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List of works by David Nickerson

A Computational Model of Cardiac Electromechanics

article

A brief history of COMBINE

A physiome standards-based model publication paradigm

scientific article published on May 2009

A semantics, energy-based approach to automate biomodel composition

scientific article published in 2022

A tool for multi-scale modelling of the renal nephron

scientific article published on 30 March 2011

An overview of the CellML API and its implementation

scientific article

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

scientific article

Cardiac Electromechanical Coupling

Cardiac electro-mechanics: from CellML to the whole heart ⬇️

2005 doctoral thesis by David Phillip Nickerson at University of Auckland

CellML 2.0.

scientific article published on 07 August 2020

CellML and associated tools and techniques

scientific article published on September 2008

CellML metadata standards, associated tools and repositories.

scientific article published on May 2009

Comparison of the Gibbs and Suga formulations of cardiac energetics: the demise of "isoefficiency"

scientific article published on 09 August 2012

Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices

scientific article published on 01 January 2019

Harmonizing semantic annotations for computational models in biology

Harmonizing semantic annotations for computational models in biology

scientific article published on 01 March 2019

Improving reproducibility in computational biology research

scientific article published on 19 May 2020

Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)

article by Dagmar Waltemath et al published 15 March 2014 in Standards in genomic sciences

Minimum Information About a Simulation Experiment (MIASE)

scientific article

Model annotation and discovery with the Physiome Model Repository

scientific article published on 06 September 2019

Modeling cardiac electrical activity at the cell and tissue levels

scientific article published on October 2006

Modelling the passive and nerve activated response of the rectus femoris muscle to a flexion loading: a finite element framework.

scientific article

Modular modelling with Physiome standards.

scientific article

Myocardial twitch duration and the dependence of oxygen consumption on pressure-volume area: experiments and modelling.

scientific article published on 8 May 2012

New developments in a strongly coupled cardiac electromechanical model

scientific article published in September 2005

OMEX metadata specification (version 1.2)

scientific article published in 2021

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

scientific article published on 25 June 2020

OpenCMISS: a multi-physics & multi-scale computational infrastructure for the VPH/Physiome project.

scientific article published on 07 July 2011

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

scientific article published on 04 October 2023

Practical application of CellML 1.1: The integration of new mechanisms into a human ventricular myocyte model

scientific article published on 23 June 2008

Practical resources for enhancing the reproducibility of mechanistic modeling in systems biology

scientific article published in September 2021

Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative

scientific article (publication date: 2015)

Reference descriptions of cellular electrophysiology models

scientific article published in March 2008

Relating components of pressure-volume area in Suga's formulation of cardiac energetics to components of the stress-time integral.

scientific article

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

scientific article

Revision history aware repositories of computational models of biological systems.

scientific article

SED-ML Web Tools: Generate, modify and export standard-compliant simulation studies

SED-ML Web Tools: Generate, modify and export standard-compliant simulation studies

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

scientific article published on 2 January 2017

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

scientific article published on 04 September 2015

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

scientific article published on 19 March 2018

Specifications of Standards in Systems and Synthetic Biology

scientific article published on 04 September 2015

Specifications of Standards in Systems and Synthetic Biology

scientific article published in June 2015

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

scientific article published on 18 December 2016

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

scientific article published in September 2016

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

scientific article published on 13 July 2019

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

scientific article published on 29 June 2020

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

scientific article published in March 2023

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

Standards and tools supporting collaborative development of the virtual physiological human

scientific article published on January 2013

The CellML 1.1 Specification

scientific article published on 04 September 2015

The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable.

scientific article published on April 2016

The Noble cardiac ventricular electrophysiology models in CellML.

scientific article

The Open Physiology workflow: modeling processes over physiology circuitboards of interoperable tissue units

scientific article

The Physiome Model Repository 2.

scientific article

The VPH-Physiome Project: Standards, tools and databases for multi-scale physiological modelling

article

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

scientific article published on 29 June 2020

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

scientific article published in 2021

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

scientific article published in March 2024

Toward a curated CellML model repository

scientific article published in January 2006

eSolv, a CellML-based simulation front-end for online teaching

scientific article published on 01 September 2017

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