LibSBML: an API Library for SBML

By B. Bornstein, Sarah M. Keating, Akiya Jouraku, Michael Hucka. Bioinform., 2008

419 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/0c5318ad67194db7a8bdb734aa92340f439a0a05

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Citations in the corpus

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0 (2007, neutral): “Importing the models into MATLAB is dependent on libSBM”
COBRApy: COnstraints-Based Reconstruction and Analysis for Python (2013, methodology): “Project name: COBRApy version 0.2.1 Project home page: http://opencobra.sourceforge.net Operating systems: Platform independent, including Java Programming language: Python ( ≥ 2.6) / Jython ( ≥ 2.5) Other requirements: Python : libSBML ≥ 5.5.0 [32].”
Fast automated reconstruction of genome-scale metabolic models for microbial species and communities (2018, methodology): “It requires the framed python package (version 0.4) for metabolic modeling, which provides an interface to common solvers (Gurobi, CPLEX), and import / export of SBML files through the libSBML API (46).”
BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models (2010, methodology): “Further consistency checks are performed on the model using libSBML [42] and SBMLeditor [43].”
A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology (2008, methodology): “The SBML has been checked using libSBML 53,54 (see also http://sbml.org/software/libsbml/).”
The Reactome pathway knowledgebase (2013, positive): “Reactome is open-source and open-data, and we have continuously supported the major open-data standards in the domain, including BioPAX levels 2 and 3 (24), PSI MITAB (18), Protégé (http://protege.stanford.edu), SBML-ML (25) and SBGN export format.”
Controlled vocabularies and semantics in systems biology (2011, methodology): “Use of SBO terms in SBML is supported by the software libraries libSBML (Bornstein et al , 2008) and JSBML (Dra¨ger et al , 2011), which provide methods to check for instance whether a term is a subelement of another term, whether a term ﬁts to a certain model component, or to query model elements…”
RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor (2018, methodology): “Various file formats are supported for import and export of models, including Microsoft Excel through Apache POI (The Apache Software Foundation, Wakefield, Massachusetts), the community standard SBML Level 3 Version 1 FBC Package Version 2 through libSBML [46] and YAML for easy tracking of differen”
Lessons Learned from Quantitative Dynamical Modeling in Systems Biology (2013, methodology): “The novel format is compliant with the SBML standard [34], i.”