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List of works by Michael Hucka

A Profile of Today's SBML-Compatible Software

scholarly article published December 2011

A brief history of COMBINE

A community-driven global reconstruction of human metabolism. ⬇️

scientific article

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

scientific article

BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models

scientific article

BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems

scientific article

BioModels: ten-year anniversary

scientific article

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

scientific article

CellML2SBML: conversion of CellML into SBML.

scientific article published on 10 February 2006

Challenges for Modeling and Simulation Methods in Systems Biology

Controlled vocabularies and semantics in systems biology

scientific article (publication date: 25 October 2011)

Corrigendum: The BioPAX community standard for pathway data sharing

correction; published 7 December 2010

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

scientific article published on 01 January 2019

Do genome-scale models need exact solvers or clearer standards?

scientific article published on 14 October 2015

Erratum: Corrigendum: The BioPAX community standard for pathway data sharing

scholarly article published in Nature Biotechnology

Erratum: The Systems Biology Graphical Notation

scholarly article published in Nature Biotechnology

Escalating model sizes and complexities call for standardized forms of representation

scientific article

Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project

scientific article

Harmonizing semantic annotations for computational models in biology

Harmonizing semantic annotations for computational models in biology

scientific article published on 01 March 2019

JSBML 1.0: providing a smorgasbord of options to encode systems biology models

scientific article

JSBML: a flexible Java library for working with SBML.

scientific article

JSBML: a flexible and entirely Java-based library for working with SBML

JSBML: a flexible and entirely Java-based library for working with SBML

LibSBML: an API library for SBML.

scientific article

MOCCASIN: converting MATLAB ODE models to SBML.

scientific article published on 9 February 2016

MathSBML: a package for manipulating SBML-based biological models

scientific article

Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE).

scientific article published on November 2011

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

Minimum information requested in the annotation of biochemical models (MIRIAM)

scientific article

Modeling the E. coli cell: The need for computing, cooperation, and consortia

Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration

scientific article

Nostril: A nonsense string evaluator written in Python

Path2Models: large-scale generation of computational models from biochemical pathway maps

scientific article

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

scientific article (publication date: 2015)

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

scientific article

Rules for modeling signal-transduction systems

scientific article

SBML Level 3 Package Proposal: Annotation

SBML Level 3 package: Groups, Version 1 Release 1.

scientific article

SBML Level 3 package: Hierarchical Model Composition, Version 1 Release 3

article

SBML Level 3 package: Hierarchical Model Composition, Version 1 Release 3.

scientific article

SBML Level 3: an extensible format for the exchange and reuse of biological models

scientific article published on 01 August 2020

SBML Models and MathSBML

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools

scientific article

SBML2L(A)T(E)X: conversion of SBML files into human-readable reports

scientific article

SBMLPkgSpec: a LaTeX style file for SBML package specification documents

scientific article published on 6 September 2017

SBMLToolbox: an SBML toolbox for MATLAB users

scientific article published on 30 March 2006

Software Infrastructure for Effective Communication and Reuse of Computational Models

Software that goes with the flow in systems biology

scientific article

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 2022 and the COMBINE meeting 2022

scientific article published in March 2023

Spiral: splitters for identifiers in source code files

Systems Biology Markup Language (SBML)

Systems Biology Markup Language (SBML)

Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions

scientific article

Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions

Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions

Systems Biology Markup Language (SBML) Level 3 Package: Distributions, Version 1, Release 1

scientific article published on 04 August 2020

Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2

scientific article published on 06 July 2020

The BioPAX community standard for pathway data sharing

scientific article (publication date: September 2010)

The Modeler's Workspace: Making Model-Based Studies of the Nervous System More Accessible

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core

scientific article

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2

scientific article published on 20 June 2019

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core.

scientific article published on 9 March 2018

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 systems biology markup language (SBML): a medium for representation and exchange of biochemical network models

scientific article (publication date: March 2003)

Toward Community Standards and Software for Whole-Cell Modeling

scientific article

Trends and Tools for Modeling in Modern Biology

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