LibSBML: an API Library for SBML

Cited by (373)

Items 301–373 of 373

  1. In Silico Models on Algal Cultivation and Processing
    Lamiaa H.S. Hassan, Imran Ahmad, Mostafa Mohamed El-Sheekh, Norhayati Abdullah · 2023 · IGI Global eBooks
  2. SBMLToolkit.jl: a Julia package for importing SBML into the SciML ecosystem
    Paul F. Lang, Anand Jain, Christopher Rackauckas · 2024 · Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics
  3. Systems Metabolic Engineering of Arabidopsis for Increased Cellulose Production
    Jiun Yang Yen, Glenda E. Gillaspy, Ryan S. Senger · 2015 · The FASEB Journal
  4. Controlled Vocabularies and Semantics in Systems Biology
    2023 · Royal Society of Chemistry eBooks
  5. SEML: A Simplified English Modeling Language for Constructing Biological Models in Julia
    Zhiping Zhang, Jeffrey D. Varner · 2019 · IFAC-PapersOnLine
  6. Modular Modeling of Genetic Circuits in SBML Level 3
    Mario Andrea Marchisio · 2020 · Methods in molecular biology
  7. Review of construction methods for whole-cell computational models
    Jingru Zhou, Xingcun Fan, Lingfeng Cao, Huijie Sun, Jianye Xia, XueFeng Yan · 2021 · Systems Microbiology and Biomanufacturing
  8. SBMLWebApp: Web-Based Simulation, Steady-State Analysis, and Parameter Estimation of Systems Biology Models
    Takahiro Yamada, Kaito Ii, Matthias König, Martina Feierabend, Andreas Dräger, Akira Funahashi · 2021 · Processes
  9. eBCSgen 2.0: Modelling and Analysis of Regulated Rule-Based Systems
    Matej Troják, David Šafránek, Branislav Brozmann, Luboš Brim · 2022 · Lecture notes in computer science
  10. Size Dependent Growth in Metabolic Networks
    Henry Dorrian, Kieran Smallbone, Jon Borresen · 2012 · arXiv (Cornell University)
  11. R and Bioconductor Packages in Bioinformatics: Towards Systems Biology
    Nolweim LeMeur, Michael F. Lawrence, Merav Bar, Muneesh Tewari, Robert C. Gentleman · 2010
  12. Coupling metabolic footprinting and flux balance analysis to predict how single gene knockouts perturb microbial metabolism
    Gonçalo dos Santos Correia · 2012 · Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT)
  13. A Modular Approach to Heterogeneous Biochemical Model Simulation on an FPGA
    Hideki 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)
  14. Variance-based sensitivity analysis and orthogonal approximations for stochastic models
    Tomasz Badowski · 2013 · arXiv (Cornell University)
  15. Proceedings of the IJCAI-09 Workshop on Nonmonotonic Reasoning, Action and Change
    Andrew Herzig, Benjamin Johnston · 2009 · UTS ePRESS eBooks
  16. A portable library to support the SBML Layout Extension
    Kyle Medley, Kiri Choi, Herbert M. Sauro · 2016 · bioRxiv (Cold Spring Harbor Laboratory)
  17. Trecento : in silico network-driven identification of target combinations for combination therapy
    Huey Eng Chua · 2015 · DR-NTU (Nanyang Technological University)
  18. SimpleSBML: A Python package for creating, editing, and interrogating SBML models: Version 2.0
    Herbert M. Sauro · 2020 · arXiv (Cornell University)
  19. Therapy for septic shock.
    Hylton Miller, Wilbur W. Oaks · 1979 · PubMed
  20. Structural and Metabolic Characterization of Ni(I)-inhibitors Provide a Robust Anti-Methanogenicity Scoring System
    Randy 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)
  21. BoolDog: integrated Boolean and semi-quantitative network modelling in Python
    Carissa Bleker, Maja Zagorščak, Andrej Blejec, Kristina Gruden, Anže Županič · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  22. Biological Pathway Analysis: An Overview of Reactome and Other Integrative Pathway Knowledge Bases
    Robin Haw, Marc E. Gillespie, Michael A. Caudy · 2010
  23. PathCase-MAW
    A. 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)
  24. A datapath classification method for FPGA-based scientific application accelerator systems
    Yui 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)
  25. A distributed software package for global sensitivity analysis of biological models
    Quang Tung Thai, Seok-Jong Yu, Yongseong Cho · 2012 · IEEE International Conference on Bioinformatics and Bioengineering (BIBE)
  26. PathCase-SB
    Xin 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
  27. Interoperable and Easy-to-Use Web Services for the Bioinformatics Community - A Case Study
    Mikael Åsberg, Lena Strömbäck · 2010 · Databases, Knowledge, and Data Applications
  28. Simulation, Characterization, and Optimization of Metabolic Models with the High Performance Systems Biology Toolkit
    Monte Lunacek, Ambarish Nag, David M. Alber, Kenny Gruchalla, Christopher H. Chang, Peter A Graf · 2011 · SIAM Journal on Scientific Computing
  29. Toward a fast stochastic simulation processor for biochemical reaction networks
    Hyungman Park, Andreas Gerstlauer · 2013 · IEEE International Conference on Application-specific Systems, Architectures and Processors (ASAP)
  30. A Software Tool for the Simulation and Optimization of Dynamic Metabolic Models
    Pedro Evangelista, Isabel Rocha, Eugénio Campos Ferreira, Miguel Rocha · 2009 · Lecture notes in computer science
  31. Flux balance analysis to model microbial metabolism for electricity generation
    Longfei Mao · 2013 · Lincoln University Research Archive (Lincoln University)
  32. A cross-species study of the evolutionary conservation of essential genes in bacteria
    Beverly Sackler · 2013
  33. CONTRIBUTIONS IN COMPUTATIONAL BIOLOGY
    ‬‬‬‬‬‬Eva Sciacca · 2009
  34. Computing project Group report SBML-ABC, a package for data simulation, parameter inference and model selection
    Nathan Harmston, David A. Knowles, S. Travis Langley, Hang Phan · 2008
  35. An Automatic Multi-dimensional Global Optimisation Implementation With Dynamic Task Mapping Model
    Xiaotian Xu · 2010
  36. Metabolic Modeling of Inborn Errors of Metabolism: Carnitine Palmitoyltransferase II Deficiency and Respiratory Chain Complex I Deficiency
    Judy McKinley Brewer · 2015 · Digital Access to Scholarship at Harvard (DASH) (Harvard University)
  37. Development, calibration and validation of a dynamic genome-scale metabolic model of saccharomyces cerevisiae
    Benjamín J. Sánchez · 2014
  38. Exact Bayesian lineage tree-based inference identifies Nanog negative autoregulation in mouse embryonic stem cells
    Justin 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)
  39. A Linearized constraint based approach for modeling
    Beverly Sackler · 2011
  40. Parameter Balancing in Kinetic Models
    Timo Lubitz · 2010
  41. Comparative Analysis of Biochemical Network Reconstructions
    Martins Mednis · 2016 · Baltic Journal of Modern Computing
  42. Corso di Laurea Specialistica in Informatica Within European Masters in Informatics
    Corrado Priami, Kanimozhi Ellavarason, Federica Ciocchetta · 2008
  43. 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)
  44. The MONGOOSE Rational Arithmetic Toolbox
    Christopher Le, Leonid Chindelevitch · 2017 · Methods in molecular biology
  45. Annotation-based storage and retrieval of models and simulation descriptions in computational biology
    Dagmar Waltemath · 2011 · Ros Dok Rostocker Dokumentenserver (Universitätsbibliothek Rostock)
  46. Accelerated construction of kinetic models for cell metabolism
    Chuan Fu Yap · 2019 · Research Explorer (The University of Manchester)
  47. Oncogenic memory underlying minimal residual disease in breast cancer
    Ksenija 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)
  48. Hybrid Reactions Modeling for Top-down Design Framework
    Löıc Matthey · 2008
  49. SED-ML Validator: tool for debugging simulation experiments
    Bilal 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)
  50. 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
  51. In Silico Models on Algal Cultivation and Processing
    Lamiaa H.S. Hassan, Imran Ahmad, Mostafa Mohamed El-Sheekh, Norhayati Abdullah · 2022 · Practice, progress, and proficiency in sustainability
  52. Desenvolvimento de um arcabouço para inferência e seleção de modelos dinâmicos de vias de sinalização celular
    Marcelo B. Lima · 2023
  53. Standards and Models for Biological Data: SBML
    Giuseppe Agapito · 2024 · Elsevier eBooks
  54. Curating models from BioModels: Developing a workflow for creating OMEX files
    Jin Hua Xu, Lucian P. Smith · 2024 · PLoS ONE
  55. Neural Ordinary Differential Equations Inspired Parameterization of Kinetic Models
    Paul van Lent, Olga Bunkova, Léon Planken, Joep P. J. Schmitz, Thomas Abeel · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  56. jax-smfsb: A Python library for stochastic systems biology modelling and inference
    Darren J. Wilkinson · 2025 · The Journal of Open Source Software
  57. Mathematical Modeling and Simulation of Naphthalene Biodegradation Using Pseudomonas aeruginosa
    Arun Kumar, M. R. Chandana, S. B. Gunapriya, R. Spoorthi, Sasmita Sabat · 2025 · Innovations in Sustainable Technologies and Computing
  58. SBMLtoOdin and Menelmacar: interactive visualisation of systems biology models for expert and non-expert audiences
    Leonie Johanna Lorenz, Antoine Andréoletti, Tung V. N. Nguyen, Henning Hermjakob, Richard G. FitzJohn, Rahuman S. Malik‐Sheriff, John A. Lees · 2025 · Bioinformatics
  59. Parameterization of cell-free systems with time-series data using KETCHUP
    Mengqi Hu, Syed Bilal Jilani, Daniel G. Olson, Costas D. Maranas · 2025 · PLoS Computational Biology
  60. Additional file 1 of gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models
    Johannes Zimmermann, Kaleta, Christoph, Silvio Waschina · 2021 · Figshare
  61. Additional file 1 of From quantitative SBML models to Boolean networks
    Athénaïs Vaginay, Taha Boukhobza, Malika Smaïl‐Tabbone · 2022 · Figshare
  62. Additional file 1 of Biology System Description Language (BiSDL): a modeling language for the design of multicellular synthetic biological systems
    Leonardo Giannantoni, Roberta Bardini, Alessandro Savino, Di Carlo, Stefano · 2024 · Figshare
  63. Additional file 3 of gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models
    Johannes Zimmermann, Kaleta, Christoph, Silvio Waschina · 2021 · Figshare
  64. Genome-scale metabolic reconstruction and analysis of the Trypanosoma brucei metabolism from a Systems biology perspective
    Sanu Shameer · 2016 · theses.fr (ABES)
  65. Knowledge-based scaling for biological models. (Généralisation de modèles métaboliques par connaissances)
    A. Zhukova · 2014
  66. Modélisation mathématique du réseau transcriptionnel contrôlé par MYB30 et MYB96, deux facteurs de transcription impliqués dans la réponse de la plante modèle arabidopsis thaliana
    Lucas Marmiesse · 2016 · theses.fr (ABES)
  67. Synthesis of Boolean Networks from the Structure and Dynamics of Reaction Networks
    Athénaïs Vaginay · 2023 · theses.fr (ABES)
  68. Logic programming tools for metabolic fluxes analysis and biological applications
    Maxime Mahout · 2023 · theses.fr (ABES)
  69. Transcriptome-guided modeling reveals insulin-related metabolic dysfunction in SCA3 mouse cerebellum
    Shin‐Hung Pan, Jui‐Chih Chang, Wen-Ling Cheng, An‐Chi Wei, Chin‐San Liu · 2026 · Brain Research
  70. Analysis of Biochemical Pathway Perturbations with Network Propagation
    Niccolò De Paolis, Paolo Milazzo · 2026 · Communications in computer and information science
  71. Integrating genome-scale metabolic models into multi-scale simulations
    Marco Ruscone, Othmane Hayoun-Mya, Randy W. Heiland, Paul Macklin, Alfonso Valencia, Miguel Ponce-de-León · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  72. Antimony 3: Extending human-readable model definitions for SBML Level 3 Core and Packages
    Adel Heydarabadipour, Lucian P. Smith, Joseph L. Hellerstein, Herbert M. Sauro · 2026 · PLoS Computational Biology
  73. Computational modelling of brain energy metabolism and circulation in the neonatal animal model
    Tracy Moroz · 2014 · UCL Discovery (University College London)