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Alan Garny
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Journal Articles
- 2024
- [j13]Lucian P. Smith
, Frank T. Bergmann
, Alan Garny
, Tomás Helikar, Jonathan R. Karr
, David P. Nickerson
, Herbert M. Sauro
, Dagmar Waltemath
, Matthias König:
The simulation experiment description markup language (SED-ML): language specification for level 1 version 5. J. Integr. Bioinform. 21(1) (2024) - 2023
- [j12]Michael Clerx, Michael T. Cooling, Jonathan Cooper, Alan Garny, Keri R. Moyle, David P. Nickerson
, Poul M. F. Nielsen, Hugh Sorby:
CellML 2.0.1. J. Integr. Bioinform. 20(1) (2023) - 2022
- [j11]Bilal Shaikh
, Lucian P. Smith
, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson
, Eran Agmon
, Henry Agnew
, Steven S. Andrews
, Azraf Anwar, Moritz E. Beber
, Frank T. Bergmann
, David Brooks
, Lutz Brusch
, Laurence Calzone
, Kiri Choi
, Joshua Cooper, John Detloff, Brian Drawert
, Michel Dumontier
, G. Bard Ermentrout
, James R. Faeder
, Andrew P. Freiburger
, Fabian Fröhlich
, Akira Funahashi
, Alan Garny
, John H. Gennari
, Padraig Gleeson
, Anne Goelzer
, Zachary B. Haiman
, Jan Hasenauer
, Joseph L. Hellerstein
, Henning Hermjakob
, Stefan Hoops
, Jon C. Ison
, Diego Jahn
, Henry V. Jakubowski
, Ryann Jordan, Matús Kalas
, Matthias König
, Wolfram Liebermeister
, Rahuman S. Malik-Sheriff
, Synchon Mandal
, Robert A. McDougal
, J. Kyle Medley, Pedro Mendes
, Robert Müller, Chris J. Myers
, Aurélien Naldi
, Tung V. N. Nguyen
, David P. Nickerson
, Brett G. Olivier
, Drashti Patoliya, Loïc Paulevé
, Linda R. Petzold
, Ankita Priya, Anand K. Rampadarath
, Johann M. Rohwer
, Ali Sinan Saglam
, Dilawar Singh
, Ankur Sinha
, Jacky L. Snoep
, Hugh Sorby
, Ryan K. Spangler
, Jörn Starruß
, Payton J. Thomas
, David D. van Niekerk, Daniel Weindl
, Fengkai Zhang
, Anna Zhukova
, Arthur P. Goldberg
, James C. Schaff
, Michael L. Blinov
, Herbert M. Sauro
, Ion I. Moraru
, Jonathan R. Karr
:
BioSimulators: a central registry of simulation engines and services for recommending specific tools. Nucleic Acids Res. 50(W1): 108-114 (2022) - 2021
- [j10]Lucian P. Smith
, Frank T. Bergmann, Alan Garny, Tomás Helikar, Jonathan R. Karr, David P. Nickerson
, Herbert M. Sauro, Dagmar Waltemath
, Matthias König
:
The simulation experiment description markup language (SED-ML): language specification for level 1 version 4. J. Integr. Bioinform. 18(3) (2021) - 2020
- [j9]Michael Clerx
, Michael T. Cooling
, Jonathan Cooper
, Alan Garny
, Keri R. Moyle
, David P. Nickerson
, Poul M. F. Nielsen
, Hugh Sorby
:
CellML 2.0. J. Integr. Bioinform. 17(2-3) (2020) - 2019
- [j8]Maxwell Lewis Neal
, Matthias König
, David P. Nickerson
, Goksel Misirli
, Reza Kalbasi, Andreas Dräger
, Koray Atalag, Vijayalakshmi Chelliah, Michael T. Cooling
, Daniel L. Cook, Sharon M. Crook
, Miguel de Alba, Samuel H. Friedman
, Alan Garny, John H. Gennari
, Padraig Gleeson
, Martin Golebiewski, Michael Hucka
, Nick S. Juty, Chris J. Myers, Brett G. Olivier
, Herbert M. Sauro, Martin Scharm, Jacky L. Snoep
, Vasundra Touré, Anil Wipat
, Olaf Wolkenhauer
, Dagmar Waltemath
:
Harmonizing semantic annotations for computational models in biology. Briefings Bioinform. 20(2): 540-550 (2019) - 2011
- [j7]Tommy Yu, Catherine M. Lloyd, David P. Nickerson
, Mike T. Cooling
, Andrew K. Miller, Alan Garny, Jonna R. Terkildsen, James R. Lawson
, Randall Britten, Peter J. Hunter
, Poul M. F. Nielsen:
The Physiome Model Repository 2. Bioinform. 27(5): 743-744 (2011) - [j6]Andrew K. Miller, Tommy Yu, Randall Britten, Mike T. Cooling
, James R. Lawson
, Dougal Cowan, Alan Garny, Matt D. B. Halstead, Peter J. Hunter
, David P. Nickerson
, Geoff Nunns, Sarala M. Wimalaratne
, Poul M. F. Nielsen:
Revision history aware repositories of computational models of biological systems. BMC Bioinform. 12: 22 (2011) - [j5]Dagmar Waltemath, Richard R. Adams
, Daniel A. Beard
, Frank T. Bergmann
, Upinder S. Bhalla, Randall Britten, Vijayalakshmi Chelliah
, Mike T. Cooling
, Jonathan Cooper
, Edmund J. Crampin, Alan Garny, Stefan Hoops, Michael Hucka
, Peter J. Hunter
, Edda Klipp, Camille Laibe
, Andrew K. Miller, Ion I. Moraru
, David P. Nickerson
, Poul M. F. Nielsen, Macha Nikolski, Sven Sahle, Herbert M. Sauro
, Henning Schmidt, Jacky L. Snoep
, Dominic P. Tolle
, Olaf Wolkenhauer
, Nicolas Le Novère:
Minimum Information About a Simulation Experiment (MIASE). PLoS Comput. Biol. 7(4) (2011) - 2010
- [j4]Andrew K. Miller, Justin Marsh, Adam Reeve, Alan Garny, Randall Britten, Matt D. B. Halstead, Jonathan Cooper
, David P. Nickerson
, Poul M. F. Nielsen:
An overview of the CellML API and its implementation. BMC Bioinform. 11: 178 (2010) - 2009
- [j3]Joe Pitt-Francis
, Pras Pathmanathan, Miguel O. Bernabeu, Rafel Bordas
, Jonathan Cooper
, Alexander G. Fletcher
, Gary R. Mirams
, Philip J. Murray
, James M. Osborne
, Alex Walter, S. Jonathan Chapman
, Alan Garny, Ingeborg M. M. van Leeuwen, Philip K. Maini, Blanca Rodríguez, Sarah L. Waters
, Jonathan P. Whiteley, Helen M. Byrne
, David Gavaghan
:
Chaste: A test-driven approach to software development for biological modelling. Comput. Phys. Commun. 180(12): 2452-2471 (2009) - 2003
- [j2]Alan Garny, Peter Kohl
, Denis Noble:
Cellular Open Resource (COR): a Public CellML Based Environment for Modeling Biological Function. Int. J. Bifurc. Chaos 13(12): 3579-3590 (2003) - [j1]Olga Solovyova, Nathalie Vikulova
, Leonid B. Katsnelson
, Vladimir S. Markhasin, P. J. Noble, Alan Garny, Peter Kohl
, Denis Noble:
Mechanical Interaction of Heterogeneous Cardiac Muscle Segments in silico: Effects on CA2+ Handling and Action Potential. Int. J. Bifurc. Chaos 13(12): 3757-3782 (2003)
Conference and Workshop Papers
- 2013
- [c2]David P. Nickerson
, Alan Garny, Poul M. F. Nielsen, Peter J. Hunter
:
Standards and tools supporting collaborative development of the virtual physiological human. EMBC 2013: 5541-5544 - 2006
- [c1]Jonathan Cooper
, Steve McKeever, Alan Garny:
On the application of partial evaluation to the optimisation of cardiac electrophysiological simulations. PEPM 2006: 12-20
Informal and Other Publications
- 2022
- [i1]Bilal Shaikh, Lucian P. Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Eran Agmon, Henry Agnew, Steven S. Andrews, Azraf Anwar, Moritz E. Beber, Frank T. Bergmann, David Brooks, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G. Bard Ermentrout, James R. Faeder, Andrew P. Freiburger, Fabian Fröhlich
, Akira Funahashi, Alan Garny, John H. Gennari, Padraig Gleeson, Anne Goelzer, Zachary B. Haiman, Joseph L. Hellerstein, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry V. Jakubowski, Ryann Jordan, Matús Kalas, Matthias König, Wolfram Liebermeister, Synchon Mandal, Robert A. McDougal, J. Kyle Medley, Pedro Mendes, Robert Müller, Chris J. Myers, Aurélien Naldi, Tung V. N. Nguyen, David P. Nickerson, Brett G. Olivier, Drashti Patoliya, Loïc Paulevé, Linda R. Petzold, Ankita Priya, Anand K. Rampadarath, Johann M. Rohwer, Ali Sinan Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David D. van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr:
BioSimulators: a central registry of simulation engines and services for recommending specific tools. CoRR abs/2203.06732 (2022)
Coauthor Index
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