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Hucka, Michael
König, Matthias and Gleeson, Padraig, el al. (2023) Specifications of standards in systems and synthetic biology: status and developments in 2022 and the COMBINE meeting 2022 ; Journal of Integrative Bioinformatics; Vol. 20; No. 1; Art. No. 20230004; PMCID PMC10063176; 10.1515/jib-2023-0004
Garijo, Daniel and Ménager, Hervé, el al. (2022) Nine best practices for research software registries and repositories ; PeerJ Computer Science; Vol. 8; Art. No. e1023; 10.7717/peerj-cs.1023
Schreiber, Falk and Gleeson, Padraig, el al. (2021) Specifications of standards in systems and synthetic biology: status and developments in 2021 ; Journal of Integrative Bioinformatics; Vol. 18; No. 3; Art. No. 20210026; PMCID PMC8573232; 10.1515/jib-2021-0026
Keating, Sarah M. and Waltemath, Dagmar, el al. (2020) SBML Level 3: an extensible format for the exchange and reuse of biological models ; Molecular Systems Biology; Vol. 16; No. 8; Art. No. e9110; 10.15252/msb.20199110
Waltemath, Dagmar and Golebiewski, Martin, el al. (2020) The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE) ; Journal of Integrative Bioinformatics; Vol. 17; No. 2-3; Art. No. 20200005; 10.1515/jib-2020-0005
Schreiber, Falk and Sommer, Björn, el al. (2020) Specifications of standards in systems and synthetic biology: status and developments in 2020 ; Journal of Integrative Bioinformatics; Vol. 17; No. 2-3; Art. No. 20200022; 10.1515/jib-2020-0022
Zhang, Fengkai and Smith, Lucian P., el al. (2020) Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2 ; Journal of Integrative Bioinformatics; Vol. 17; No. 2-3; Art. No. 20200015; 10.1515/jib-2020-0015
Smith, Lucian P. and Moodie, Stuart L., el al. (2020) Systems Biology Markup Language (SBML) Level 3 Package: Distributions, Version 1, Release 1 ; Journal of Integrative Bioinformatics; Vol. 17; No. 2-3; Art. No. 20200018; 10.1515/jib-2020-0018
Malik-Sheriff, Rahuman S. and Glont, Mihai, el al. (2020) BioModels—15 years of sharing computational models in life science ; Nucleic Acids Research; Vol. 48; No. D1; D407-D415; PMCID PMC7145643; 10.1093/nar/gkz1055
Stanford, Natalie J. and Scharm, Martin, el al. (2019) Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices ; ISBN 978-1-4939-9735-0; Yeast Systems Biology: Methods and Protocols; 285-314; 10.1007/978-1-4939-9736-7_17
Hucka, Michael and Bergmann, Frank T., el al. (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, el al. (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
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
Schreiber, Falk and Bader, Gary D., el al. (2018) Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017 ; Journal of Integrative Bioinformatics; Vol. 15; No. 1; Art. No. 20180013; 10.1515/jib-2018-0013
Hucka, Michael and Bergmann, Frank T., el al. (2018) The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core ; Journal of Integrative Bioinformatics; Vol. 15; No. 1; Art. No. 20170081; PMCID PMC6167032; 10.1515/jib-2017-0081
Sansone, Susanna-Assunta and Hucka, Michael (2018) FAIRsharing, a cohesive community approach to the growth in standards, repositories and policies ; 10.1101/245183
Myers, Chris J. and Bader, Gary, el al. (2017) A brief history of COMBINE ; ISBN 978-1-5386-3428-8; Proceedings of the 2017 Winter Simulation Conference; 884-895; 10.1109/WSC.2017.8247840
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
Schreiber, Falk and Bader, Gary D., el al. (2016) Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016 ; Journal of Integrative Bioinformatics; Vol. 13; No. 3; Art. No. 289; PMCID PMC5431574; 10.2390/biecoll-jib-2016-289
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., el al. (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
Gómez, Harold F. and Hucka, Michael, el al. (2016) MOCCASIN: converting MATLAB ODE models to SBML ; Bioinformatics; Vol. 32; No. 12; 1905-1906; PMCID PMC4908318; 10.1093/bioinformatics/btw056
Rodriguez, Nicolas and Thomas, Alex, el al. (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., el al. (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
Chelliah, Vijayalakshmi and Juty, Nick, el al. (2015) BioModels: ten-year anniversary ; Nucleic Acids Research; Vol. 43; No. D1; D542-D548; PMCID PMC4383975; 10.1093/nar/gku1181
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
Bergmann, Frank T. and Adams, Richard, el al. (2014) COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project ; BMC Bioinformatics; Vol. 15; Art. No. 369; PMCID PMC4272562; 10.1186/s12859-014-0369-z
Waltemath, Dagmar and Bergmann, Frank T., el al. (2014) Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE) ; Standards in Genomics Sciences (SIGS); Vol. 9; No. 3; 10.4056/sigs.5279417
Chaouiya, Claudine and Berénguier, Duncan, el al. (2013) SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools ; BMC Systems Biology; Vol. 7; Art. No. 135; PMCID PMC3892043; 10.1186/1752-0509-7-135
Smith, Lucian P. and Hucka, Michael, el al. (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 (2013) Approximate Spatial Layout Processing in the Visual System: Modeling Texture-Based Segmentation and Shape Estimation
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, el al. (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., el al. (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
Le Novère, Nicolas and Hucka, Michael, el al. (2011) Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE) ; Standards in Genomics Sciences (SIGS); Vol. 5; No. 2; PMCID PMC3235518; 10.4056/sigs.2034671
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
Smith, Lucian P. and Hucka, Michael (2011) SBML Level 3 Package Specification: Hierarchical Model Composition, Version 1 Draft
Dräger, Andreas and Rodriguez, Nicolas, el al. (2011) JSBML: a flexible Java library for working with SBML ; Bioinformatics; Vol. 27; No. 15; 2167-2168; PMCID PMC3137227; 10.1093/bioinformatics/btr361
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, el al. (2011) SBML Level 3 Package Proposal: Annotation ; Nature Precedings; 10.1038/npre.2011.5610.1
Hucka, Michael and Bergmann, Frank T., el al. (2010) The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core
Hucka, Michael and Bergmann, Frank T., el al. (2010) The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core ; Nature Precedings; Art. No. 4959; 10.1038/npre.2010.4959.1
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
Li, Chen and Donizelli, Marco, el al. (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models ; BMC Systems Biology; Vol. 4; Art. No. 92; PMCID PMC2909940; 10.1186/1752-0509-4-92
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, el al. (2009) The Systems Biology Graphical Notation ; Nature Biotechnology; Vol. 27; No. 8; 735-741; 10.1038/nbt.1558
Dräger, Andreas and Planatscher, Hannes, el al. (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, el al. (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, el al. (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
Le Novère, Nicolas and Moodie, Stuart, el al. (2008) Systems Biology Graphical Notation: Process Diagram Level 1 ; Nature Precedings
Bornstein, Benjamin J. and Keating, Sarah M., el al. (2008) LibSBML: an API library for SBML ; Bioinformatics; Vol. 24; No. 6; 880-881; PMCID PMC2517632; 10.1093/bioinformatics/btn051
Hucka, Michael and Finney, Andrew M., el al. (2007) Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions ; Nature Precedings
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
Hucka, Michael (2007) Evolving standards and infrastructure for systems biology: SBML, SBGN, and BioModels.net ; Nature Precedings; 10.1038/npre.2007.20.1
Shapiro, Bruce E. and Finney, Andrew, el al. (2007) SBML Models and MathSBML ; ISBN 9781597455312; Introduction to Systems Biology; 395-421
Sauro, Herbert M. and Uhrmacher, Adelinde M., el al. (2006) Challenges for Modeling and Simulation Methods in Systems Biology ; ISBN 1-4244-0500-9; Proceedings of the 2006 Winter Simulation Conference; 1720-1730; 10.1109/WSC.2006.322948
Hucka, Michael and Finney, Andrew, el al. (2006) Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions
Hlavacek, William S. and Faeder, James R., el al. (2006) Rules for Modeling Signal-Transduction Systems ; Science's STKE: signal transduction knowledge environment; Vol. 2006; No. 344; re6; 10.1126/stke.3442006re6
Keating, Sarah M. and Bornstein, Benjamin J., el al. (2006) SBMLToolbox: an SBML toolbox for MATLAB users ; Bioinformatics; Vol. 22; No. 10; 1275-1277; 10.1093/bioinformatics/btl111
Schilstra, Maria J. and Li, Lu, el al. (2006) CellML2SBML: conversion of CellML into SBML ; Bioinformatics; Vol. 22; No. 8; 1018-1020; 10.1093/bioinformatics/btl047
Le Novère, Nicolas and Bornstein, Benjamin, el al. (2006) BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems ; Nucleic Acids Research; Vol. 34; No. Databa; D689-D691; PMCID PMC1347454; 10.1093/nar/gkj092
Finney, Andrew and Hucka, Michael, el al. (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
Le Novère, Nicolas and Finney, Andrew, el al. (2005) Minimum information requested in the annotation of biochemical models (MIRIAM) ; Nature Biotechnology; Vol. 23; No. 12; 1509-1515; 10.1038/nbt1156
Hucka, Michael and Finney, Andrew (2005) Escalating model sizes and complexities call for standardized forms of representation ; Molecular Systems Biology; Vol. 1; Art. No. 2005.0011; PMCID PMC1360139; 10.1038/msb4100015
Wanner, Barry L. and Finney, Andrew, el al. (2005) Modeling the E. coli cell: The need for computing, cooperation, and consortia ; ISBN 978-3-540-22968-1; Systems Biology: Definitions and Perspectives; 163-189; 10.1007/b138743
Shapiro, Bruce E. and Hucka, Michael, el al. (2004) MathSBML: a package for manipulating SBML-based biological models ; Bioinformatics; Vol. 20; No. 16; 2829-2831; PMCID PMC1409765; 10.1093/bioinformatics/bth271
Hucka, M. and Finney, A., el al. (2004) Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project ; Systems Biology; Vol. 1; No. 1; 41-53; 10.1049/sb:20045008
Sauro, Herbert M. and Hucka, Michael, el al. (2003) Next Generation Simulation Tools: The Systems Biology Workbench and BioSPICE Integration ; OMICS: A Journal of Integrative Biology; Vol. 7; No. 4; 355-372; 10.1089/153623103322637670
Hucka, Michael and Finney, Andrew, el al. (2003) Systems Biology Markup Language (SBML) Level 1: Structures and Facilities for Basic Model Definitions
Hucka, Michael and Finney, Andrew (2003) Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions
Hucka, M. and Finney, A., el al. (2003) The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models ; Bioinformatics; Vol. 19; No. 4; 524-531; 10.1093/bioinformatics/btg015
Bower, James M. and Beeman, David, el al. (2003) The GENESIS Simulation System ; ISBN 9780262267267; The Handbook of Brain Theory and Neural Networks; 475-478
Goddard, N. H. and Beeman, D., el al. (2002) NeuroML for plug and play neuronal modeling ; Neurocomputing; Vol. 44-46; 1077-1081; 10.1016/S0925-2312(02)00420-4
Hucka, Michael and Finney, Andrew, el al. (2002) The ERATO Systems Biology Workbench: Enabling Interaction and Exchange Between Software Tools for Computational Biology ; ISBN 9789812799623; Pacific Symposium on Biocomputing 2002; 450-461
Hucka, Michael and Shankar, Kavita, el al. (2002) The Modeler's Workspace: Making model-based studies of the nervous system more accessible ; ISBN 9781588290007; Computational Neuroanatomy: Principles and Methods; 83-103
Hucka, Michael and Finney, Andrew, el al. (2001) The ERATO Systems Biology Workbench: Architectural Evolution ; ISBN 9781591350002; Proceedings of the second International Conference on Systems Biology; 352-361
Goddard, Nigel H. and Hucka, Michael, el al. (2001) Towards NeuroML: Model Description Methods for Collaborative Modelling in Neuroscience ; Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences; Vol. 356; No. 1412; 1209-1228; PMCID PMC1088511; 10.1098/rstb.2001.0910
Finney, Andrew M. and Hucka, Michael, el al. (2001) An Overview of the ERATO Systems Biology Workbench Project ; ISBN 9783897226487; 2nd Workshop on Computation and Biochemical Pathways; 115-122
Hucka, Michael and Finney, Andrew, el al. (2001) Systems Biology Markup Language (SBML) Level 1: Structures and Facilities for Basic Model Definitions
Hucka, Michael and Finney, Andrew, el al. (2001) The ERATO Systems Biology Workbench: An Integrated Environment for Multiscale and Multitheoretic Simulations in Systems Biology ; ISBN 978-0262112666; Foundations of Systems Biology; 125-143
Hucka, Michael and Forss, Jenny, el al. (2000) The Modeler's Workspace: Making model-based studies of the nervous system more accessible ; FASEB Journal; Vol. 14; Art. No. A543
Hucka, Michael and Kaplan, Stephen (1996) Approximate Spatial Layout Processing in Early Vision ; ISBN 978-0805825411; Proceedings of the Eighteenth Annual Meeting of the Cognitive Science Society
Hucka, Michael and Kaplan, Stephen (1996) Texture-Based Processing in Early Vision and a Proposed Role for Coarse-Scale Segmentation
Hucka, Michael and Weaver, Mark, el al. (1995) Hebb's Accomplishments Misunderstood ; Behavioral and Brain Sciences; Vol. 18; No. 04; 635-636; 10.1017/S0140525X00040267
Laird, John E. and Yager, Eric S., el al. (1993) Robo-Soar: An Integration of External Interaction, Planning, and Learning using Soar ; ISBN 9780262720175; Toward Learning Robots; 113-129
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Laird, John E. and Hucka, Michael, el al. (1990) Correcting and extending domain knowledge using outside guidance ; ISBN 9781558601413; Proceedings of the Seventh International Conference (1990) on Machine Learning; 235-243
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