Michael Hucka

According to our database1, Michael Hucka authored at least 55 papers between 1990 and 2023.

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Bibliography

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

2022
Nine best practices for research software registries and repositories.
PeerJ Comput. Sci., 2022

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

2020
BioModels - 15 years of sharing computational models in life science.
Nucleic Acids Res., 2020

Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2.
J. Integr. Bioinform., 2020

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

Systems Biology Markup Language (SBML) Level 3 Package: Distributions, Version 1, Release 1.
J. Integr. Bioinform., 2020

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

Nine Best Practices for Research Software Registries and Repositories: A Concise Guide.
CoRR, 2020

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

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2.
J. Integr. Bioinform., 2019

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

2018
Software search is not a science, even among scientists: A survey of how scientists and engineers find software.
J. Syst. Softw., 2018

Nostril: A nonsense string evaluator written in Python.
J. Open Source Softw., 2018

Spiral: splitters for identifiers in source code files.
J. Open Source Softw., 2018

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

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core.
J. Integr. Bioinform., 2018

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core.
J. Integr. Bioinform., 2018

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

2016
Toward Community Standards and Software for Whole-Cell Modeling.
IEEE Trans. Biomed. Eng., 2016

Software vs. data in the context of citation.
PeerJ Prepr., 2016

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016.
J. Integr. Bioinform., 2016

SBML Level 3 package: Groups, Version 1 Release 1.
J. Integr. Bioinform., 2016

Software search is not a science, even among scientists.
CoRR, 2016

MOCCASIN: converting MATLAB ODE models to SBML.
Bioinform., 2016

2015
BioModels: ten-year anniversary.
Nucleic Acids Res., 2015

SBML Level 3 package: Hierarchical Model Composition, Version 1 Release 3.
J. Integr. Bioinform., 2015

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

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core.
J. Integr. Bioinform., 2015

Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions.
J. Integr. Bioinform., 2015

JSBML 1.0: providing a smorgasbord of options to encode systems biology models.
Bioinform., 2015

2014
Systems Biology Markup Language (SBML).
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
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.
BMC Syst. Biol., 2013

Path2Models: large-scale generation of computational models from biochemical pathway maps.
BMC Syst. Biol., 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

JSBML: a flexible Java library for working with SBML.
Bioinform., 2011

A Profile of Today's SBML-Compatible Software.
Proceedings of the IEEE 7th International Conference on E-Science, 2011

2010
BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models.
BMC Syst. Biol., 2010

2009
SBML2L<sup>A</sup>T<sub>E</sub>X: Conversion of SBML files into human-readable reports.
Bioinform., 2009

2008
LibSBML: an API Library for SBML.
Bioinform., 2008

2006
BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems.
Nucleic Acids Res., 2006

CellML2SBML: conversion of CellML into SBML.
Bioinform., 2006

SBMLToolbox: an SBML toolbox for MATLAB users.
Bioinform., 2006

Challenges for modeling and simulation methods in systems biology.
Proceedings of the Winter Simulation Conference WSC 2006, 2006

2004
MathSBML: a package for manipulating SBML-based biological models.
Bioinform., 2004

2003
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.
Bioinform., 2003

2002
NeuroML for plug and play neuronal modeling.
Neurocomputing, 2002

The ERATO Systems Biology Workbench: Enabling Interaction and Exchange Between Software Tools for Computational Biology.
Proceedings of the 7th Pacific Symposium on Biocomputing, 2002

1998
Approximate spatial layout processing in the visual system: Modeling texture-based segmentation and shape estimation.
PhD thesis, 1998

1991
An Analysis of Soar as an Integrated Architecture.
SIGART Bull., 1991

Robo-Soar: An integration of external interaction, planning, and learning using Soar.
Robotics Auton. Syst., 1991

1990
Correcting and Extending Domain Knowledge using Outside Guidance.
Proceedings of the Machine Learning, 1990


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