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Journal Articles
- 2024
[j37]Martin Golebiewski
, Gary D. Bader, Padraig Gleeson, Thomas E. Gorochowski, Sarah M. Keating, Matthias König, Chris J. Myers, David P. Nickerson, Björn Sommer, Dagmar Waltemath, Falk Schreiber:
Specifications of standards in systems and synthetic biology: status, developments, and tools in 2024. J. Integr. Bioinform. 21(1) (2024)- [j36]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
- [j35]Yuda Munarko, Anand K. Rampadarath, David P. Nickerson:
CASBERT: BERT-based retrieval for compositely annotated biosimulation model entities. Frontiers Bioinform. 3 (2023) - [j34]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) - [j33]Matthias König, Padraig Gleeson, Martin Golebiewski, Thomas E. Gorochowski, Michael Hucka, Sarah M. Keating, Chris J. Myers, David P. Nickerson, Björn Sommer, Dagmar Waltemath, Falk Schreiber:
Specifications of standards in systems and synthetic biology: status and developments in 2022 and the COMBINE meeting 2022. J. Integr. Bioinform. 20(1) (2023) - 2022
- [j32]Anna Niarakis, Dagmar Waltemath, James A. Glazier, Falk Schreiber, Sarah M. Keating, David P. Nickerson, Claudine Chaouiya, Anne Siegel, Vincent Noël, Henning Hermjakob, Tomás Helikar, Sylvain Soliman, Laurence Calzone:
Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology. Briefings Bioinform. 23(4) (2022) - [j31]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
- [j30]Ciaran M. Welsh, David P. Nickerson, Anand K. Rampadarath, Maxwell Lewis Neal, Herbert M. Sauro, John H. Gennari:
libOmexMeta: enabling semantic annotation of models to support FAIR principles. Bioinform. 37(24): 4898-4900 (2021) - [j29]John H. Gennari, Matthias König, Goksel Misirli, Maxwell Lewis Neal, David P. Nickerson, Dagmar Waltemath:
OMEX metadata specification (version 1.2). J. Integr. Bioinform. 18(3) (2021) - [j28]Falk Schreiber, Padraig Gleeson, Martin Golebiewski, Thomas E. Gorochowski, Michael Hucka, Sarah M. Keating, Matthias König, Chris J. Myers, David P. Nickerson, Björn Sommer, Dagmar Waltemath:
Specifications of standards in systems and synthetic biology: status and developments in 2021. J. Integr. Bioinform. 18(3) (2021) - [j27]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) - [j26]Niloofar Shahidi, Michael Pan, Soroush Safaei, Kenneth Tran, Edmund J. Crampin, David P. Nickerson:
Hierarchical semantic composition of biosimulation models using bond graphs. PLoS Comput. Biol. 17(5) (2021) - 2020
- [j25]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) - [j24]Maxwell Lewis Neal, John H. Gennari, Dagmar Waltemath, David P. Nickerson, Matthias König:
Open modeling and exchange (OMEX) metadata specification version 1.0. J. Integr. Bioinform. 17(2-3) (2020) - [j23]Falk Schreiber, Björn Sommer, Tobias Czauderna, Martin Golebiewski, Thomas E. Gorochowski, Michael Hucka, Sarah M. Keating, Matthias König, Chris J. Myers, David P. Nickerson, Dagmar Waltemath:
Specifications of standards in systems and synthetic biology: status and developments in 2020. J. Integr. Bioinform. 17(2-3) (2020) - [j22]Dagmar Waltemath, Martin Golebiewski, Michael L. Blinov, Padraig Gleeson, Henning Hermjakob, Michael Hucka, Esther Thea Inau, Sarah M. Keating, Matthias König, Olga Krebs, Rahuman S. Malik-Sheriff, David P. Nickerson, Ernst Oberortner, Herbert M. Sauro, Falk Schreiber, Lucian P. Smith, Melanie I. Stefan, Ulrike Wittig, Chris J. Myers:
The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE). J. Integr. Bioinform. 17(2-3) (2020) - [j21]Jason A. Papin, Feilim Mac Gabhann, Herbert M. Sauro, David P. Nickerson, Anand K. Rampadarath:
Improving reproducibility in computational biology research. PLoS Comput. Biol. 16(5) (2020) - 2019
- [j20]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) - [j19]Marek Ostaszewski, Stephan Gebel, Inna Kuperstein, Alexander Mazein, Andrei Yu. Zinovyev, Ugur Dogrusoz, Jan Hasenauer, Ronan M. T. Fleming, Nicolas Le Novère, Piotr Gawron, Thomas S. Ligon, Anna Niarakis, David P. Nickerson, Daniel Weindl, Rudi Balling, Emmanuel Barillot, Charles Auffray, Reinhard Schneider:
Community-driven roadmap for integrated disease maps. Briefings Bioinform. 20(2): 659-670 (2019) - [j18]Dewan M. Sarwar, Reza Kalbasi, John H. Gennari, Brian E. Carlson, Maxwell Lewis Neal, Bernard de Bono, Koray Atalag, Peter J. Hunter, David P. Nickerson:
Model annotation and discovery with the Physiome Model Repository. BMC Bioinform. 20(1): 457:1-457:10 (2019) - [j17]Falk Schreiber, Björn Sommer, Gary D. Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Sarah M. Keating, Matthias König, Chris J. Myers, David P. Nickerson, Dagmar Waltemath:
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019. J. Integr. Bioinform. 16(2) (2019) - 2018
- [j16]Frank T. Bergmann, Jonathan Cooper, Matthias König, Ion I. Moraru, David P. Nickerson, Nicolas Le Novère, Brett G. Olivier, Sven Sahle, Lucian P. Smith, Dagmar Waltemath:
Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3). J. Integr. Bioinform. 15(1) (2018) - [j15]Falk Schreiber, Gary D. Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Sarah M. Keating, Nicolas Le Novère, Chris J. Myers, David P. Nickerson, Björn Sommer, Dagmar Waltemath:
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017. J. Integr. Bioinform. 15(1) (2018) - 2017
- [j14]Frank T. Bergmann, David P. Nickerson, Dagmar Waltemath, Martin Scharm:
SED-ML web tools: generate, modify and export standard-compliant simulation studies. Bioinform. 33(8): 1253-1254 (2017) - 2016
- [j13]Falk Schreiber, Gary D. Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nicolas Le Novère, Chris J. Myers, David P. Nickerson, Björn Sommer, Dagmar Waltemath:
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016. J. Integr. Bioinform. 13(3) (2016) - 2015
- [j12]Frank T. Bergmann, Jonathan Cooper, Nicolas Le Novère, David P. Nickerson, Dagmar Waltemath:
Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2. J. Integr. Bioinform. 12(2) (2015) - [j11]Autumn A. Cuellar, Warren Hedley, Melanie Nelson, Catherine M. Lloyd, Matt D. B. Halstead, David P. Bullivant, David P. Nickerson, Peter J. Hunter, Poul M. F. Nielsen:
The CellML 1.1 Specification. J. Integr. Bioinform. 12(2) (2015) - [j10]Falk Schreiber, Gary D. Bader, Martin Golebiewski, Michael Hucka, Benjamin Kormeier, Nicolas Le Novère, Chris J. Myers, David P. Nickerson, Björn Sommer, Dagmar Waltemath, Stephan Weise:
Specifications of Standards in Systems and Synthetic Biology. J. Integr. Bioinform. 12(2) (2015) - 2014
- [j9]Frank T. Bergmann, Richard R. Adams, Stuart L. Moodie, Jonathan Cooper, Mihai Glont, Martin Golebiewski, Michael Hucka, Camille Laibe, Andrew K. Miller, David P. Nickerson, Brett G. Olivier, Nicolas Rodriguez, Herbert M. Sauro, Martin Scharm, Stian Soiland-Reyes, Dagmar Waltemath, Florent Yvon, Nicolas Le Novère:
COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project. BMC Bioinform. 15: 369 (2014) - 2011
- [j8]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) - [j7]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) - [j6]Dagmar Waltemath, Richard R. Adams, Frank T. Bergmann, Michael Hucka, Fedor A. Kolpakov, Andrew K. Miller, Ion I. Moraru, David P. Nickerson, Sven Sahle, Jacky L. Snoep, Nicolas Le Novère:
Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language. BMC Syst. Biol. 5: 198 (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) - 2008
- [j3]David P. Nickerson, Alberto Corrias, Martin L. Buist:
Reference descriptions of cellular electrophysiology models. Bioinform. 24(8): 1112-1114 (2008) - 2006
- [j2]David P. Nickerson, Martyn P. Nash, Poul M. F. Nielsen, Nicolas Smith, Peter J. Hunter:
Computational multiscale modeling in the IUPS Physiome Project: Modeling cardiac electromechanics. IBM J. Res. Dev. 50(6): 617-630 (2006) - 2003
- [j1]Autumn A. Cuellar, Catherine M. Lloyd, Poul M. F. Nielsen, David P. Bullivant, David P. Nickerson, Peter J. Hunter:
An Overview of CellML 1.1, a Biological Model Description Language. Simul. 79(12): 740-747 (2003)
Conference and Workshop Papers
- 2023
- [c8]Reza Kalbasi, David P. Nickerson, Koray Atalag:
PhysioMed: A Semantic Web based Framework for Linking Healthcare Information with Computational Physiology Models. BCB 2023: 85:1 - [c7]Thiranja P. Babarenda Gamage, Ayah Elsayed, Chinchien Lin, Alan Wu, Yuan Feng, Jianwei Yu, Linkun Gao, Savindi Wijenayaka, Martyn P. Nash, Anthony J. Doyle, David P. Nickerson:
Vision for the 12 LABOURS Digital Twin Platform. EMBC 2023: 1-4 - 2017
- [c6]David Phillip Nickerson, Peter John Hunter:
Introducing the Physiome Journal: Improving Reproducibility, Reuse, and Discovery of Computational Models. eScience 2017: 448-449 - [c5]Chris J. Myers, Gary D. Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nicolas Le Novère, David P. Nickerson, Falk Schreiber, Dagmar Waltemath:
A brief history of COMBINE. WSC 2017: 884-895 - 2013
- [c4]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
- [c3]David P. Nickerson, Carey Stevens, Matt D. B. Halstead, Peter J. Hunter, Poul M. F. Nielsen:
Toward a Curated CellML Model Repository. EMBC 2006: 4237-4240 - [c2]David P. Nickerson, Steven A. Niederer, Carey Stevens, Martyn P. Nash, Peter J. Hunter:
A Computational Model of Cardiac Electromechanics. EMBC 2006: 5311-5314 - 2005
- [c1]Shane Blackett, David P. Bullivant, David P. Nickerson, Peter J. Hunter:
Multi-scale and multi-physics visualization. SIGGRAPH Posters 2005: 136
Reference Works
- 2014
- [r1]Tommy Yu, Randall D. Britten, David P. Nickerson, Peter J. Hunter, Poul M. F. Nielsen:
Physiome Repository. Encyclopedia of Computational Neuroscience 2014
Informal and Other Publications
- 2023
- [i3]Yuda Munarko, Anand K. Rampadarath, David P. Nickerson:
Building a search tool for compositely annotated entities using Transformer-based approach: Case study in Biosimulation Model Search Engine (BMSE). F1000Research 12: 162 (2023) - 2022
- [i2]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) - 2014
- [i1]Frank T. Bergmann, Richard Adams, Stuart L. Moodie, Jonathan Cooper, Mihai Glont, Martin Golebiewski, Michael Hucka, Camille Laibe, Andrew K. Miller, David P. Nickerson, Brett G. Olivier, Nicolas Rodriguez, Herbert M. Sauro, Martin Scharm, Stian Soiland-Reyes, Dagmar Waltemath, Florent Yvon, Nicolas Le Novère:
COMBINE archive: One File To Share Them All. CoRR abs/1407.4992 (2014)
Coauthor Index
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