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Michael Hucka
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The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
M Hucka, A Finney, HM Sauro, H Bolouri, JC Doyle, H Kitano, AP Arkin, ...
Bioinformatics 19 (4), 524-531, 2003
37932003
A community-driven global reconstruction of human metabolism
I Thiele, N Swainston, RMT Fleming, A Hoppe, S Sahoo, MK Aurich, ...
Nature biotechnology 31 (5), 419-425, 2013
11712013
The systems biology graphical notation
N Le Novère, M Hucka, H Mi, S Moodie, F Schreiber, A Sorokin, E Demir, ...
Nature biotechnology 27 (8), 735-741, 2009
10482009
Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v. 3.0
L Heirendt, S Arreckx, T Pfau, SN Mendoza, A Richelle, A Heinken, ...
Nature protocols 14 (3), 639-702, 2019
9772019
BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems
N Le Novère, B Bornstein, A Broicher, M Courtot, M Donizelli, H Dharuri, ...
Nucleic Acids Research 34 (suppl 1), D689-D691, 2006
9742006
The BioPAX community standard for pathway data sharing
E Demir, MP Cary, S Paley, K Fukuda, C Lemer, I Vastrik, G Wu, ...
Nature biotechnology 28 (9), 935-942, 2010
7822010
Mutsuki Amano
K Bettenbrock, H Bolouri, D Bray, J Bruck, J Doyle, A Finney, ED Gilles, ...
7622001
Minimum information requested in the annotation of biochemical models (MIRIAM)
N Le Novère, A Finney, M Hucka, US Bhalla, F Campagne, ...
Nature biotechnology 23 (12), 1509-1515, 2005
6902005
BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models
C Li, M Donizelli, N Rodriguez, H Dharuri, L Endler, V Chelliah, L Li, E He, ...
BMC systems biology 4 (1), 92, 2010
6842010
A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology
MJ Herrgård, N Swainston, P Dobson, WB Dunn, KY Arga, M Arvas, ...
Nature biotechnology 26 (10), 1155-1160, 2008
6782008
LibSBML: an API library for SBML
BJ Bornstein, SM Keating, A Jouraku, M Hucka
Bioinformatics 24 (6), 880, 2008
4852008
Rules for modeling signal-transduction systems
WS Hlavacek, JR Faeder, ML Blinov, RG Posner, M Hucka, W Fontana
Sci STKE 344, 2006, 2006
4502006
Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration
HM Sauro, M Hucka, A Finney, C Wellock, H Bolouri, J Doyle, H Kitano
Omics A Journal of Integrative Biology 7 (4), 355-372, 2003
3472003
Controlled vocabularies and semantics in systems biology
M Courtot, N Juty, C Knüpfer, D Waltemath, A Zhukova, A Dräger, ...
Molecular systems biology 7 (1), 2011
3332011
Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project
M Hucka, A Finney, BJ Bornstein, SM Keating, BE Shapiro, J Matthews, ...
Systems Biology 1 (1), 41-53, 2004
3272004
BioModels: ten-year anniversary
V Chelliah, N Juty, I Ajmera, R Ali, M Dumousseau, M Glont, M Hucka, ...
Nucleic acids research 43 (D1), D542-D548, 2015
3202015
BioModels—15 years of sharing computational models in life science
RS Malik-Sheriff, M Glont, TVN Nguyen, K Tiwari, MG Roberts, A Xavier, ...
Nucleic acids research 48 (D1), D407-D415, 2020
2942020
Reproducible computational biology experiments with SED-ML-the simulation experiment description markup language
D Waltemath, R Adams, FT Bergmann, M Hucka, F Kolpakov, AK Miller, ...
BMC systems biology 5, 1-10, 2011
2902011
FAIRsharing as a community approach to standards, repositories and policies
Nature Biotechnology 37 (4), 358, 2019
2842019
Systems biology markup language: Level 2 and beyond
A Finney, M Hucka
Biochemical Society Transactions 31 (6), 1472-1473, 2003
2722003
SBML Level 3: an extensible format for the exchange and reuse of biological models
SM Keating, D Waltemath, M König, F Zhang, A Dräger, C Chaouiya, ...
Molecular systems biology 16 (8), e9110, 2020
1962020
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools
C Chaouiya, D Bérenguier, SM Keating, A Naldi, MP Van Iersel, ...
BMC systems biology 7, 1-15, 2013
1892013
SBMLToolbox: an SBML toolbox for MATLAB users
SM Keating, BJ Bornstein, A Finney, M Hucka
Bioinformatics 22 (10), 1275-1277, 2006
1832006
Towards NeuroML: model description methods for collaborative modelling in neuroscience
NH Goddard, M Hucka, F Howell, H Cornelis, K Shankar, D Beeman
Philosophical Transactions of the Royal Society of London. Series B …, 2001
1802001
Path2Models: large-scale generation of computational models from biochemical pathway maps
F Büchel, N Rodriguez, N Swainston, C Wrzodek, T Czauderna, R Keller, ...
BMC systems biology 7, 1-19, 2013
1752013
Minimum Information About a Simulation Experiment (MIASE)
D Waltemath, R Adams, DA Beard, FT Bergmann, US Bhalla, R Britten, ...
PLoS computational biology 7 (4), e1001122, 2011
1632011
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core
M Hucka, FT Bergmann, S Hoops, SM Keating, S Sahle, JC Schaff, ...
Nature Publishing Group, 2010
163*2010
COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project
FT Bergmann, R Adams, S Moodie, J Cooper, M Glont, M Golebiewski, ...
BMC bioinformatics 15, 1-9, 2014
1462014
The ERATO Systems Biology Workbench: enabling interaction and exchange between software tools for computational biology
M Hucka, A Finney, HM Sauro, H Bolouri, J Doyle, H Kitano
Pac Symp Biocomput 1, 450-461, 2002
1182002
JSBML: a flexible Java library for working with SBML
A Dräger, N Rodriguez, M Dumousseau, A Dörr, C Wrzodek, N Le Novère, ...
Bioinformatics 27 (15), 2167-2168, 2011
1162011
The systems biology markup language (SBML): language specification for level 3 version 2 core release 2
M Hucka, FT Bergmann, C Chaouiya, A Dräger, S Hoops, SM Keating, ...
Journal of integrative bioinformatics 16 (2), 20190021, 2019
1072019
Robo-Soar: An integration of external interaction, planning, and learning using Soar
JE Laird, ES Yager, M Hucka, CM Tuck
Robotics and Autonomous Systems 8 (1-2), 113-129, 1991
981991
Systems Biology Markup Language (SBML) Level 1: Structures and facilities for basic model definitions
M Hucka, A Finney, H Sauro, H Bolouri
August, 2003
912003
Promoting coordinated development of community-based information standards for modeling in biology: the COMBINE initiative
M Hucka, DP Nickerson, GD Bader, FT Bergmann, J Cooper, E Demir, ...
Frontiers in bioengineering and biotechnology 3, 19, 2015
852015
The systems biology markup language (SBML): language specification for level 3 version 2 core
M Hucka, FT Bergmann, A Dräger, S Hoops, SM Keating, N Le Novère, ...
Journal of integrative bioinformatics 15 (1), 20170081, 2018
812018
The genesis simulation system
JM Bower, D Beeman, M Hucka
The Handbook of Brain Theory and Neural Networks 2, 2002
752002
MathSBML: a package for manipulating SBML-based biological models
BE Shapiro, M Hucka, A Finney, J Doyle
Bioinformatics 20 (16), 2829, 2004
742004
Systems biology markup language (SBML) Level 2: structures and facilities for model definitions
M Hucka, S Hoops, SM Keating, N Le Novère, S Sahle, D Wilkinson
Nature Publishing Group, 2008
662008
Toward community standards and software for whole-cell modeling
D Waltemath, JR Karr, FT Bergmann, V Chelliah, M Hucka, M Krantz, ...
IEEE Transactions on Biomedical Engineering 63 (10), 2007-2014, 2016
642016
Do genome‐scale models need exact solvers or clearer standards?
A Ebrahim, E Almaas, E Bauer, A Bordbar, AP Burgard, RL Chang, ...
Molecular systems biology 11 (10), 831, 2015
642015
Harmonizing semantic annotations for computational models in biology
ML Neal, M König, D Nickerson, G Mısırlı, R Kalbasi, A Dräger, K Atalag, ...
Briefings in bioinformatics 20 (2), 540-550, 2019
622019
Learning in tele-autonomous systems using Soar
J LAIRD, E YAGER, C TUCK, M Hucka
JPL, California Inst. of Tech, Proceedings of the NASA Conference on Space …, 1989
601989
Systems biology markup language (sbml) level 2: Structures and facilities for model definitions
A Finney, M Hucka, H Bolouri
June, 2003
532003
Correcting and extending domain knowledge using outside guidance
JE Laird, M Hucka, ES Yager, CM Tuck
Machine Learning Proceedings 1990, 235-243, 1990
521990
SBML level 3 package: hierarchical model composition, version 1 release 3
LP Smith, M Hucka, S Hoops, A Finney, M Ginkel, CJ Myers, I Moraru, ...
Journal of integrative bioinformatics 12 (2), 603-659, 2015
512015
CellML2SBML: conversion of CellML into SBML
MJ Schilstra, L Li, J Matthews, A Finney, M Hucka, N Le Novère
Bioinformatics 22 (8), 1018-1020, 2006
492006
the rest of the SBML Forum:, AP Arkin, BJ Bornstein, D
M Hucka, A Finney, HM Sauro, H Bolouri, JC Doyle, H Kitano
Bray, A. Cornish-Bowden, AA Cuellar, S. Dronov, ED Gilles, M. Ginkel, V. Gor …, 2003
47*2003
JSBML 1.0: providing a smorgasbord of options to encode systems biology models
N Rodriguez, A Thomas, L Watanabe, IY Vazirabad, V Kofia, HF Gómez, ...
Bioinformatics 31 (20), 3383-3386, 2015
462015
Challenges for modeling and simulation methods in systems biology
HM Sauro, D Harel, M Kwiatkowska, CA Shaffer, AM Uhrmacher, M Hucka, ...
Proceedings of the 2006 Winter Simulation Conference, 1720-1730, 2006
462006
Specifications of standards in systems and synthetic biology: status and developments in 2020
F Schreiber, B Sommer, T Czauderna, M Golebiewski, TE Gorochowski, ...
Journal of integrative bioinformatics 17 (2-3), 20200022, 2020
372020
SBML2LaTEX: Conversion of SBML files into human-readable reports
A Dräger, H Planatscher, D Motsou Wouamba, A Schröder, M Hucka, ...
Bioinformatics 25 (11), 1455, 2009
352009
The systems biology markup language (SBML): language specification for level 3 version 1 core (release 1 candidate)
M Hucka, F Bergmann, S Hoops, S Keating, S Sahle, D Wilkinson
Nature Precedings, 1-1, 2010
332010
Software vs. data in the context of citation
DS Katz, KE Niemeyer, AM Smith, WL Anderson, C Boettiger, K Hinsen, ...
PeerJ Preprints 4, e2630v1, 2016
322016
The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE)
D Waltemath, M Golebiewski, ML Blinov, P Gleeson, H Hermjakob, ...
Journal of integrative bioinformatics 17 (2-3), 20200005, 2020
312020
SBML level 3 package: groups, version 1 release 1
M Hucka, LP Smith
Journal of integrative bioinformatics 13 (3), 8-29, 2016
292016
The ERATO Systems Biology Workbench: An integrated environment for multiscale and multitheoretic simulations in systems biology
M Hucka, A Finney, H Sauro, H Bolouri, J Doyle, H Kitano
Foundations of Systems Biology, 125, 2001
292001
A Specification of the Soar Cognitive Architecture in Z
BG Milnes, G Pelton, R Doorenbos, M Hucka, J Laird, P Rosenbloom, ...
291992
Systems biology markup language (SBML) level 2 version 5: structures and facilities for model definitions
M Hucka, FT Bergmann, A Dräger, S Hoops, SM Keating, N Le Novere, ...
Journal of integrative bioinformatics 12 (2), 731-901, 2015
282015
An analysis of SOAR as an integrated architecture
J Laird, M Hucka, S Huffman, P Rosenbloom
ACM SIGART Bulletin 2 (4), 98-103, 1991
281991
Systems biology markup language (SBML) level 2: structures and facilities for model definitions
M Hucka, A Finney, S Hoops, S Keating, N Le Novere
Nature Precedings, 1-1, 2007
272007
Software Infrastructure for Effective Communication and Reuse of Computational Models
A Finney, M Hucka, BJ Bornstein, SM Keating, BE Shapiro, J Matthews, ...
272006
Software search is not a science, even among scientists: A survey of how scientists and engineers find software
M Hucka, MJ Graham
Journal of Systems and Software 141, 171-191, 2018
262018
Specifications of standards in systems and synthetic biology
F Schreiber, GD Bader, M Golebiewski, M Hucka, B Kormeier, ...
Journal of integrative bioinformatics 12 (2), 1-3, 2015
262015
Systems biology markup language (SBML)
M Hucka, R Jung
Neuroinformatics 6 (4), 257-277, 2017
212017
Meeting report from the fourth meeting of the computational modeling in biology network (COMBINE)
D Waltemath, FT Bergmann, C Chaouiya, T Czauderna, P Gleeson, ...
Standards in Genomic Sciences 9, 1285-1301, 2014
212014
Systems biology graphical notation: process diagram level 1
N Le Novere, S Moodie, A Sorokin, M Hucka, F Schreiber, E Demir, H Mi, ...
Nature Precedings, 1-1, 2008
202008
Introduction to the Systems Biology Workbench
M Hucka, A Finney, HM Sauro, H Bolouri
Available via the World Wide Web at http://www. cds. caltech. edu/erato/sbw …, 2001
182001
Escalating model sizes and complexities call for standardized forms of representation
M Hucka, A Finney
Molecular Systems Biology 1 (1), 2005.0011, 2005
162005
Moccasin: converting matlab ode models to sbml
HF Gómez, M Hucka, SM Keating, G Nudelman, D Iber, SC Sealfon
Bioinformatics 32 (12), 1905-1906, 2016
152016
The systems biology markup language
AM Finney, M Hucka, HM Sauro, J Doyle, H Kitano, H Bolouri
Mol. Biol. Cell 12, 708S, 2001
152001
The erato systems biology workbench: Architectural evolution
M Hucka, A Finney, H Sauro, H Bolouri, JC Doyle, H Kitano
Proc. 2nd Int. Conf. on Systems Biology, 352-361, 2001
142001
Systems biology markup language (sbml) level 3 package: distributions, version 1, release 1
LP Smith, SL Moodie, FT Bergmann, C Gillespie, SM Keating, M König, ...
Journal of Integrative Bioinformatics 17 (2-3), 20200018, 2020
122020
Software search is not a science, even among scientists
M Hucka, MJ Graham
arXiv preprint arXiv:1605.02265, 2016
122016
A profile of today's SBML-compatible software
M Hucka, FT Bergmann, SM Keating, LP Smith
2011 IEEE Seventh International Conference on e-Science Workshops, 143-150, 2011
122011
Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE)
N Le Novère, M Hucka, N Anwar, GD Bader, E Demir, S Moodie, ...
Standards in genomic sciences 5, 230-242, 2011
122011
Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2
F Zhang, LP Smith, ML Blinov, J Faeder, WS Hlavacek, J Juan Tapia, ...
Journal of Integrative Bioinformatics 17 (2-3), 20200015, 2020
112020
An xml-based model description language for systems biology simulations
A Finney, H Sauro, M Hucka, H Bolouri
Available via the World Wide Web at http://www. cds. caltech. edu/erato, 2000
112000
Goryanin, II, WJ Hedley, TC Hodgman, JH Hofmeyr, PJ Hunter, NS Juty, JL Kasberger, A
M Hucka, A Finney, HM Sauro, H Bolouri, JC Doyle, H Kitano, AP Arkin, ...
Mjolsness, Y. Nakayama, MR Nelson, PF Nielsen, T. Sakurada, JC Schaff, BE …, 2003
92003
SCHUCS: An UML-based approach for describing data representations intended for XML encoding
M Hucka
Sys. Biol. Workbench Develop. Group, 2000
92000
A brief history of COMBINE
CJ Myers, G Bader, P Gleeson, M Golebiewski, M Hucka, N Le Novere, ...
2017 Winter Simulation Conference (WSC), 884-895, 2017
82017
Modeling the E. coli cell: The need for computing, cooperation, and consortia
B Wanner, A Finney, M Hucka
Systems Biology, 1353-1355, 2005
82005
Nine best practices for research software registries and repositories
D Garijo, H Ménager, L Hwang, A Trisovic, M Hucka, T Morrell, A Allen
PeerJ Computer Science 8, e1023, 2022
72022
Data management in computational systems biology: exploring standards, tools, databases, and packaging best practices
NJ Stanford, M Scharm, PD Dobson, M Golebiewski, M Hucka, ...
Yeast Systems Biology: Methods and Protocols, 285-314, 2019
72019
SBML Level 3 Hierarchical Model Composition
LP Smith, M Hucka
Nature Publishing Group, 2010
72010
Hierarchical model composition
LP Smith, M Hucka, S Hoops, A Finney, M Ginkel, CJ Myers
Available via the World Wide Web at http://www. sbml 26, 2010
72010
Systems Biology Markup Language (SBML) Level 1
M Hucka, A Finney, H Sauro, H Bolouri
Version 1 (2), 2001
72001
The Soar development environment
M Hucka, JE Laird
Ann Arbor, MI: Artificial Intelligence Laboratory, U. of Michigan. Also …, 1994
71994
SBMLPkgSpec: a LaTeX style file for SBML package specification documents
M Hucka
BMC research notes 10, 1-4, 2017
62017
Software that goes with the flow in systems biology
M Hucka, N Le Novère
BMC biology 8, 1-3, 2010
62010
The Modeler's Workspace: making model-based studies of the nervous system more accessible
M Hucka, K Shankar, D Beeman, JM Bower
Computational neuroanatomy: principles and methods (ed. G. Ascoli). Humana Press, 2001
62001
Foundations of Systems Biology
M Hucka, A Finney, H Sauro, H Bolouri, J Doyle, K Kitano
First International Symposium on Computational Cell Biology, Lenox …, 2001
62001
Nine best practices for research software registries and repositories: a concise guide
A Monteil, A Gonzalez-Beltran, A Ioannidis, A Allen, A Lee, A Bandrowski, ...
arXiv preprint arXiv:2012.13117, 2020
52020
The Systems Biology Markup Language (SBML): language specification for level 3 version 1 Core (release 1 candidate). Nature Precedings. 2010
M Hucka, A Finney, BJ Bornstein
precedings. nature. com/documents/4123/version/1, 2014
52014
The Systems Biology Workbench concept demonstrator: Design and implementation
HM Sauro, M Hucka, A Finney, H Bolouri
Available via the World Wide Web at http://www. cds. caltech. edu/erato/sbw …, 2001
52001
SBML level 3 package proposal: annotation
D Waltemath, N Swainston, AL Lister, F Bergmann, R Henkel, S Hoops, ...
Nature Publishing Group, 2011
42011
NeuroML for plug and play neuronal modeling
NH Goddard, D Beeman, R Cannon, H Cornelis, MO Gewaltig, G Hood, ...
Neurocomputing 44, 1077-1081, 2002
42002
Soar-mode manual
FE Ritter, M Hucka, TF McGinnis
CMU-CS-92-205. School of Computer Science, Carnegie-Mellon University, 1992
41992
Trends and tools for modeling in modern biology
M Hucka, J Schaff
Photosynthesis in silico: Understanding Complexity from Molecules to …, 2009
32009
A Practical Introduction to SBML
MJ Schilstra, A Finney, M Hucka
EBI Industry Forum Workshop on Biomolecular Networks 29, 31, 2003
32003
Systems Biology Workbench Java programmer’s manual
M Hucka, A Finney, HM Sauro, H Bolouri, F Bergmann
Available via the World Wide Web at http://www. cds. caltech. edu/erato/sbw/docs, 2002
32002
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