Coveney PV. Multiscale computing for science and engineering in the era of exascale performance. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2019;377:20180144. [PMID: 30967040 PMCID: PMC6388008 DOI: 10.1098/rsta.2018.0144] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/09/2018] [Indexed: 05/18/2023]
11
Bragard J, Sankarankutty AC, Sachse FB. Extended Bidomain Modeling of Defibrillation: Quantifying Virtual Electrode Strengths in Fibrotic Myocardium. Front Physiol 2019;10:337. [PMID: 31001135 PMCID: PMC6456788 DOI: 10.3389/fphys.2019.00337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 03/13/2019] [Indexed: 11/17/2022]  Open
12
Shi Y, Lawford P, Hose DR. Construction of lumped-parameter cardiovascular models using the CellML language. J Med Eng Technol 2019;42:525-531. [PMID: 30774016 DOI: 10.1080/03091902.2019.1576792] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
13
Stanford NJ, Scharm M, Dobson PD, Golebiewski M, Hucka M, Kothamachu VB, Nickerson D, Owen S, Pahle J, Wittig U, Waltemath D, Goble C, Mendes P, Snoep J. Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices. Methods Mol Biol 2019;2049:285-314. [PMID: 31602618 DOI: 10.1007/978-1-4939-9736-7_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
14
Ghosh S, Tran K, Delbridge LMD, Hickey AJR, Hanssen E, Crampin EJ, Rajagopal V. Insights on the impact of mitochondrial organisation on bioenergetics in high-resolution computational models of cardiac cell architecture. PLoS Comput Biol 2018;14:e1006640. [PMID: 30517098 PMCID: PMC6296675 DOI: 10.1371/journal.pcbi.1006640] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 12/17/2018] [Accepted: 11/13/2018] [Indexed: 01/05/2023]  Open
15
Reproducible model development in the cardiac electrophysiology Web Lab. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018;139:3-14. [PMID: 29842853 PMCID: PMC6288479 DOI: 10.1016/j.pbiomolbio.2018.05.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 05/01/2018] [Accepted: 05/23/2018] [Indexed: 12/18/2022]
16
Zaniboni M. Short-term action potential memory and electrical restitution: A cellular computational study on the stability of cardiac repolarization under dynamic pacing. PLoS One 2018;13:e0193416. [PMID: 29494628 PMCID: PMC5832261 DOI: 10.1371/journal.pone.0193416] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 02/09/2018] [Indexed: 01/24/2023]  Open
17
Chase JG, Preiser JC, Dickson JL, Pironet A, Chiew YS, Pretty CG, Shaw GM, Benyo B, Moeller K, Safaei S, Tawhai M, Hunter P, Desaive T. Next-generation, personalised, model-based critical care medicine: a state-of-the art review of in silico virtual patient models, methods, and cohorts, and how to validation them. Biomed Eng Online 2018;17:24. [PMID: 29463246 PMCID: PMC5819676 DOI: 10.1186/s12938-018-0455-y] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 02/12/2018] [Indexed: 01/17/2023]  Open
18
MarkoLAB: A simulator to study ionic channel's stochastic behavior. Comput Biol Med 2017;87:258-270. [PMID: 28618338 DOI: 10.1016/j.compbiomed.2017.05.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 05/28/2017] [Accepted: 05/30/2017] [Indexed: 11/22/2022]
19
Onal B, Gratz D, Hund T. LongQt: A cardiac electrophysiology simulation platform. MethodsX 2016;3:589-599. [PMID: 27942465 PMCID: PMC5137180 DOI: 10.1016/j.mex.2016.11.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]  Open
20
Cooper J, Scharm M, Mirams GR. The Cardiac Electrophysiology Web Lab. Biophys J 2016;110:292-300. [PMID: 26789753 PMCID: PMC4724653 DOI: 10.1016/j.bpj.2015.12.012] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 12/09/2015] [Accepted: 12/11/2015] [Indexed: 12/21/2022]  Open
21
Roehner N, Beal J, Clancy K, Bartley B, Misirli G, Grünberg R, Oberortner E, Pocock M, Bissell M, Madsen C, Nguyen T, Zhang M, Zhang Z, Zundel Z, Densmore D, Gennari JH, Wipat A, Sauro HM, Myers CJ. Sharing Structure and Function in Biological Design with SBOL 2.0. ACS Synth Biol 2016;5:498-506. [PMID: 27111421 DOI: 10.1021/acssynbio.5b00215] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
22
da Silva RR, Bissaco MAS, Goroso DG. MioLab, a rat cardiac contractile force simulator: Applications to teaching cardiac cell physiology and biophysics. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2015;122:480-490. [PMID: 26428599 DOI: 10.1016/j.cmpb.2015.09.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 08/21/2015] [Accepted: 09/11/2015] [Indexed: 06/05/2023]
23
Zhang Z, Nguyen T, Roehner N, Misirli G, Pocock M, Oberortner E, Samineni M, Zundel Z, Beal J, Clancy K, Wipat A, Myers CJ. libSBOLj 2.0: A Java Library to Support SBOL 2.0. ACTA ACUST UNITED AC 2015. [DOI: 10.1109/lls.2016.2546546] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
24
Punzalan FR, Kunieda Y, Amano A. Program Code Generator for Cardiac Electrophysiology Simulation with Automatic PDE Boundary Condition Handling. PLoS One 2015;10:e0136821. [PMID: 26356082 PMCID: PMC4565589 DOI: 10.1371/journal.pone.0136821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 08/10/2015] [Indexed: 11/21/2022]  Open
25
Holzem KM, Madden EJ, Efimov IR. Human cardiac systems electrophysiology and arrhythmogenesis: iteration of experiment and computation. Europace 2015;16 Suppl 4:iv77-iv85. [PMID: 25362174 DOI: 10.1093/europace/euu264] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]  Open
26
McKeever S, Johnson D. The role of markup for enabling interoperability in health informatics. Front Physiol 2015;6:152. [PMID: 26042043 PMCID: PMC4434901 DOI: 10.3389/fphys.2015.00152] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 04/27/2015] [Indexed: 11/13/2022]  Open
27
Garny A, Hunter PJ. OpenCOR: a modular and interoperable approach to computational biology. Front Physiol 2015;6:26. [PMID: 25705192 PMCID: PMC4319394 DOI: 10.3389/fphys.2015.00026] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Accepted: 01/16/2015] [Indexed: 11/26/2022]  Open
28
Cooper J, Spiteri RJ, Mirams GR. Cellular cardiac electrophysiology modeling with Chaste and CellML. Front Physiol 2015;5:511. [PMID: 25610400 PMCID: PMC4285015 DOI: 10.3389/fphys.2014.00511] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 12/09/2014] [Indexed: 11/18/2022]  Open
29
Nickerson DP, Ladd D, Hussan JR, Safaei S, Suresh V, Hunter PJ, Bradley CP. Using CellML with OpenCMISS to Simulate Multi-Scale Physiology. Front Bioeng Biotechnol 2015;2:79. [PMID: 25601911 PMCID: PMC4283644 DOI: 10.3389/fbioe.2014.00079] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 12/11/2014] [Indexed: 11/13/2022]  Open
30
De Lazzari C, Genuini I, Pisanelli DM, D'Ambrosi A, Fedele F. Interactive simulator for e-Learning environments: a teaching software for health care professionals. Biomed Eng Online 2014;13:172. [PMID: 25522902 PMCID: PMC4280694 DOI: 10.1186/1475-925x-13-172] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 12/05/2014] [Indexed: 11/23/2022]  Open
31
Neal ML, Cooling MT, Smith LP, Thompson CT, Sauro HM, Carlson BE, Cook DL, Gennari JH. A reappraisal of how to build modular, reusable models of biological systems. PLoS Comput Biol 2014;10:e1003849. [PMID: 25275523 PMCID: PMC4183381 DOI: 10.1371/journal.pcbi.1003849] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
32
Castiglione F, Pappalardo F, Bianca C, Russo G, Motta S. Modeling biology spanning different scales: an open challenge. BIOMED RESEARCH INTERNATIONAL 2014;2014:902545. [PMID: 25143952 PMCID: PMC4124842 DOI: 10.1155/2014/902545] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 06/25/2014] [Indexed: 02/03/2023]
33
Pathmanathan P, Gray RA. Verification of computational models of cardiac electro-physiology. INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN BIOMEDICAL ENGINEERING 2014;30:525-544. [PMID: 24259465 DOI: 10.1002/cnm.2615] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 07/23/2013] [Accepted: 10/20/2013] [Indexed: 06/02/2023]
34
Hunter P, Chapman T, Coveney PV, de Bono B, Diaz V, Fenner J, Frangi AF, Harris P, Hose R, Kohl P, Lawford P, McCormack K, Mendes M, Omholt S, Quarteroni A, Shublaq N, Skår J, Stroetmann K, Tegner J, Thomas SR, Tollis I, Tsamardinos I, van Beek JHGM, Viceconti M. A vision and strategy for the virtual physiological human: 2012 update. Interface Focus 2014;3:20130004. [PMID: 24427536 DOI: 10.1098/rsfs.2013.0004] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]  Open
35
Modeling the chemoelectromechanical behavior of skeletal muscle using the parallel open-source software library OpenCMISS. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2013;2013:517287. [PMID: 24348739 PMCID: PMC3855958 DOI: 10.1155/2013/517287] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 08/28/2013] [Accepted: 09/13/2013] [Indexed: 11/18/2022]
36
Britten RD, Christie GR, Little C, Miller AK, Bradley C, Wu A, Yu T, Hunter P, Nielsen P. FieldML, a proposed open standard for the Physiome project for mathematical model representation. Med Biol Eng Comput 2013;51:1191-207. [PMID: 23900627 PMCID: PMC3825639 DOI: 10.1007/s11517-013-1097-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 07/02/2013] [Indexed: 11/28/2022]
37
Beattie KA, Luscombe C, Williams G, Munoz-Muriedas J, Gavaghan DJ, Cui Y, Mirams GR. Evaluation of an in silico cardiac safety assay: using ion channel screening data to predict QT interval changes in the rabbit ventricular wedge. J Pharmacol Toxicol Methods 2013;68:88-96. [PMID: 23624022 PMCID: PMC4142193 DOI: 10.1016/j.vascn.2013.04.004] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 04/08/2013] [Accepted: 04/17/2013] [Indexed: 12/22/2022]
38
Mirams GR, Arthurs CJ, Bernabeu MO, Bordas R, Cooper J, Corrias A, Davit Y, Dunn SJ, Fletcher AG, Harvey DG, Marsh ME, Osborne JM, Pathmanathan P, Pitt-Francis J, Southern J, Zemzemi N, Gavaghan DJ. Chaste: an open source C++ library for computational physiology and biology. PLoS Comput Biol 2013;9:e1002970. [PMID: 23516352 PMCID: PMC3597547 DOI: 10.1371/journal.pcbi.1002970] [Citation(s) in RCA: 204] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Accepted: 01/20/2013] [Indexed: 01/23/2023]  Open
39
Punzalan FR, Yamashita Y, Kawabata M, Shimayoshi T, Kuwabara H, Kunieda Y, Amano A. Code generator for distributed parameter biological model simulation with PDE numerical schemes. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2013;2013:1494-1497. [PMID: 24109982 DOI: 10.1109/embc.2013.6609795] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
40
Connecting Models to Data in Multiscale Multicellular Tissue Simulations. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.procs.2013.05.235] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
41
Blätke MA, Dittrich A, Rohr C, Heiner M, Schaper F, Marwan W. JAK/STAT signalling – an executable model assembled from molecule-centred modules demonstrating a module-oriented database concept for systems and synthetic biology. MOLECULAR BIOSYSTEMS 2013;9:1290-307. [DOI: 10.1039/c3mb25593j] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
42
Brette R, Goodman DFM. Simulating spiking neural networks on GPU. NETWORK (BRISTOL, ENGLAND) 2012;23:167-182. [PMID: 23067314 DOI: 10.3109/0954898x.2012.730170] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
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Frangi AF, Coatrieux JL, Peng GCY, D'Argenio DZ, Marmarelis VZ, Michailova A. Editorial: Special issue on multiscale modeling and analysis in computational biology and medicine--part-1. IEEE Trans Biomed Eng 2012;58:2936-42. [PMID: 21937299 DOI: 10.1109/tbme.2011.2165151] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Niederer SA, Smith NP. At the heart of computational modelling. J Physiol 2012;590:1331-8. [PMID: 22271869 DOI: 10.1113/jphysiol.2011.225045] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]  Open
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Levin M. Molecular bioelectricity in developmental biology: new tools and recent discoveries: control of cell behavior and pattern formation by transmembrane potential gradients. Bioessays 2012;34:205-17. [PMID: 22237730 DOI: 10.1002/bies.201100136] [Citation(s) in RCA: 171] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Corrias A, Pathmanathan P, Gavaghan DJ, Buist ML. Modelling tissue electrophysiology with multiple cell types: applications of the extended bidomain framework. Integr Biol (Camb) 2012;4:192-201. [PMID: 22222297 DOI: 10.1039/c2ib00100d] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Marchisio MA. In silico implementation of synthetic gene networks. Methods Mol Biol 2012;813:3-21. [PMID: 22083733 DOI: 10.1007/978-1-61779-412-4_1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Levin M, Stevenson CG. Regulation of cell behavior and tissue patterning by bioelectrical signals: challenges and opportunities for biomedical engineering. Annu Rev Biomed Eng 2012;14:295-323. [PMID: 22809139 PMCID: PMC10472538 DOI: 10.1146/annurev-bioeng-071811-150114] [Citation(s) in RCA: 129] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Chang DC, Dokos S, Lovell NH. Temporo-spatial model construction using the MML and software framework. IEEE Trans Biomed Eng 2011;58:3528-31. [PMID: 21947514 DOI: 10.1109/tbme.2011.2168955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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