Works matching AU Hucka, Michael

Results: 35

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

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

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

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

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

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

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

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

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

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

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

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: 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 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: 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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