David P. Nickerson

According to our database, David P. Nickerson authored at least 49 papers between 2003 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

The simulation experiment description markup language (SED-ML): language specification for level 1 version 5.

Lucian P. Smith, Frank T. Bergmann, Alan Garny, Tomás Helikar, Jonathan R. Karr, David P. Nickerson, Herbert M. Sauro, Dagmar Waltemath, Matthias König

J. Integr. Bioinform., 2024

Specifications of standards in systems and synthetic biology: status, developments, and tools in 2024.

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

J. Integr. Bioinform., 2024

2023

CASBERT: BERT-based retrieval for compositely annotated biosimulation model entities.

Yuda Munarko, Anand K. Rampadarath, David P. Nickerson

Frontiers Bioinform., May, 2023

Specifications of standards in systems and synthetic biology: status and developments in 2022 and the COMBINE meeting 2022.

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

J. Integr. Bioinform., March, 2023

CellML 2.0.1.

Michael Clerx, Michael T. Cooling, Jonathan Cooper, Alan Garny, Keri R. Moyle, David P. Nickerson, Poul M. F. Nielsen, Hugh Sorby

J. Integr. Bioinform., March, 2023

Building a search tool for compositely annotated entities using Transformer-based approach: Case study in Biosimulation Model Search Engine (BMSE).

Yuda Munarko, Anand K. Rampadarath, David P. Nickerson

F1000Research, 2023

Vision for the 12 LABOURS Digital Twin Platform.

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

Proceedings of the 45th Annual International Conference of the IEEE Engineering in Medicine & Biology Society, 2023

PhysioMed: A Semantic Web based Framework for Linking Healthcare Information with Computational Physiology Models.

Reza Kalbasi, David P. Nickerson, Koray Atalag

Proceedings of the 14th ACM International Conference on Bioinformatics, 2023

2022

BioSimulators: a central registry of simulation engines and services for recommending specific tools.

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

Nucleic Acids Res., 2022

BioSimulators: a central registry of simulation engines and services for recommending specific tools.

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

CoRR, 2022

Addressing <i>barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology</i>.

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

Briefings Bioinform., 2022

2021

Hierarchical semantic composition of biosimulation models using bond graphs.

Niloofar Shahidi, Michael Pan, Soroush Safaei, Kenneth Tran, Edmund J. Crampin, David P. Nickerson

PLoS Comput. Biol., 2021

The simulation experiment description markup language (SED-ML): language specification for level 1 version 4.

Lucian P. Smith, Frank T. Bergmann, Alan Garny, Tomás Helikar, Jonathan R. Karr, David P. Nickerson, Herbert M. Sauro, Dagmar Waltemath, Matthias König

J. Integr. Bioinform., 2021

Specifications of standards in systems and synthetic biology: status and developments in 2021.

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

J. Integr. Bioinform., 2021

OMEX metadata specification (version 1.2).

John H. Gennari, Matthias König, Goksel Misirli, Maxwell Lewis Neal, David P. Nickerson, Dagmar Waltemath

J. Integr. Bioinform., 2021

libOmexMeta: enabling semantic annotation of models to support FAIR principles.

Ciaran M. Welsh, David P. Nickerson, Anand K. Rampadarath, Maxwell Lewis Neal, Herbert M. Sauro, John H. Gennari

Bioinform., 2021

2020

Improving reproducibility in computational biology research.

Jason A. Papin, Feilim Mac Gabhann, Herbert M. Sauro, David P. Nickerson, Anand K. Rampadarath

PLoS Comput. Biol., 2020

The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE).

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

J. Integr. Bioinform., 2020

Specifications of standards in systems and synthetic biology: status and developments in 2020.

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

J. Integr. Bioinform., 2020

Open modeling and exchange (OMEX) metadata specification version 1.0.

Maxwell Lewis Neal, John H. Gennari, Dagmar Waltemath, David P. Nickerson, Matthias König

J. Integr. Bioinform., 2020

CellML 2.0.

Michael Clerx, Michael T. Cooling, Jonathan Cooper, Alan Garny, Keri R. Moyle, David P. Nickerson, Poul M. F. Nielsen, Hugh Sorby

J. Integr. Bioinform., 2020

2019

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019.

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

J. Integr. Bioinform., 2019

Model annotation and discovery with the Physiome Model Repository.

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

BMC Bioinform., 2019

Community-driven roadmap for integrated disease maps.

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

Briefings Bioinform., 2019

Harmonizing semantic annotations for computational models in biology.

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

Briefings Bioinform., 2019

2018

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017.

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

J. Integr. Bioinform., 2018

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3).

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

J. Integr. Bioinform., 2018

2017

SED-ML web tools: generate, modify and export standard-compliant simulation studies.

Frank T. Bergmann, David P. Nickerson, Dagmar Waltemath, Martin Scharm

Bioinform., 2017

A brief history of COMBINE.

Chris J. Myers, Gary D. Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nicolas Le Novère, David P. Nickerson, Falk Schreiber, Dagmar Waltemath

Proceedings of the 2017 Winter Simulation Conference, 2017

Introducing the Physiome Journal: Improving Reproducibility, Reuse, and Discovery of Computational Models.

David Phillip Nickerson, Peter John Hunter

Proceedings of the 13th IEEE International Conference on e-Science, 2017

2016

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016.

Falk Schreiber, Gary D. Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nicolas Le Novère, Chris J. Myers, David P. Nickerson, Björn Sommer, Dagmar Waltemath

J. Integr. Bioinform., 2016

2015

Specifications of Standards in Systems and Synthetic Biology.

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

J. Integr. Bioinform., 2015

The CellML 1.1 Specification.

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

J. Integr. Bioinform., 2015

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2.

Frank T. Bergmann, Jonathan Cooper, Nicolas Le Novère, David P. Nickerson, Dagmar Waltemath

J. Integr. Bioinform., 2015

2014

Physiome Repository.

Tommy Yu, Randall D. Britten, David P. Nickerson, Peter J. Hunter, Poul M. F. Nielsen

Proceedings of the Encyclopedia of Computational Neuroscience, 2014

COMBINE archive: One File To Share Them All.

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

CoRR, 2014

COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project.

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

BMC Bioinform., 2014

2013

Standards and tools supporting collaborative development of the virtual physiological human.

David P. Nickerson, Alan Garny, Poul M. F. Nielsen, Peter J. Hunter

Proceedings of the 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 2013

2011

Minimum Information About a Simulation Experiment (MIASE).

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

PLoS Comput. Biol., 2011

Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language.

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

BMC Syst. Biol., 2011

Revision history aware repositories of computational models of biological systems.

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

BMC Bioinform., 2011

The Physiome Model Repository 2.

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

Bioinform., 2011

2010

An overview of the CellML API and its implementation.

Andrew K. Miller, Justin Marsh, Adam Reeve, Alan Garny, Randall Britten, Matt D. B. Halstead, Jonathan Cooper, David P. Nickerson, Poul M. F. Nielsen

BMC Bioinform., 2010

2008

Reference descriptions of cellular electrophysiology models.

David P. Nickerson, Alberto Corrias, Martin L. Buist

Bioinform., 2008

2006

Computational multiscale modeling in the IUPS Physiome Project: Modeling cardiac electromechanics.

David P. Nickerson, Martyn P. Nash, Poul M. F. Nielsen, Nicolas Smith, Peter J. Hunter

IBM J. Res. Dev., 2006

Toward a Curated CellML Model Repository.

David P. Nickerson, Carey Stevens, Matt D. B. Halstead, Peter J. Hunter, Poul M. F. Nielsen

Proceedings of the 28th International Conference of the IEEE Engineering in Medicine and Biology Society, 2006

A Computational Model of Cardiac Electromechanics.

David P. Nickerson, Steven A. Niederer, Carey Stevens, Martyn P. Nash, Peter J. Hunter

Proceedings of the 28th International Conference of the IEEE Engineering in Medicine and Biology Society, 2006

2005

Multi-scale and multi-physics visualization.

Shane Blackett, David P. Bullivant, David P. Nickerson, Peter J. Hunter

Proceedings of the International Conference on Computer Graphics and Interactive Techniques, 2005

2003

An Overview of CellML 1.1, a Biological Model Description Language.

Autumn A. Cuellar, Catherine M. Lloyd, Poul M. F. Nielsen, David P. Bullivant, David P. Nickerson, Peter J. Hunter

Simul., 2003