LibSBML: an API Library for SBML
Cited by (373)
Items 301–373 of 373
- In Silico Models on Algal Cultivation and ProcessingLamiaa H.S. Hassan, Imran Ahmad, Mostafa Mohamed El-Sheekh, Norhayati Abdullah · 2023 · IGI Global eBooks
- SBMLToolkit.jl: a Julia package for importing SBML into the SciML ecosystemPaul F. Lang, Anand Jain, Christopher Rackauckas · 2024 · Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics
- Systems Metabolic Engineering of Arabidopsis for Increased Cellulose ProductionJiun Yang Yen, Glenda E. Gillaspy, Ryan S. Senger · 2015 · The FASEB Journal
- Controlled Vocabularies and Semantics in Systems Biology2023 · Royal Society of Chemistry eBooks
- SEML: A Simplified English Modeling Language for Constructing Biological Models in JuliaZhiping Zhang, Jeffrey D. Varner · 2019 · IFAC-PapersOnLine
- Modular Modeling of Genetic Circuits in SBML Level 3Mario Andrea Marchisio · 2020 · Methods in molecular biology
- Review of construction methods for whole-cell computational modelsJingru Zhou, Xingcun Fan, Lingfeng Cao, Huijie Sun, Jianye Xia, XueFeng Yan · 2021 · Systems Microbiology and Biomanufacturing
- SBMLWebApp: Web-Based Simulation, Steady-State Analysis, and Parameter Estimation of Systems Biology ModelsTakahiro Yamada, Kaito Ii, Matthias König, Martina Feierabend, Andreas Dräger, Akira Funahashi · 2021 · Processes
- eBCSgen 2.0: Modelling and Analysis of Regulated Rule-Based SystemsMatej Troják, David Šafránek, Branislav Brozmann, Luboš Brim · 2022 · Lecture notes in computer science
- Size Dependent Growth in Metabolic NetworksHenry Dorrian, Kieran Smallbone, Jon Borresen · 2012 · arXiv (Cornell University)
- R and Bioconductor Packages in Bioinformatics: Towards Systems BiologyNolweim LeMeur, Michael F. Lawrence, Merav Bar, Muneesh Tewari, Robert C. Gentleman · 2010
- Coupling metabolic footprinting and flux balance analysis to predict how single gene knockouts perturb microbial metabolismGonçalo dos Santos Correia · 2012 · Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT)
- A Modular Approach to Heterogeneous Biochemical Model Simulation on an FPGAHideki Yamada, Yasunori Osana, Tomoya Ishimori, Tomonori Ooya, Masato Yoshimi, Yuri Nishikawa, Akira Funahashi, Noriko F. Hiroi, Hideharu Amano, Yuichiro Shibata et al. · 2009 · International Conference on ReConFigurable Computing and FPGAs (ReConFig)
- Variance-based sensitivity analysis and orthogonal approximations for stochastic modelsTomasz Badowski · 2013 · arXiv (Cornell University)
- Proceedings of the IJCAI-09 Workshop on Nonmonotonic Reasoning, Action and ChangeAndrew Herzig, Benjamin Johnston · 2009 · UTS ePRESS eBooks
- A portable library to support the SBML Layout ExtensionKyle Medley, Kiri Choi, Herbert M. Sauro · 2016 · bioRxiv (Cold Spring Harbor Laboratory)
- Trecento : in silico network-driven identification of target combinations for combination therapyHuey Eng Chua · 2015 · DR-NTU (Nanyang Technological University)
- SimpleSBML: A Python package for creating, editing, and interrogating SBML models: Version 2.0Herbert M. Sauro · 2020 · arXiv (Cornell University)
- Therapy for septic shock.Hylton Miller, Wilbur W. Oaks · 1979 · PubMed
- Structural and Metabolic Characterization of Ni(I)-inhibitors Provide a Robust Anti-Methanogenicity Scoring SystemRandy Aryee, Mohammad Reza Zargar, Vaishnavey SR, B. Arunraj, Noor S. Mohammed, Supantha Dey, Karuna Anna Sajeevan, Angel Frazier, Jacek A. Koziel, Matthew R Beck et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
- BoolDog: integrated Boolean and semi-quantitative network modelling in PythonCarissa Bleker, Maja Zagorščak, Andrej Blejec, Kristina Gruden, Anže Županič · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
- Biological Pathway Analysis: An Overview of Reactome and Other Integrative Pathway Knowledge BasesRobin Haw, Marc E. Gillespie, Michael A. Caudy · 2010
- PathCase-MAWA. Ercüment Çiçek, Xinjian Qi, Ali Cakmak, Stephen R. Johnson, Han Xu, Sami Alshalwi, Gültekin Özsoyoğlu · 2013 · ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB)
- A datapath classification method for FPGA-based scientific application accelerator systemsYui Ogawa, Tomonori Ooya, Yasunori Osana, Masato Yoshimi, Yuri Nishikawa, Akira Funahashi, Noriko F. Hiroi, Hideharu Amano, Yuichiro Shibata, Kiyoshi Oguri · 2010 · International Conference on Field-Programmable Technology (FPT)
- A distributed software package for global sensitivity analysis of biological modelsQuang Tung Thai, Seok-Jong Yu, Yongseong Cho · 2012 · IEEE International Conference on Bioinformatics and Bioengineering (BIBE)
- PathCase-SBXin Qi, Sarp A Coskun, Ali Cakmak, En Cheng, E. A. Cicek, M. Das, Lu Yang, Rishiraj Jadeja, S. Syed, Ranjan K. Dash et al. · 2012 · ACM SIGBioinformatics Record
- Interoperable and Easy-to-Use Web Services for the Bioinformatics Community - A Case StudyMikael Åsberg, Lena Strömbäck · 2010 · Databases, Knowledge, and Data Applications
- Simulation, Characterization, and Optimization of Metabolic Models with the High Performance Systems Biology ToolkitMonte Lunacek, Ambarish Nag, David M. Alber, Kenny Gruchalla, Christopher H. Chang, Peter A Graf · 2011 · SIAM Journal on Scientific Computing
- Toward a fast stochastic simulation processor for biochemical reaction networksHyungman Park, Andreas Gerstlauer · 2013 · IEEE International Conference on Application-specific Systems, Architectures and Processors (ASAP)
- A Software Tool for the Simulation and Optimization of Dynamic Metabolic ModelsPedro Evangelista, Isabel Rocha, Eugénio Campos Ferreira, Miguel Rocha · 2009 · Lecture notes in computer science
- Flux balance analysis to model microbial metabolism for electricity generationLongfei Mao · 2013 · Lincoln University Research Archive (Lincoln University)
- A cross-species study of the evolutionary conservation of essential genes in bacteriaBeverly Sackler · 2013
- CONTRIBUTIONS IN COMPUTATIONAL BIOLOGYEva Sciacca · 2009
- Computing project Group report SBML-ABC, a package for data simulation, parameter inference and model selectionNathan Harmston, David A. Knowles, S. Travis Langley, Hang Phan · 2008
- An Automatic Multi-dimensional Global Optimisation Implementation With Dynamic Task Mapping ModelXiaotian Xu · 2010
- Metabolic Modeling of Inborn Errors of Metabolism: Carnitine Palmitoyltransferase II Deficiency and Respiratory Chain Complex I DeficiencyJudy McKinley Brewer · 2015 · Digital Access to Scholarship at Harvard (DASH) (Harvard University)
- Development, calibration and validation of a dynamic genome-scale metabolic model of saccharomyces cerevisiaeBenjamín J. Sánchez · 2014
- Exact Bayesian lineage tree-based inference identifies Nanog negative autoregulation in mouse embryonic stem cellsJustin S. Feigelman, Stefan Ganscha, Simon Hastreiter, Michael Schwarzfischer, Adam A. Filipczyk, Timm Schroeder, Fabian Joachim Theis, Carsten Marr, Manfred Claassen · 2016 · bioRxiv (Cold Spring Harbor Laboratory)
- A Linearized constraint based approach for modelingBeverly Sackler · 2011
- Parameter Balancing in Kinetic ModelsTimo Lubitz · 2010
- Comparative Analysis of Biochemical Network ReconstructionsMartins Mednis · 2016 · Baltic Journal of Modern Computing
- Corso di Laurea Specialistica in Informatica Within European Masters in InformaticsCorrado Priami, Kanimozhi Ellavarason, Federica Ciocchetta · 2008
- Computer simulation of a large-scale signalling network regulating translation Initiation in the mammalian cell.David Ward Taylor · 2017 · Surrey Research Insight Open Access (The University of Surrey)
- The MONGOOSE Rational Arithmetic ToolboxChristopher Le, Leonid Chindelevitch · 2017 · Methods in molecular biology
- Annotation-based storage and retrieval of models and simulation descriptions in computational biologyDagmar Waltemath · 2011 · Ros Dok Rostocker Dokumentenserver (Universitätsbibliothek Rostock)
- Accelerated construction of kinetic models for cell metabolismChuan Fu Yap · 2019 · Research Explorer (The University of Manchester)
- Oncogenic memory underlying minimal residual disease in breast cancerKsenija Radic Shechter, Eleni Kafkia, Katharina Zirngibl, Sylwia Gawrzak, Ashna Alladin, Daniel Machado, Christian Lüchtenborg, Daniel C. Sévin, Britta Brügger, Kiran Raosaheb Patil et al. · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
- Hybrid Reactions Modeling for Top-down Design FrameworkLöıc Matthey · 2008
- SED-ML Validator: tool for debugging simulation experimentsBilal Shaikh, Andrew Freiburger, Matthias König, Frank Bergmann, David Phillip Nickerson, Herbert M. Sauro, Michael L. Blinov, Lucian P. Smith, Ion I. Moraru, Jonathan R. Karr · 2021 · arXiv (Cornell University)
- Faculty Opinions recommendation of Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language.Herbert M. Sauro · 2019 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
- In Silico Models on Algal Cultivation and ProcessingLamiaa H.S. Hassan, Imran Ahmad, Mostafa Mohamed El-Sheekh, Norhayati Abdullah · 2022 · Practice, progress, and proficiency in sustainability
- Desenvolvimento de um arcabouço para inferência e seleção de modelos dinâmicos de vias de sinalização celularMarcelo B. Lima · 2023
- Standards and Models for Biological Data: SBMLGiuseppe Agapito · 2024 · Elsevier eBooks
- Curating models from BioModels: Developing a workflow for creating OMEX filesJin Hua Xu, Lucian P. Smith · 2024 · PLoS ONE
- Neural Ordinary Differential Equations Inspired Parameterization of Kinetic ModelsPaul van Lent, Olga Bunkova, Léon Planken, Joep P. J. Schmitz, Thomas Abeel · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
- jax-smfsb: A Python library for stochastic systems biology modelling and inferenceDarren J. Wilkinson · 2025 · The Journal of Open Source Software
- Mathematical Modeling and Simulation of Naphthalene Biodegradation Using Pseudomonas aeruginosaArun Kumar, M. R. Chandana, S. B. Gunapriya, R. Spoorthi, Sasmita Sabat · 2025 · Innovations in Sustainable Technologies and Computing
- SBMLtoOdin and Menelmacar: interactive visualisation of systems biology models for expert and non-expert audiencesLeonie Johanna Lorenz, Antoine Andréoletti, Tung V. N. Nguyen, Henning Hermjakob, Richard G. FitzJohn, Rahuman S. Malik‐Sheriff, John A. Lees · 2025 · Bioinformatics
- Parameterization of cell-free systems with time-series data using KETCHUPMengqi Hu, Syed Bilal Jilani, Daniel G. Olson, Costas D. Maranas · 2025 · PLoS Computational Biology
- Additional file 1 of gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic modelsJohannes Zimmermann, Kaleta, Christoph, Silvio Waschina · 2021 · Figshare
- Additional file 1 of From quantitative SBML models to Boolean networksAthénaïs Vaginay, Taha Boukhobza, Malika Smaïl‐Tabbone · 2022 · Figshare
- Additional file 1 of Biology System Description Language (BiSDL): a modeling language for the design of multicellular synthetic biological systemsLeonardo Giannantoni, Roberta Bardini, Alessandro Savino, Di Carlo, Stefano · 2024 · Figshare
- Additional file 3 of gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic modelsJohannes Zimmermann, Kaleta, Christoph, Silvio Waschina · 2021 · Figshare
- Genome-scale metabolic reconstruction and analysis of the Trypanosoma brucei metabolism from a Systems biology perspectiveSanu Shameer · 2016 · theses.fr (ABES)
- Knowledge-based scaling for biological models. (Généralisation de modèles métaboliques par connaissances)A. Zhukova · 2014
- Modélisation mathématique du réseau transcriptionnel contrôlé par MYB30 et MYB96, deux facteurs de transcription impliqués dans la réponse de la plante modèle arabidopsis thalianaLucas Marmiesse · 2016 · theses.fr (ABES)
- Synthesis of Boolean Networks from the Structure and Dynamics of Reaction NetworksAthénaïs Vaginay · 2023 · theses.fr (ABES)
- Logic programming tools for metabolic fluxes analysis and biological applicationsMaxime Mahout · 2023 · theses.fr (ABES)
- Transcriptome-guided modeling reveals insulin-related metabolic dysfunction in SCA3 mouse cerebellumShin‐Hung Pan, Jui‐Chih Chang, Wen-Ling Cheng, An‐Chi Wei, Chin‐San Liu · 2026 · Brain Research
- Analysis of Biochemical Pathway Perturbations with Network PropagationNiccolò De Paolis, Paolo Milazzo · 2026 · Communications in computer and information science
- Integrating genome-scale metabolic models into multi-scale simulationsMarco Ruscone, Othmane Hayoun-Mya, Randy W. Heiland, Paul Macklin, Alfonso Valencia, Miguel Ponce-de-León · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
- Antimony 3: Extending human-readable model definitions for SBML Level 3 Core and PackagesAdel Heydarabadipour, Lucian P. Smith, Joseph L. Hellerstein, Herbert M. Sauro · 2026 · PLoS Computational Biology
- Computational modelling of brain energy metabolism and circulation in the neonatal animal modelTracy Moroz · 2014 · UCL Discovery (University College London)