Found: 35

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  • Specifications of standards in systems and synthetic biology: status and developments in 2022 and the COMBINE meeting 2022.

    Published in:
    Journal of Integrative Bioinformatics, 2023, v. 20, n. 1, p. 1, doi. 10.1515/jib-2023-0004
    By:
    • König, Matthias;
    • Gleeson, Padraig;
    • Golebiewski, Martin;
    • Gorochowski, Thomas E.;
    • Hucka, Michael;
    • Keating, Sarah M.;
    • Myers, Chris J.;
    • Nickerson, David P.;
    • Sommer, Björn;
    • Waltemath, Dagmar;
    • Schreiber, Falk
    Publication type:
    Article

  • Specifications of standards in systems and synthetic biology: status and developments in 2021.

    Published in:
    2021
    By:
    • Schreiber, Falk;
    • Gleeson, Padraig;
    • Golebiewski, Martin;
    • Gorochowski, Thomas E.;
    • Hucka, Michael;
    • Keating, Sarah M.;
    • König, Matthias;
    • Myers, Chris J.;
    • Nickerson, David P.;
    • Sommer, Björn;
    • Waltemath, Dagmar
    Publication type:
    Editorial

  • Specifications of standards in systems and synthetic biology: status and developments in 2020.

    Published in:
    Journal of Integrative Bioinformatics, 2020, v. 17, n. 2/3, p. 1, doi. 10.1515/jib-2020-0022
    By:
    • Schreiber, Falk;
    • Sommer, Björn;
    • Czauderna, Tobias;
    • Golebiewski, Martin;
    • Gorochowski, Thomas E.;
    • Hucka, Michael;
    • Keating, Sarah M.;
    • König, Matthias;
    • Myers, Chris;
    • Nickerson, David;
    • Waltemath, Dagmar
    Publication type:
    Article

  • Systems Biology Markup Language (SBML) Level 3 Package: Distributions, Version 1, Release 1.

    Published in:
    Journal of Integrative Bioinformatics, 2020, v. 17, n. 2/3, p. 1, doi. 10.1515/jib-2020-0018
    By:
    • Smith, Lucian P.;
    • Moodie, Stuart L.;
    • Bergmann, Frank T.;
    • Gillespie, Colin;
    • Keating, Sarah M.;
    • König, Matthias;
    • Myers, Chris J.;
    • Swat, Maciek J.;
    • Wilkinson, Darren J.;
    • Hucka, Michael
    Publication type:
    Article

  • The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE).

    Published in:
    Journal of Integrative Bioinformatics, 2020, v. 17, n. 2/3, p. 1, doi. 10.1515/jib-2020-0005
    By:
    • Waltemath, Dagmar;
    • Golebiewski, Martin;
    • Blinov, Michael L;
    • Gleeson, Padraig;
    • Hermjakob, Henning;
    • Hucka, Michael;
    • Inau, Esther Thea;
    • Keating, Sarah M;
    • König, Matthias;
    • Krebs, Olga;
    • Malik-Sheriff, Rahuman S;
    • Nickerson, David;
    • Oberortner, Ernst;
    • Sauro, Herbert M;
    • Schreiber, Falk;
    • Smith, Lucian;
    • Stefan, Melanie I;
    • Wittig, Ulrike;
    • Myers, Chris J
    Publication type:
    Article

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

    Published in:
    Journal of Integrative Bioinformatics, 2020, v. 17, n. 2/3, p. 1, doi. 10.1515/jib-2020-0015
    By:
    • Zhang, Fengkai;
    • Smith, Lucian P.;
    • Blinov, Michael L.;
    • Faeder, James;
    • Hlavacek, William S.;
    • Juan Tapia, Jose;
    • Keating, Sarah M.;
    • Rodriguez, Nicolas;
    • Dräger, Andreas;
    • Harris, Leonard A.;
    • Finney, Andrew;
    • Hu, Bin;
    • Hucka, Michael;
    • Meier-Schellersheim, Martin
    Publication type:
    Article

  • The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2.

    Published in:
    Journal of Integrative Bioinformatics, 2019, v. 16, n. 2, p. 1, doi. 10.1515/jib-2019-0021
    By:
    • Hucka, Michael;
    • Bergmann, Frank T.;
    • Chaouiya, Claudine;
    • Dräger, Andreas;
    • Hoops, Stefan;
    • Keating, Sarah M.;
    • König, Matthias;
    • Le Novère, Nicolas;
    • Myers, Chris J.;
    • Olivier, Brett G.;
    • Sahle, Sven;
    • Schaff, James C.;
    • Sheriff, Rahuman;
    • Smith, Lucian P.;
    • Waltemath, Dagmar;
    • Wilkinson, Darren J.;
    • Zhang, Fengkai
    Publication type:
    Article

  • Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019.

    Published in:
    Journal of Integrative Bioinformatics, 2019, v. 16, n. 2, p. 1, doi. 10.1515/jib-2019-0035
    By:
    • Schreiber, Falk;
    • Sommer, Björn;
    • Bader, Gary D.;
    • Gleeson, Padraig;
    • Golebiewski, Martin;
    • Hucka, Michael;
    • Keating, Sarah M.;
    • König, Matthias;
    • Myers, Chris;
    • Nickerson, David;
    • Waltemath, Dagmar
    Publication type:
    Article

  • Harmonizing semantic annotations for computational models in biology.

    Published in:
    Briefings in Bioinformatics, 2019, v. 20, n. 2, p. 540, doi. 10.1093/bib/bby087
    By:
    • Neal, Maxwell Lewis;
    • König, Matthias;
    • Nickerson, David;
    • Mısırlı, Göksel;
    • Kalbasi, Reza;
    • Dräger, Andreas;
    • Atalag, Koray;
    • Chelliah, Vijayalakshmi;
    • Cooling, Michael T;
    • Cook, Daniel L;
    • Crook, Sharon;
    • Alba, Miguel de;
    • Friedman, Samuel H;
    • Garny, Alan;
    • Gennari, John H;
    • Gleeson, Padraig;
    • Golebiewski, Martin;
    • Hucka, Michael;
    • Juty, Nick;
    • Myers, Chris
    Publication type:
    Article

  • Correction to: Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE).

    Published in:
    2018
    By:
    • Waltemath, Dagmar;
    • Bergmann, Frank T.;
    • Chaouiya, Claudine;
    • Czauderna, Tobias;
    • Gleeson, Padraig;
    • Goble, Carole;
    • Golebiewski, Martin;
    • Hucka, Michael;
    • Juty, Nick;
    • Krebs, Olga;
    • Le Novère, Nicolas;
    • Mi, Huaiyu;
    • Moraru, Ion I.;
    • Myers, Chris J.;
    • Nickerson, David;
    • Olivier, Brett G.;
    • Rodriguez, Nicolas;
    • Schreiber, Falk;
    • Smith, Lucian;
    • Zhang, Fengkai
    Publication type:
    Correction Notice

  • SBMLPkgSpec: a LaTeX style file for SBML package specification documents.

    Published in:
    BMC Research Notes, 2017, v. 10, n. 1, p. 1, doi. 10.1186/s13104-017-2788-1
    By:
    • Hucka, Michael
    Publication type:
    Article

  • MOCCASIN: converting MATLAB ODE models to SBML.

    Published in:
    Bioinformatics, 2016, v. 32, n. 12, p. 1905, doi. 10.1093/bioinformatics/btw056
    By:
    • Gómez, Harold F.;
    • Hucka, Michael;
    • Keating, Sarah M.;
    • Nudelman, German;
    • Iber, Dagmar;
    • Sealfon, Stuart C.
    Publication type:
    Article

  • Do genome-scale models need exact solvers or clearer standards?

    Published in:
    2015
    By:
    • Ebrahim, Ali;
    • Almaas, Eivind;
    • Bauer, Eugen;
    • Bordbar, Aarash;
    • Burgard, Anthony P;
    • Chang, Roger L;
    • Dräger, Andreas;
    • Famili, Iman;
    • Feist, Adam M;
    • Fleming, Ronan MT;
    • Fong, Stephen S;
    • Hatzimanikatis, Vassily;
    • Herrgård, Markus J;
    • Holder, Allen;
    • Hucka, Michael;
    • Hyduke, Daniel;
    • Jamshidi, Neema;
    • Lee, Sang Yup;
    • Le Novère, Nicolas;
    • Lerman, Joshua A
    Publication type:
    Letter to the Editor

  • BioModels: ten-year anniversary.

    Published in:
    Nucleic Acids Research, 2015, v. 43, n. D1, p. D542, doi. 10.1093/nar/gku1181
    By:
    • Chelliah, Vijayalakshmi;
    • Juty, Nick;
    • Ajmera, Ishan;
    • Ali, Raza;
    • Dumousseau, Marine;
    • Glont, Mihai;
    • Hucka, Michael;
    • Jalowicki, Gaël;
    • Keating, Sarah;
    • Knight-Schrijver, Vincent;
    • Lloret-Villas, Audald;
    • Natarajan, Kedar Nath;
    • Pettit, Jean-Baptiste;
    • Rodriguez, Nicolas;
    • Schubert, Michael;
    • Wimalaratne, Sarala M.;
    • Zhao, Yangyang;
    • Hermjakob, Henning;
    • Le Novère, Nicolas;
    • Laibe, Camille
    Publication type:
    Article

  • COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project.

    Published in:
    BMC Bioinformatics, 2014, v. 15, n. 1, p. 61, doi. 10.1186/s12859-014-0369-z
    By:
    • Bergmann, Frank T.;
    • Adams, Richard;
    • Moodie, Stuart;
    • Cooper, Jonathan;
    • Glont, Mihai;
    • Golebiewski, Martin;
    • Hucka, Michael;
    • Laibe, Camille;
    • Miller, Andrew K.;
    • Nickerson, David P.;
    • Olivier, Brett G.;
    • Rodriguez, Nicolas;
    • Sauro, Herbert M.;
    • Scharm, Martin;
    • Soiland-Reyes, Stian;
    • Waltemath, Dagmar;
    • Yvon, Florent;
    • Le Novère, Nicolas
    Publication type:
    Article

  • Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE).

    Published in:
    Standards in Genomic Sciences, 2014, v. 9, n. 3, p. 1285, doi. 10.4056/sigs.5279417
    By:
    • Waltemath, Dagmar;
    • Bergmann, Frank;
    • Chaouiya, Claudine;
    • Czauderna, Tobias;
    • Gleeson, Padraig;
    • Goble, Carole;
    • Golebiewski, Martin;
    • Hucka, Michael;
    • Juty, Nick;
    • Krebs, Olga;
    • Novère, Nicolas;
    • Mi, Huaiyu;
    • Moraru, Ion;
    • Myers, Chris;
    • Nickerson, David;
    • Olivier, Brett;
    • Rodriguez, Nicolas;
    • Schreiber, Falk;
    • Smith, Lucian;
    • Zhang, Fengkai
    Publication type:
    Article

  • Path2Models: large-scale generation of computational models from biochemical pathway maps.

    Published in:
    BMC Systems Biology, 2013, v. 7, n. 1, p. 3, doi. 10.1186/1752-0509-7-116
    By:
    • Büchel, Finja;
    • Rodriguez, Nicolas;
    • Swainston, Neil;
    • Wrzodek, Clemens;
    • Czauderna, Tobias;
    • Keller, Roland;
    • Mittag, Florian;
    • Schubert, Michael;
    • Glont, Mihai;
    • Golebiewski, Martin;
    • van Iersel, Martijn;
    • Keating, Sarah;
    • Rall, Matthias;
    • Wybrow, Michael;
    • Hermjakob, Henning;
    • Hucka, Michael;
    • Kell, Douglas B.;
    • Müller, Wolfgang;
    • Mendes, Pedro;
    • Zell, Andreas
    Publication type:
    Article

  • A community-driven global reconstruction of human metabolism.

    Published in:
    Nature Biotechnology, 2013, v. 31, n. 5, p. 419, doi. 10.1038/nbt.2488
    By:
    • Thiele, Ines;
    • Swainston, Neil;
    • Fleming, Ronan M T;
    • Hoppe, Andreas;
    • Sahoo, Swagatika;
    • Aurich, Maike K;
    • Haraldsdottir, Hulda;
    • Mo, Monica L;
    • Rolfsson, Ottar;
    • Stobbe, Miranda D;
    • Thorleifsson, Stefan G;
    • Agren, Rasmus;
    • Bölling, Christian;
    • Bordel, Sergio;
    • Chavali, Arvind K;
    • Dobson, Paul;
    • Dunn, Warwick B;
    • Endler, Lukas;
    • Hala, David;
    • Hucka, Michael
    Publication type:
    Article

  • SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.

    Published in:
    BMC Systems Biology, 2013, v. 7, n. 1, p. 3, doi. 10.1186/1752-0509-7-135
    By:
    • Chaouiya, Claudine;
    • Berenguier, Duncan;
    • Keating, Sarah M.;
    • Naldi, Aurelien;
    • Van Iersel, Martijn P.;
    • Rodriguez, Nicolas;
    • Dräger, Andreas;
    • Büchel, Finja;
    • Cokelaer, Thomas;
    • Kowal, Bryan;
    • Wicks, Benjamin;
    • Gonçalves, Emanuel;
    • Dorier, Julien;
    • Page, Michel;
    • Monteiro, Pedro T.;
    • Kamp, Axel von;
    • Xenarios, Ioannis;
    • Jong, Hidde de;
    • Hucka, Michael;
    • Klamt, Steffen
    Publication type:
    Article

  • JSBML: a flexible Java library for working with SBML.

    Published in:
    Bioinformatics, 2011, v. 27, n. 15, p. 2167, doi. 10.1093/bioinformatics/btr361
    By:
    • Dräger, Andreas;
    • Rodriguez, Nicolas;
    • Dumousseau, Marine;
    • Dörr, Alexander;
    • Wrzodek, Clemens;
    • Le Novère, Nicolas;
    • Zell, Andreas;
    • Hucka, Michael
    Publication type:
    Article

  • Minimum Information About a Simulation Experiment (MIASE).

    Published in:
    PLoS Computational Biology, 2011, v. 7, n. 4, p. 1, doi. 10.1371/journal.pcbi.1001122
    By:
    • Waltemath, Dagmar;
    • Adams, Richard;
    • Beard, Daniel A.;
    • Bergmann, Frank T.;
    • Bhalla, Upinder S.;
    • Britten, Randall;
    • Chelliah, Vijayalakshmi;
    • Cooling, Michael T.;
    • Cooper, Jonathan;
    • Crampin, Edmund J.;
    • Garny, Alan;
    • Hoops, Stefan;
    • Hucka, Michael;
    • Hunter, Peter;
    • Klipp, Edda;
    • Laibe, Camille;
    • Miller, Andrew K.;
    • Moraru, Ion;
    • Nickerson, David;
    • Nielsen, Poul
    Publication type:
    Article

  • Software that goes with the flow in systems biology.

    Published in:
    BMC Biology, 2010, v. 8, p. 140, doi. 10.1186/1741-7007-8-140
    By:
    • Hucka, Michael;
    • Le Novère, Nicolas
    Publication type:
    Article

  • BioModels Database: An enhanced, curated andannotated resource for published quantitativekinetic models.

    Published in:
    BMC Systems Biology, 2010, v. 4, p. 92, doi. 10.1186/1752-0509-4-92
    By:
    • Chen Li;
    • Donizelli, Marco;
    • Rodriguez, Nicolas;
    • Dharuri, Harish;
    • Endler, Lukas;
    • Chelliah, Vijayalakshmi;
    • Lu Li;
    • Enuo He;
    • Henry, Arnaud;
    • Stefan, Melanie I.;
    • Snoep, Jacky L.;
    • Hucka, Michael.;
    • Le Novère1, Nicolas;
    • Laibe, Camille
    Publication type:
    Article

  • Erratum: The Systems Biology Graphical Notation.

    Published in:
    2009
    By:
    • Le Novère, Nicolas;
    • Hucka, Michael;
    • Mi, Huaiyu;
    • Moodie, Stuart;
    • Schreiber, Falk;
    • Sorokin, Anatoly;
    • Demir, Emek;
    • Wegner, Katja;
    • Aladjem, Mirit I;
    • Wimalaratne, Sarala M;
    • Bergman, Frank T;
    • Gauges, Ralph;
    • Ghazal, Peter;
    • Kawaji, Hideya;
    • Li, Lu;
    • Matsuoka, Yukiko;
    • Villéger, Alice;
    • Boyd, Sarah E;
    • Calzone, Laurence;
    • Courtot, Melanie
    Publication type:
    Correction notice

  • The Systems Biology Graphical Notation.

    Published in:
    Nature Biotechnology, 2009, v. 27, n. 8, p. 735, doi. 10.1038/nbt.1558
    By:
    • Le Novére, Nicolas;
    • Hucka, Michael;
    • Mi, Huaiyu;
    • Moodie, Stuart;
    • Schreiber, Falk;
    • Sorokin, Anatoly;
    • Demir, Emek;
    • Wegner, Katja;
    • Aladjem, Mirit I.;
    • Wimalaratne, Sarala M.;
    • Bergman, Frank T.;
    • Gauges, Ralph;
    • Ghazal, Peter;
    • Kawaji, Hideya;
    • Li, Lu;
    • Matsuoka, Yukiko;
    • Villéger, Alice;
    • Boyd, Sarah E.;
    • Calzone, Laurence;
    • Courtot, Melanie
    Publication type:
    Article

  • SBML2LATEX: Conversion of SBML files into human-readable reports.

    Published in:
    Bioinformatics, 2009, v. 25, n. 11, p. 1455, doi. 10.1093/bioinformatics/btp170
    By:
    • Andreas Dräger;
    • Hannes Planatscher;
    • Dieudonné Motsou Wouamba;
    • Adrian Schröder;
    • Michael Hucka;
    • Lukas Endler;
    • Martin Golebiewski;
    • Wolfgang Müller;
    • Andreas Zell
    Publication type:
    Article

  • A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology.

    Published in:
    Nature Biotechnology, 2008, v. 26, n. 10, p. 1155, doi. 10.1038/nbt1492
    By:
    • Herrgård, Markus J;
    • Swainston, Neil;
    • Dobson, Paul;
    • Dunn, Warwick B;
    • Arga, K Yalçin;
    • Arvas, Mikko;
    • Büthgen, Nils;
    • Borger, Simon;
    • Costenoble, Roeland;
    • Heinemann, Matthias;
    • Hucka, Michael;
    • Le Novère, Nicolas;
    • Li, Peter;
    • Liebermeister, Wolfram;
    • Mo, Monica L;
    • Oliveira, Ana Paula;
    • Petranovic, Dina;
    • Pettifer, Stephen;
    • Simeonidis, Evangelos;
    • Smallbone, Kieran
    Publication type:
    Article

  • LibSBML: an API Library for SBML.

    Published in:
    Bioinformatics, 2008, v. 24, n. 6, p. 880
    By:
    • Benjamin J. Bornstein;
    • Sarah M. Keating;
    • Akiya Jouraku;
    • Michael Hucka
    Publication type:
    Article

  • SBMLToolbox: an SBML toolbox for MATLAB users.

    Published in:
    Bioinformatics, 2006, v. 22, n. 10, p. 1275, doi. 10.1093/bioinformatics/btl111
    By:
    • Sarah M. Keating;
    • Benjamin J. Bornstein;
    • Andrew Finney;
    • Michael Hucka
    Publication type:
    Article

  • CellML2SBML: conversion of CellML into SBML.

    Published in:
    Bioinformatics, 2006, v. 22, n. 8, p. 1018, doi. 10.1093/bioinformatics/btl047
    By:
    • Maria J. Schilstra;
    • Lu Li;
    • Joanne Matthews;
    • Andrew Finney;
    • Michael Hucka;
    • Nicolas Le Novère
    Publication type:
    Article

  • BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems.

    Published in:
    Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d689, doi. 10.1093/nar/gkj092
    By:
    • Le Novère, Nicolas;
    • Bornstein, Benjamin;
    • Broicher, Alexander;
    • Courtot, Mélanie;
    • Donizelli, Marco;
    • Dharuri, Harish;
    • Li, Lu;
    • Sauro, Herbert;
    • Schilstra, Maria;
    • Shapiro, Bruce;
    • Snoep, Jacky L.;
    • Hucka, Michael
    Publication type:
    Article

  • Escalating model sizes and complexities call for standardized forms of representation.

    Published in:
    Molecular Systems Biology, 2005, v. 1, n. 1, p. E1, doi. 10.1038/msb4100015
    By:
    • Hucka, Michael;
    • Finney, Andrew
    Publication type:
    Article

  • Minimum information requested in the annotation of biochemical models (MIRIAM).

    Published in:
    Nature Biotechnology, 2005, v. 23, n. 12, p. 1509, doi. 10.1038/nbt1156
    By:
    • Novère, Nicolas Le;
    • Finney, Andrew;
    • Hucka, Michael;
    • Bhalla, Upinder S.;
    • Campagne, Fabien;
    • Collado-Vides, Julio;
    • Crampin, Edmund J.;
    • Halstead, Matt;
    • Klipp, Edda;
    • Mendes, Pedro;
    • Nielsen, Poul;
    • Sauro, Herbert;
    • Shapiro, Bruce;
    • Snoep, Jacky L.;
    • Spence, Hugh D.;
    • Wanner, Barry L.
    Publication type:
    Article

  • MathSBML: a package for manipulating SBML-based biological models.

    Published in:
    Bioinformatics, 2004, v. 20, n. 16, p. 2829, doi. 10.1093/bioinformatics/bth271
    By:
    • Bruce E. Shapiro;
    • Michael Hucka;
    • Andrew Finney;
    • John Doyle
    Publication type:
    Article

  • Hebb's accomplishments misunderstood.

    Published in:
    Behavioral & Brain Sciences, 1995, v. 18, n. 4, p. 635, doi. 10.1017/S0140525X00040267
    By:
    • Hucka, Michael;
    • Weaver, Mark;
    • Kaplan, Stephen
    Publication type:
    Article