Hucka, Michael
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- Hucka, Michael and Bergmann, Frank T., et el. (2019) Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2; Journal of Integrative Bioinformatics; Vol. 16; No. 2; Art. No. 20190021; PMCID PMC6798823; 10.1515/jib-2019-0021
- Neal, Maxwell Lewis and Hucka, Michael (2019) Harmonizing semantic annotations for computational models in biology; Briefings in Bioinformatics; Vol. 20; No. 2; 540-550; 10.1093/bib/bby087
- Heirendt, Laurent and Arreckx, Sylvain, et el. (2019) Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0; Nature Protocols; Vol. 14; No. 3; 639-702; PMCID PMC6635304; 10.1038/s41596-018-0098-2
- Sansone, Susanna-Assunta and Hucka, Michael (2018) FAIRsharing, a cohesive community approach to the growth in standards, repositories and policies; 10.1101/245183
- Hucka, M. and Graham, M. J. (2018) Software search is not a science, even among scientists: A survey of how scientists and engineers find software; Journal of Systems and Software; Vol. 141; 171-191; 10.1016/j.jss.2018.03.047
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- Hucka, Michael (2017) SBMLPkgSpec: a LaTeX style file for SBML package specification documents; BMC Research Notes; Vol. 10; Art. No. 451; PMCID PMC5588604; 10.1186/s13104-017-2788-1
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- Hucka, Michael and Smith, Lucian P. (2016) SBML Level 3 package: Groups, Version 1 Release 1; Journal of Integrative Bioinformatics; Vol. 13; No. 3; Art. No. 290; 10.2390/biecoll-jib-2016-290
- Waltemath, Dagmar and Karr, Jonathan R., et el. (2016) Toward community standards and software for whole-cell modeling; IEEE Transactions on Biomedical Engineering; Vol. 63; No. 10; 2007-2014; PMCID PMC5451320; 10.1109/TBME.2016.2560762
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- Rodriguez, Nicolas and Thomas, Alex, et el. (2015) JSBML 1.0: providing a smorgasbord of options to encode systems biology models; Bioinformatics; Vol. 31; No. 20; 3380-3383; PMCID PMC4595895; 10.1093/bioinformatics/btv341
- Ebrahim, Ali and Hucka, Michael (2015) Do genome-scale models need exact solvers or clearer standards?; Molecular Systems Biology; Vol. 11; No. 10; Art. No. 831; PMCID PMC4631202; 10.15252/msb.20156157
- Hucka, Michael (2015) Systems Biology Markup Language (SBML); ISBN 978-1-4614-6674-1; Encyclopedia of Computational Neuroscience; 2943-2944; 10.1007/978-1-4614-6675-8_376
- Hucka, Michael and Nickerson, David P., et el. (2015) Promoting coordinated development of community-based information standards for modeling in biology: the COMBINE initiative; Frontiers in Bioengineering and Biotechnology; Vol. 3; No. 2; Art. No. 19; PMCID PMC4338824; 10.3389/fbioe.2015.00019
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- Hucka, Michael (2015) Organizing Community-Based Data Standards: Lessons from Developing a Successful Open Standard in Systems Biology; ISBN 9781583818749; Astronomical Data Analysis Software and Systems XXIV; 575-578
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- Smith, Lucian P. and Hucka, Michael, et el. (2013) SBML Level 3 Package Specification: Hierarchical Model Composition
- Büchel, Finja and Hucka, Michael (2013) Path2Models: large-scale generation of computational models from biochemical pathway maps; BMC Systems Biology; Vol. 7; Art. No. 116; PMCID PMC4228421; 10.1186/1752-0509-7-116
- Thiele, Ines and Hucka, Michael (2013) A community-driven global reconstruction of human metabolism; Nature Biotechnology; Vol. 31; No. 5; 419-425; PMCID PMC3856361; 10.1038/nbt.2488
- Hucka, Michael and Finney, Andrew, et el. (2013) Systems Biology Markup Language (SBML) Level 1: Structures and Facilities for Basic Model Definitions
- Ritter, Frank E. and Hucka, Michael, et el. (2013) Soar-mode v5.0 User's Manual for Soar release 5.2 and 6.0
- Hucka, Michael (2013) Approximate Spatial Layout Processing in the Visual System: Modeling Texture-Based Segmentation and Shape Estimation
- Milnes, Brian G. and Pelton, Garrett, et el. (2013) A Specification of the Soar Cognitive Architecture in Z
- Hucka, Michael and Finney, Andrew, et el. (2013) Systems Biology Markup Language (SBML) Level 1: Structures and Facilities for Basic Model Definitions
- Hucka, Michael and Finney, Andrew (2013) Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions
- Hucka, Michael and Finney, Andrew, et el. (2013) Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions
- Smith, Lucian P. and Hucka, Michael (2013) SBML Level 3 Package Specification: Hierarchical Model Composition, Version 1 Draft
- Finney, A. and Hucka, M. (2012) Systems biology markup language: Level 2 and beyond; Biochemical Society Transactions; Vol. 31; No. 6; 1472-1473
- Waltemath, Dagmar and Adams, Richard, et el. (2011) Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language; BMC Systems Biology; Vol. 5; Art. No. 198; PMCID PMC3292844; 10.1186/1752-0509-5-198
- Hucka, Michael and Bergmann, Frank T., et el. (2011) A profile of today's SBML-compatible software; ISBN 9781467300261; 2011 IEEE Seventh International Conference on e-Science Workshops; 143-150; 10.1109/eScienceW.2011.28
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- Courtot, Mélanie and Hucka, Michael (2011) Controlled vocabularies and semantics in systems biology; Molecular Systems Biology; Vol. 7; Art. No. 543; PMCID PMC3261705; 10.1038/msb.2011.77
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- Waltemath, Dagmar and Hucka, Michael (2011) Minimum Information About a Simulation Experiment (MIASE); PLoS Computational Biology; Vol. 7; No. 4; Art. No. e1001122; PMCID PMC3084216; 10.1371/journal.pcbi.1001122
- Waltemath, Dagmar and Swainston, Neil, et el. (2011) SBML Level 3 Package Proposal: Annotation; Nature Precedings; 10.1038/npre.2011.5610.1
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- Hucka, Michael and Bergmann, Frank T., et el. (2010) The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core
- Demir, Emek and Hucka, Michael (2010) The BioPAX community standard for pathway data sharing; Nature Biotechnology; Vol. 28; No. 9; 935-942; PMCID PMC3001121; 10.1038/nbt.1666
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- Hucka, Michael and Le Novère, Nicolas (2010) Software that goes with the flow in systems biology; BMC Biology; Vol. 8; 140-142; PMCID PMC2993668; 10.1186/1741-7007-8-140
- Le Novère, Nicolas and Hucka, Michael, et el. (2009) The Systems Biology Graphical Notation; Nature Biotechnology; Vol. 27; No. 8; 735-741; 10.1038/nbt.1558
- Dräger, Andreas and Planatscher, Hannes, et el. (2009) SBML2LATEX: Conversion of SBML files into human-readable reports; Bioinformatics; Vol. 25; No. 11; 1455-1456; PMCID PMC2682517; 10.1093/bioinformatics/btp170
- Hucka, Michael (2009) An overview of several standardization efforts for systems biology; Journal of Physiological Sciences; Vol. 59; No. S1; 102-102
- Hucka, Michael and Schaff, James (2009) Trends and Tools for Modeling in Modern Biology; ISBN 978-1-4020-9236-7; Photosynthesis in silico: Understanding Complexity from Molecules to Ecosystems; 3-15; 10.1007/978-1-4020-9237-4_1
- Hucka, Michael and Hoops, Stefan, et el. (2008) Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions; Nature Precedings; 10.1038/npre.2008.2715.1
- Herrgård, Markus J. and Swainston, Neil, et el. (2008) A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology; Nature Biotechnology; Vol. 26; No. 10; 1155-1160; PMCID PMC4018421; 10.1038/nbt1492
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- Hucka, Michael and Finney, Andrew M., et el. (2007) Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions; Nature Precedings
- Hucka, Michael (2007) Evolving standards and infrastructure for systems biology: SBML, SBGN, and BioModels.net; Nature Precedings; 10.1038/npre.2007.20.1
- Hucka, Michael and Keating, Sarah (2007) A tutorial about SBML and SBML Level 2 Version 2; Nature Precedings; 10.1038/npre.2007.19.1
- Hucka, Michael (2007) SBML, BioModels.net, and SBGN; Nature Precedings; 10.1038/npre.2007.20.1
- Shapiro, Bruce E. and Finney, Andrew, et el. (2007) SBML Models and MathSBML; ISBN 9781597455312; Introduction to Systems Biology; 395-421
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- Finney, Andrew and Hucka, Michael, et el. (2006) Software Infrastructure for Effective Communication and Reuse of Computational Models; ISBN 9780262195485; System Modeling in Cell Biology: From Concepts to Nuts & Bolts; 355-378
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- Hucka, Michael and Shankar, Kavita, et el. (2002) The Modeler's Workspace: Making model-based studies of the nervous system more accessible; ISBN 9781588290007; Computational Neuroanatomy: Principles and Methods; 83-103
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