David P. Nickerson

According to our database1, David P. Nickerson authored at least 47 papers between 2003 and 2023.

Collaborative distances:
  • Dijkstra number2 of four.
  • Erdős number3 of four.

Timeline

Legend:

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PhD thesis 
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Links

Online presence:

On csauthors.net:

Bibliography

2023
CASBERT: BERT-based retrieval for compositely annotated biosimulation model entities.
Frontiers Bioinform., May, 2023

Specifications of standards in systems and synthetic biology: status and developments in 2022 and the COMBINE meeting 2022.
J. Integr. Bioinform., March, 2023

CellML 2.0.1.
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).
F1000Research, 2023

Vision for the 12 LABOURS Digital Twin Platform.
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.
Proceedings of the 14th ACM International Conference on Bioinformatics, 2023

2022
BioSimulators: a central registry of simulation engines and services for recommending specific tools.
Nucleic Acids Res., 2022

BioSimulators: a central registry of simulation engines and services for recommending specific tools.
CoRR, 2022

Addressing <i>barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology</i>.
Briefings Bioinform., 2022

2021
Hierarchical semantic composition of biosimulation models using bond graphs.
PLoS Comput. Biol., 2021

The simulation experiment description markup language (SED-ML): language specification for level 1 version 4.
J. Integr. Bioinform., 2021

Specifications of standards in systems and synthetic biology: status and developments in 2021.
J. Integr. Bioinform., 2021

OMEX metadata specification (version 1.2).
J. Integr. Bioinform., 2021

libOmexMeta: enabling semantic annotation of models to support FAIR principles.
Bioinform., 2021

2020
Improving reproducibility in computational biology research.
PLoS Comput. Biol., 2020

The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE).
J. Integr. Bioinform., 2020

Specifications of standards in systems and synthetic biology: status and developments in 2020.
J. Integr. Bioinform., 2020

Open modeling and exchange (OMEX) metadata specification version 1.0.
J. Integr. Bioinform., 2020

CellML 2.0.
J. Integr. Bioinform., 2020

2019
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019.
J. Integr. Bioinform., 2019

Model annotation and discovery with the Physiome Model Repository.
BMC Bioinform., 2019

Community-driven roadmap for integrated disease maps.
Briefings Bioinform., 2019

Harmonizing semantic annotations for computational models in biology.
Briefings Bioinform., 2019

2018
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017.
J. Integr. Bioinform., 2018

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3).
J. Integr. Bioinform., 2018

2017
SED-ML web tools: generate, modify and export standard-compliant simulation studies.
Bioinform., 2017

A brief history of COMBINE.
Proceedings of the 2017 Winter Simulation Conference, 2017

Introducing the Physiome Journal: Improving Reproducibility, Reuse, and Discovery of Computational Models.
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.
J. Integr. Bioinform., 2016

2015
Specifications of Standards in Systems and Synthetic Biology.
J. Integr. Bioinform., 2015

The CellML 1.1 Specification.
J. Integr. Bioinform., 2015

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2.
J. Integr. Bioinform., 2015

2014
Physiome Repository.
Proceedings of the Encyclopedia of Computational Neuroscience, 2014

COMBINE archive: One File To Share Them All.
CoRR, 2014

COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project.
BMC Bioinform., 2014

2013
Standards and tools supporting collaborative development of the virtual physiological human.
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).
PLoS Comput. Biol., 2011

Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language.
BMC Syst. Biol., 2011

Revision history aware repositories of computational models of biological systems.
BMC Bioinform., 2011

The Physiome Model Repository 2.
Bioinform., 2011

2010
An overview of the CellML API and its implementation.
BMC Bioinform., 2010

2008
Reference descriptions of cellular electrophysiology models.
Bioinform., 2008

2006
Computational multiscale modeling in the IUPS Physiome Project: Modeling cardiac electromechanics.
IBM J. Res. Dev., 2006

Toward a Curated CellML Model Repository.
Proceedings of the 28th International Conference of the IEEE Engineering in Medicine and Biology Society, 2006

A Computational Model of Cardiac Electromechanics.
Proceedings of the 28th International Conference of the IEEE Engineering in Medicine and Biology Society, 2006

2005
Multi-scale and multi-physics visualization.
Proceedings of the International Conference on Computer Graphics and Interactive Techniques, 2005

2003
An Overview of CellML 1.1, a Biological Model Description Language.
Simul., 2003


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