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ArticlesPeer ReviewedFull Text
SBML Level 3: an extensible format for the exchange and reuse of biological models
Author / Creator:Waltemath, Dagmar ; König, Matthias ; Zhang, Fengkai ; Dräger, Andreas ; Chaouiya, Claudine ; Bergmann, Frank T ; Finney, Andrew ; Helikar, Tomáš ; Hoops, Stefan ; Malik‐Sheriff, Rahuman S ; Moraru, Ion I ; Naldi, Aurélien ; Olivier, Brett G ; Sahle, Sven ; Smith, Lucian P ; Swat, Maciej J ; Watanabe, Leandro ; Wilkinson, Darren J ; Begley, Kimberly ; Faeder, James R ; Gómez, Harold F ; Inagaki, Yuichiro ; Lister, Allyson L ; Lucio, Daniel ; Mjolsness, Eric ; Proctor, Carole J ; Raman, Karthik ; Rodriguez, Nicolas ; Shaffer, Clifford A ; Shapiro, Bruce E ; Stelling, Joerg ; Swainston, Neil ; Tanimura, Naoki ; Wagner, John ; Meier‐Schellersheim, Martin ; Sauro, Herbert M ; Palsson, Bernhard ; Kitano, Hiroaki ; Funahashi, Akira ; Hermjakob, Henning ; Doyle, John C ; Hucka, Michael ; Adams, Richard R ; Allen, Nicholas A ; Angermann, Bastian R ; Antoniotti, Marco ; Courtot, Mélanie ; Cox, Chris D ; Dalle Pezze, Piero ; Demir, Emek ; Denney, William S ; Dharuri, Harish ; Dorier, Julien ; Drasdo, Dirk ; Ebrahim, Ali ; Eichner, Johannes ; Elf, Johan ; Flamm, Christoph ; Fleming, Ronan MT ; Fröhlich, Martina ; Gonçalves, Emanuel ; Golebiewski, Martin ; Grabski, Hovakim ; Heavner, Benjamin D ; de Jong, Hidde ; Juty, Nick ; Karp, Peter D ; Kiselev, Ilya ; Klipp, Edda ; Knüpfer, Christian ; Kolpakov, Fedor ; Lawless, Conor ; Li, Lu ; Machne, Rainer ; Mendes, Pedro ; Mittag, Florian ; Monteiro, Pedro T ; Natarajan, Kedar Nath ; Nguyen, Tramy ; Pfau, Thomas ; Phair, Robert D ; Radivoyevitch, Tomas ; Rohwer, Johann M ; Saez‐Rodriguez, Julio ; Scharm, Martin ; Schmidt, Henning ; Schreiber, Falk ; Schubert, Michael ; Sealfon, Stuart C ; Soliman, Sylvain ; Stefan, Melanie I ; Sullivan, Devin P ; Takahashi, Koichi ; Teusink, Bas ; Tolnay, David ; Vazirabad, Ibrahim ; von Kamp, Axel ; Wittig, Ulrike ; Wrzodek, Clemens ; Zucker, Jeremy
Publisher:London: Nature Publishing Group UK
Journal title:Molecular systems biology, 2020-08, Vol.16 (8), p.e9110-n/a
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SBMLKinetics: a tool for annotation-independent classification of reaction kinetics for SBML models
Author / Creator:Xu, Jin
Publisher:England: BioMed Central Ltd
Journal title:BMC bioinformatics, 2023-06, Vol.24 (1), p.248-248, Article 248
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SBML-SAT: a systems biology markup language (SBML) based sensitivity analysis tool
Author / Creator:Zi, Zhike ; Zheng, Yanan ; Rundell, Ann E ; Klipp, Edda
Publisher:England: BioMed Central Ltd
Journal title:BMC bioinformatics, 2008-08, Vol.9 (1), p.342-342, Article 342
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From quantitative SBML models to Boolean networks
Author / Creator:Vaginay, Athénaïs ; Boukhobza, Taha ; Smaïl-Tabbone, Malika
Publisher:Cham: Springer International Publishing
Journal title:Applied network science, 2022-12, Vol.7 (1), p.1-23, Article 73
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SyBLaRS: A web service for laying out, rendering and mining biological maps in SBGN, SBML and more
Author / Creator:Balci, Hasan ; Dogrusoz, Ugur ; Ozgul, Yusuf Ziya ; Atayev, Perman
Publisher:San Francisco: Public Library of Science
Journal title:PLoS computational biology, 2022-11, Vol.18 (11), p.e1010635-e1010635
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Automatic Generation of SBML Kinetic Models from Natural Language Texts Using GPT
Author / Creator:Maeda, Kazuhiro ; Kurata, Hiroyuki
Publisher:Switzerland: MDPI AG
Journal title:International journal of molecular sciences, 2023-04, Vol.24 (8), p.7296
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SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools
Author / Creator:Chaouiya, Claudine ; Bérenguier, Duncan ; Keating, Sarah M ; Naldi, Aurélien ; 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 ; von Kamp, Axel ; Xenarios, Ioannis ; de Jong, Hidde ; Hucka, Michael ; Klamt, Steffen ; Thieffry, Denis ; Le Novère, Nicolas ; Saez-Rodriguez, Julio ; Helikar, Tomáš
Publisher:England: BioMed Central Ltd
Journal title:BMC systems biology, 2013-12, Vol.7 (1), p.135-135
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tidysbml: R/Bioconductor package for SBML extraction into dataframes
Author / Creator:Paparozzi, Veronica ; Nardini, Christine
Publisher:England: Oxford University Press
Journal title:Bioinformatics advances, 2024, Vol.4 (1), p.vbae148
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A General Hybrid Modeling Framework for Systems Biology Applications: Combining Mechanistic Knowledge with Deep Neural Networks under the SBML Standard
Author / Creator:Pinto, José ; Ramos, João R. C. ; Costa, Rafael S. ; Oliveira, Rui
Publisher:Basel: MDPI AG
Journal title:AI (Basel), 2023-03, Vol.4 (1), p.303-318
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Novel Ground-Up 3D Multicellular Simulators for Synthetic Biology CAD Integrating Stochastic Gillespie Simulations Benchmarked with Topologically Variable SBML Models
Author / Creator:Matzko, Richard Oliver ; Mierla, Laurentiu ; Konur, Savas
Publisher:Switzerland: MDPI AG
Journal title:Genes, 2023-01, Vol.14 (1), p.154
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ASPASIA: A toolkit for evaluating the effects of biological interventions on SBML model behaviour
Author / Creator:Evans, Stephanie ; Alden, Kieran ; Cucurull-Sanchez, Lourdes ; Larminie, Christopher ; Coles, Mark C. ; Kullberg, Marika C. ; Timmis, Jon
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2017-02, Vol.13 (2), p.e1005351-e1005351
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SBMLPkgSpec: a LaTeX style file for SBML package specification documents
Author / Creator:Hucka, Michael
Publisher:England: BioMed Central Ltd
Journal title:BMC research notes, 2017-09, Vol.10 (1), p.451-451, Article 451
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Computational speed-up of large-scale, single-cell model simulations via a fully integrated SBML-based format
Author / Creator:Mutsuddy, Arnab ; Erdem, Cemal ; Huggins, Jonah R ; Salim, Misha ; Cook, Daniel ; Hobbs, Nicole ; Feltus, F Alex ; Birtwistle, Marc R
Publisher:England: Oxford University Press
Journal title:Bioinformatics advances, 2023, Vol.3 (1), p.vbad039-vbad039
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Annotation-based feature extraction from sets of SBML models
Author / Creator:Alm, Rebekka ; Waltemath, Dagmar ; Wolfien, Markus ; Wolkenhauer, Olaf ; Henkel, Ron
Publisher:England: BioMed Central
Journal title:Journal of biomedical semantics, 2015-04, Vol.6 (1), p.20-20, Article 20
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SBMLeditor: effective creation of models in the Systems Biology Markup Language (SBML)
Author / Creator:Rodriguez, Nicolas ; Donizelli, Marco ; Le Novère, Nicolas
Publisher:England: BioMed Central Ltd
Journal title:BMC bioinformatics, 2007-03, Vol.8 (1), p.79-79, Article 79
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Annotation of SBML models through rule-based semantic integration
Author / Creator:Lister, Allyson L ; Lord, Phillip ; Pocock, Matthew ; Wipat, Anil
Publisher:England: BioMed Central
Journal title:Journal of biomedical semantics, 2010-06, Vol.1 (Suppl 1), p.S3-S3
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Identification of components in biochemical pathways: extensive application to SBML models
Author / Creator:Pardini, Giovanni ; Milazzo, Paolo ; Maggiolo-Schettini, Andrea
Publisher:Dordrecht: Springer Netherlands
Journal title:Natural computing, 2014-09, Vol.13 (3), p.351-365
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A Versatile Platform for Multilevel Modeling of Physiological Systems: SBML-PHML Hybrid Modeling and Simulation
Author / Creator:ASAI, Yoshiyuki ; ABE, Takeshi ; OKA, Hideki ; OKITA, Masao ; HAGIHARA, Ken-ichi ; GHOSH, Samik ; MATSUOKA, Yukiko ; KURACHI, Yoshihisa ; NOMURA, Taishin ; KITANO, Hiroaki
Publisher:Kagoshima: Japanese Society for Medical and Biological Engineering
Journal title:Advanced Biomedical Engineering, 2014, Vol.3, pp.50-58
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SBML and MathML support for the stochastic reaction-diffusion simulator STEPS
Author / Creator:Hepburn, Iain ; Chen, Weiliang ; De Schutter, Erik
Publisher:BioMed Central Ltd
Journal title:BMC neuroscience, 2011-07, Vol.12 (S1), p.P57-P57, Article P57
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Integrating Systems Biology Markup Language(SBML) with NEURON
Author / Creator:Bulanova, Anna S ; McDougal, Robert A ; Neymotin, Samuel A ; Mutai, Victor K ; Lytton, William W ; Hines, Michael L
Publisher:London: BioMed Central
Journal title:BMC neuroscience, 2014-07, Vol.15 (S1), p.P144-P144, Article P144
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Showing 1 to 20 of 432 results

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SBML Level 3: an extensible format for the exchange and reuse of biological models

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SBMLKinetics: a tool for annotation-independent classification of reaction kinetics for SBML models

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SBML-SAT: a systems biology markup language (SBML) based sensitivity analysis tool

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From quantitative SBML models to Boolean networks

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SyBLaRS: A web service for laying out, rendering and mining biological maps in SBGN, SBML and more

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Automatic Generation of SBML Kinetic Models from Natural Language Texts Using GPT

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

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tidysbml: R/Bioconductor package for SBML extraction into dataframes

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A General Hybrid Modeling Framework for Systems Biology Applications: Combining Mechanistic Knowledge with Deep Neural Networks under the SBML Standard

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Novel Ground-Up 3D Multicellular Simulators for Synthetic Biology CAD Integrating Stochastic Gillespie Simulations Benchmarked with Topologically Variable SBML Models

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ASPASIA: A toolkit for evaluating the effects of biological interventions on SBML model behaviour

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SBMLPkgSpec: a LaTeX style file for SBML package specification documents

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Computational speed-up of large-scale, single-cell model simulations via a fully integrated SBML-based format

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Annotation-based feature extraction from sets of SBML models

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SBMLeditor: effective creation of models in the Systems Biology Markup Language (SBML)

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Annotation of SBML models through rule-based semantic integration

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Identification of components in biochemical pathways: extensive application to SBML models

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A Versatile Platform for Multilevel Modeling of Physiological Systems: SBML-PHML Hybrid Modeling and Simulation

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SBML and MathML support for the stochastic reaction-diffusion simulator STEPS

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Integrating Systems Biology Markup Language(SBML) with NEURON

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