Michael Hucka

Publication Activity (10 Years)

Years Active: 1990-2023
Publications (10 Years): 25

Top Topics

Markup Language

Computational Models

Systems Biology

Top Venues

J. Integr. Bioinform.

Nucleic Acids Res.

Publications

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
Specifications of standards in systems and synthetic biology: status and developments in 2022 and the COMBINE meeting 2022. J. Integr. Bioinform. 20 (1) (2023)
Daniel Garijo, Hervé Ménager, Lorraine J. Hwang, Ana Trisovic, Michael Hucka, Thomas Morrell, Alice Allen
Nine best practices for research software registries and repositories. PeerJ Comput. Sci. 8 (2022)
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
Specifications of standards in systems and synthetic biology: status and developments in 2021. J. Integr. Bioinform. 18 (3) (2021)
Rahuman S. Malik-Sheriff, Mihai Glont, Tung V. N. Nguyen, Krishna Tiwari, Matthew G. Roberts, Ashley Xavier, Manh T. Vu, Jinghao Men, Matthieu Maire, Sarubini Kananathan, Emma L. Fairbanks, Johannes P. Meyer, Chinmay Arankalle, Thawfeek M. Varusai, Vincent Knight-Schrijver, Lu Li, Corina Dueñas-Roca, Gaurhari Dass, Sarah M. Keating, Young M. Park, Nicola Buso, Nicolas Rodriguez, Michael Hucka, Henning Hermjakob
BioModels - 15 years of sharing computational models in life science. Nucleic Acids Res. 48 (Database-Issue) (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
Specifications of standards in systems and synthetic biology: status and developments in 2020. J. Integr. Bioinform. 17 (2-3) (2020)
Alain Monteil, Alejandra N. González-Beltrán, Alexandros Ioannidis, Alice Allen, Allen Lee, Anita E. Bandrowski, Bruce E. Wilson, Bryce D. Mecum, Cai Fan Du, Carly Robinson, Daniel Garijo, Daniel S. Katz, David Long, Genevieve Milliken, Hervé Ménager, Jessica Hausman, Jurriaan H. Spaaks, Katrina Fenlon, Kristin Vanderbilt, Lorraine J. Hwang, Lynn Davis, Martin Fenner, Michael R. Crusoe, Michael Hucka, Mingfang Wu, Neil P. Chue Hong, Peter J. Teuben, Shelley Stall, Stephan Druskat, Ted Carnevale, Thomas Morrell
Nine Best Practices for Research Software Registries and Repositories: A Concise Guide. CoRR (2020)
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
The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE). J. Integr. Bioinform. 17 (2-3) (2020)
Lucian P. Smith, Stuart L. Moodie, Frank T. Bergmann, Colin S. Gillespie, Sarah M. Keating, Matthias König, Chris J. Myers, Maciek J. Swat, Darren J. Wilkinson, Michael Hucka
Systems Biology Markup Language (SBML) Level 3 Package: Distributions, Version 1, Release 1. J. Integr. Bioinform. 17 (2-3) (2020)
Fengkai Zhang, Lucian P. Smith, Michael L. Blinov, James R. Faeder, William S. Hlavacek, José Juan Tapia, Sarah M. Keating, Nicolas Rodriguez, Andreas Dräger, Leonard A. Harris, Andrew Finney, Bin Hu, Michael Hucka, Martin Meier-Schellersheim
Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2. J. Integr. Bioinform. 17 (2-3) (2020)
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
Harmonizing semantic annotations for computational models in biology. Briefings Bioinform. 20 (2) (2019)
Michael Hucka, Frank T. Bergmann, Claudine Chaouiya, Andreas Dräger, Stefan Hoops, Sarah M. Keating, Matthias König, Nicolas Le Novère, Chris J. Myers, Brett G. Olivier, Sven Sahle, James C. Schaff, Rahuman S. Malik-Sheriff, Lucian P. Smith, Dagmar Waltemath, Darren J. Wilkinson, Fengkai Zhang
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2. J. Integr. Bioinform. 16 (2) (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
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019. J. Integr. Bioinform. 16 (2) (2019)
Michael Hucka
Nostril: A nonsense string evaluator written in Python. J. Open Source Softw. 3 (25) (2018)
Michael Hucka
Spiral: splitters for identifiers in source code files. J. Open Source Softw. 3 (24) (2018)
Michael Hucka, Matthew J. Graham
Software search is not a science, even among scientists: A survey of how scientists and engineers find software. J. Syst. Softw. 141 (2018)
Michael Hucka, Frank T. Bergmann, Andreas Dräger, Stefan Hoops, Sarah M. Keating, Nicolas Le Novère, Chris J. Myers, Brett G. Olivier, Sven Sahle, James C. Schaff, Lucian P. Smith, Dagmar Waltemath, Darren J. Wilkinson
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core. J. Integr. Bioinform. 15 (1) (2018)
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
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017. J. Integr. Bioinform. 15 (1) (2018)
Michael Hucka, Frank T. Bergmann, Andreas Dräger, Stefan Hoops, Sarah M. Keating, Nicolas Le Novère, Chris J. Myers, Brett G. Olivier, Sven Sahle, James C. Schaff, Lucian P. Smith, Dagmar Waltemath, Darren J. Wilkinson
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core. J. Integr. Bioinform. 15 (1) (2018)
Chris J. Myers, Gary D. Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nicolas Le Novère, David P. Nickerson, Falk Schreiber, Dagmar Waltemath
A brief history of COMBINE. WSC (2017)
Harold F. Gómez, Michael Hucka, Sarah M. Keating, German Nudelman, Dagmar Iber, Stuart C. Sealfon
MOCCASIN: converting MATLAB ODE models to SBML. Bioinform. 32 (12) (2016)
Michael Hucka, Lucian P. Smith
SBML Level 3 package: Groups, Version 1 Release 1. J. Integr. Bioinform. 13 (3) (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
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016. J. Integr. Bioinform. 13 (3) (2016)
Michael Hucka, Matthew J. Graham
Software search is not a science, even among scientists. CoRR (2016)
Dagmar Waltemath, Jonathan R. Karr, Frank T. Bergmann, Vijayalakshmi Chelliah, Michael Hucka, Marcus Krantz, Wolfram Liebermeister, Pedro Mendes, Chris J. Myers, Pinar Pir, Begum Alaybeyoglu, Naveen K. Aranganathan, Kambiz Baghalian, Arne T. Bittig, Paulo E. Pinto Burke, Matteo Cantarelli, Yin Hoon Chew, Rafael S. Costa, Joseph Cursons, Tobias Czauderna, Arthur P. Goldberg, Harold F. Gómez, Jens Hahn, Tuure Hameri, Daniel F. Hernandez Gardiol, Denis Kazakiewicz, Ilya Kiselev, Vincent Knight-Schrijver, Christian Knüpfer, Matthias König, Daewon Lee, Audald Lloret-Villas, Nikita Mandrik, J. Kyle Medley, Bertrand Moreau, Hojjat Naderi-Meshkin, Sucheendra K. Palaniappan, Daniel Priego-Espinosa, Martin Scharm, Mahesh Sharma, Kieran Smallbone, Natalie J. Stanford, Je-Hoon Song, Tom Theile, Milenko Tokic, Namrata Tomar, Vasundra Touré, Jannis Uhlendorf, Thawfeek M. Varusai, Leandro H. Watanabe, Florian Wendland, Markus Wolfien, James T. Yurkovich, Yan Zhu, Argyris Zardilis, Anna Zhukova, Falk Schreiber
Toward Community Standards and Software for Whole-Cell Modeling. IEEE Trans. Biomed. Eng. 63 (10) (2016)
Daniel S. Katz, Kyle E. Niemeyer, Arfon M. Smith, William L. Anderson, Carl Boettiger, Konrad Hinsen, Rob W. W. Hooft, Michael Hucka, Allen Lee, Frank Löffler, Tom J. Pollard, Fernando Rios
Software vs. data in the context of citation. PeerJ Prepr. 4 (2016)
Vijayalakshmi Chelliah, Nick S. Juty, Ishan Ajmera, Raza Ali, Marine Dumousseau, Mihai Glont, Michael Hucka, Gaël Jalowicki, Sarah M. Keating, Vincent Knight-Schrijver, Audald Lloret-Villas, Kedar Nath Natarajan, Jean-Baptiste Pettit, Nicolas Rodriguez, Michael Schubert, Sarala M. Wimalaratne, Yangyang Zhao, Henning Hermjakob, Nicolas Le Novère, Camille Laibe
BioModels: ten-year anniversary. Nucleic Acids Res. 43 (Database-Issue) (2015)
Nicolas Rodriguez, Alex Thomas, Leandro H. Watanabe, Ibrahim Y. Vazirabad, Victor Kofia, Harold F. Gómez, Florian Mittag, Jakob Matthes, Jan Rudolph, Finja Wrzodek, Eugen Netz, Alexander Diamantikos, Johannes Eichner, Roland Keller, Clemens Wrzodek, Sebastian Fröhlich, Nathan E. Lewis, Chris J. Myers, Nicolas Le Novère, Bernhard Ø. Palsson, Michael Hucka, Andreas Dräger
JSBML 1.0: providing a smorgasbord of options to encode systems biology models. Bioinform. 31 (20) (2015)
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
Specifications of Standards in Systems and Synthetic Biology. J. Integr. Bioinform. 12 (2) (2015)
Lucian Paul Smith, Michael Hucka, Stefan Hoops, Andrew Finney, Martin Ginkel, Chris J. Myers, Ion I. Moraru, Wolfram Liebermeister
SBML Level 3 package: Hierarchical Model Composition, Version 1 Release 3. J. Integr. Bioinform. 12 (2) (2015)
Michael Hucka, Frank T. Bergmann, Andreas Dräger, Stefan Hoops, Sarah M. Keating, Nicolas Le Novère, Chris J. Myers, Brett G. Olivier, Sven Sahle, James C. Schaff, Lucian P. Smith, Dagmar Waltemath, Darren J. Wilkinson
Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions. J. Integr. Bioinform. 12 (2) (2015)
Michael Hucka, Frank T. Bergmann, Stefan Hoops, Sarah M. Keating, Sven Sahle, James C. Schaff, Lucian P. Smith, Darren J. Wilkinson
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core. J. Integr. Bioinform. 12 (2) (2015)
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
COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project. BMC Bioinform. 15 (2014)
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
COMBINE archive: One File To Share Them All. CoRR (2014)
Finja Büchel, Nicolas Rodriguez, Neil Swainston, Clemens Wrzodek, Tobias Czauderna, Roland Keller, Florian Mittag, Michael Schubert, Mihai Glont, Martin Golebiewski, Martijn P. van Iersel, Sarah M. Keating, Matthias Rall, Michael Wybrow, Henning Hermjakob, Michael Hucka, Douglas B. Kell, Wolfgang Müller, Pedro Mendes, Andreas Zell, Claudine Chaouiya, Julio Saez-Rodriguez, Falk Schreiber, Camille Laibe, Andreas Dräger, Nicolas Le Novère
Path2Models: large-scale generation of computational models from biochemical pathway maps. BMC Syst. Biol. 7 (2013)
Claudine Chaouiya, Duncan Bérenguier, Sarah M. Keating, Aurélien Naldi, Martijn P. van Iersel, Nicolas Rodriguez, Andreas Dräger, Finja Büchel, Thomas Cokelaer, Bryan M. Kowal, Benjamin Wicks, Emanuel J. V. Gonçalves, Julien Dorier, Michel Page, Pedro T. Monteiro, Axel von Kamp, Ioannis Xenarios, Hidde de Jong, Michael Hucka, Steffen Klamt, Denis Thieffry, Nicolas Le Novère, Julio Saez-Rodriguez, Tomás Helikar
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. BMC Syst. Biol. 7 (2013)
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
Minimum Information About a Simulation Experiment (MIASE). PLoS Comput. Biol. 7 (4) (2011)
Michael Hucka, Frank T. Bergmann, Sarah M. Keating, Lucian P. Smith
A Profile of Today's SBML-Compatible Software. e-Science Workshops (2011)
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
Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language. BMC Syst. Biol. 5 (2011)
Andreas Dräger, Nicolas Rodriguez, Marine Dumousseau, Alexander Dörr, Clemens Wrzodek, Nicolas Le Novère, Andreas Zell, Michael Hucka
JSBML: a flexible Java library for working with SBML. Bioinform. 27 (15) (2011)
Chen Li, Marco Donizelli, Nicolas Rodriguez, Harish Dharuri, Lukas Endler, Vijayalakshmi Chelliah, Lu Li, Enuo He, Arnaud Henry, Melanie I. Stefan, Jacky L. Snoep, Michael Hucka, Nicolas Le Novère, Camille Laibe
BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst. Biol. 4 (2010)
Andreas Dräger, Hannes Planatscher, Dieudonné Motsou Wouamba, Adrian Schröder, Michael Hucka, Lukas Endler, Martin Golebiewski, Wolfgang Müller, Andreas Zell
X: Conversion of SBML files into human-readable reports. Bioinform. 25 (11) (2009)
Benjamin J. Bornstein, Sarah M. Keating, Akiya Jouraku, Michael Hucka
LibSBML: an API Library for SBML. Bioinform. 24 (6) (2008)
Herbert M. Sauro, David Harel, Marta Z. Kwiatkowska, Clifford A. Shaffer, Adelinde M. Uhrmacher, Michael Hucka, Pedro Mendes, Lena Strömbäck, John J. Tyson
Challenges for modeling and simulation methods in systems biology. WSC (2006)
Sarah M. Keating, Benjamin J. Bornstein, Andrew Finney, Michael Hucka
SBMLToolbox: an SBML toolbox for MATLAB users. Bioinform. 22 (10) (2006)
Nicolas Le Novère, Benjamin J. Bornstein, Alexander Broicher, Mélanie Courtot, Marco Donizelli, Harish Dharuri, Lu Li, Herbert M. Sauro, Maria J. Schilstra, Bruce E. Shapiro, Jacky L. Snoep, Michael Hucka
BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Res. 34 (Database-Issue) (2006)
Maria J. Schilstra, Lu Li, Joanne Matthews, Andrew Finney, Michael Hucka, Nicolas Le Novère
CellML2SBML: conversion of CellML into SBML. Bioinform. 22 (8) (2006)
Bruce E. Shapiro, Michael Hucka, Andrew Finney, John Doyle
MathSBML: a package for manipulating SBML-based biological models. Bioinform. 20 (16) (2004)
Michael Hucka, Andrew Finney, Herbert M. Sauro, H. Bolouri, John C. Doyle, Hiroaki Kitano, Adam P. Arkin, Benjamin J. Bornstein, D. Bray, Athel Cornish-Bowden, Autumn A. Cuellar, Serge Dronov, Ernst Dieter Gilles, Martin Ginkel, Victoria Gor, Igor Goryanin, W. J. Hedley, T. Charles Hodgman, Jan-Hendrik S. Hofmeyr, Peter J. Hunter, Nick S. Juty, J. L. Kasberger, Andreas Kremling, Ursula Kummer, Nicolas Le Novère, Leslie M. Loew, D. Lucio, Pedro Mendes, E. Minch, Eric Mjolsness, Yoichi Nakayama, M. R. Nelson, Poul M. F. Nielsen, T. Sakurada, James C. Schaff, Bruce E. Shapiro, Thomas Simon Shimizu, Hugh D. Spence, Jörg Stelling, Koichi Takahashi, Masaru Tomita, J. Wagner, J. Wang
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinform. 19 (4) (2003)
Nigel H. Goddard, David Beeman, Robert C. Cannon, Hugo Cornelis, Marc-Oliver Gewaltig, Greg Hood, Fredrick W. Howell, P. Rogister, Erik De Schutter, K. Shankar, Michael Hucka
NeuroML for plug and play neuronal modeling. Neurocomputing (2002)
Michael Hucka, Andrew Finney, Herbert M. Sauro, H. Bolouri, John C. Doyle, Hiroaki Kitano
The ERATO Systems Biology Workbench: Enabling Interaction and Exchange Between Software Tools for Computational Biology. Pacific Symposium on Biocomputing (2002)
John E. Laird, Eric S. Yager, Michael Hucka, Christopher M. Tuck
Robo-Soar: An integration of external interaction, planning, and learning using Soar. Robotics Auton. Syst. 8 (1-2) (1991)
John E. Laird, Michael Hucka, Scott B. Huffman, Paul S. Rosenbloom
An Analysis of Soar as an Integrated Architecture. SIGART Bull. 2 (4) (1991)
John E. Laird, Michael Hucka, Eric S. Yager, Christopher M. Tuck
Correcting and Extending Domain Knowledge using Outside Guidance. ML (1990)