JSBML: a flexible Java library for working with SBML

Dräger, Andreas; Rodríguez, Nicolás; Dumousseau, Marine; Dörr, Alexander; Wrzodek, Clemens; Novère, Nicolas Le; Zell, Andreas; Hucka, Michael

doi:10.1093/bioinformatics/btr361

Cited by 72 publications

(54 citation statements)

References 10 publications

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“…The latest specification document for SBML Qual can be found on the package homepage ( http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/Qualitative_Models_(qual)). Support for importing models stored in SBML Qual format is achieved using the jSBML library 16 and the respective SBML Qual package. Supplementary material 1 provides a step-by-step tutorial and an example on how to use the workflow.…”

Section: Resultsmentioning

confidence: 99%

Cyrface: An interface from Cytoscape to R that provides a user interface to R packages

Gonçalvès

Sáez-Rodríguez

2013

F1000Res

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There is an increasing number of software packages to analyse biological experimental data in the R environment. In particular, Bioconductor, a repository of curated R packages, is one of the most comprehensive resources for bioinformatics and biostatistics. The use of these packages is increasing, but it requires a basic understanding of the R language, as well as the syntax of the specific package used. The availability of user graphical interfaces for these packages would decrease the learning curve and broaden their application. Here, we present a Cytoscape plug-in termed Cyrface that allows Cytoscape plug-ins to connect to any function and package developed in R. Cyrface can be used to run R packages from within the Cytoscape environment making use of a graphical user interface. Moreover, it links the R packages with the capabilities of Cytoscape and its plug-ins, in particular network visualization and analysis. Cyrface’s utility has been demonstrated for two Bioconductor packages (CellNOptR and DrugVsDisease), and here we further illustrate its usage by implementing a workflow of data analysis and visualization. Download links, installation instructions and user guides can be accessed from the Cyrface homepage ( http://www.ebi.ac.uk/saezrodriguez/cyrface/).

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Section: Resultsmentioning

confidence: 99%

Cyrface: An interface from Cytoscape to R that provides a user interface to R packages

Gonçalvès

Sáez-Rodríguez

2013

F1000Res

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“…The simulation of a model is done with the SBSCL [5] and JSBML [27] is used as internal data structure for model representation. The SBSCL outputs the simulation results in a specific format, which enables SBMLsimulator to plot the time course of the model's species.…”

Section: Methodsmentioning

confidence: 99%

SBMLSimulator: A Java Tool for Model Simulation and Parameter Estimation in Systems Biology

et al. 2014

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Abstract:The identification of suitable model parameters for biochemical reactions has been recognized as a quite difficult endeavor. Parameter values from literature or experiments can often not directly be combined in complex reaction systems. Nature-inspired optimization techniques can find appropriate sets of parameters that calibrate a model to experimentally obtained time series data. We present SBMLsimulator, a tool that combines the Systems Biology Simulation Core Library for dynamic simulation of biochemical models with the heuristic optimization framework EvA2. SBMLsimulator provides an intuitive graphical user interface with various options as well as a fully-featured command-line interface for large-scale and script-based model simulation and calibration. In a parameter estimation study based on a published model and artificial data we demonstrate the capability of SBMLsimulator to identify parameters. SBMLsimulator is useful for both, the interactive simulation and exploration of the parameter space and for the large-scale model calibration and estimation of uncertain parameter values.

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“…ACR decider takes a reaction network as input and checks if its network structure alone is sufficient for the ACR property. In ACRE, we utilized two external Java packages: JSBML (Dr€ ager et al 2011) and JAMA (http://math.nist.gov/javanumerics/jama/).…”

Section: Software Designmentioning

confidence: 99%

ACRE: Absolute concentration robustness exploration in module-based combinatorial networks

et al. 2017

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CitationKuwahara H, Umarov R, Almasri I, Gao X (2017) AbstractTo engineer cells for industrial-scale application, a deep understanding of how to design molecular control mechanisms to tightly maintain functional stability under various fluctuations is crucial. Absolute concentration robustness (ACR) is a category of robustness in reaction network models in which the steady-state concentration of a molecular species is guaranteed to be invariant even with perturbations in the other molecular species in the network. Here, we introduce a software tool, absolute concentration robustness explorer (ACRE), which efficiently explores combinatorial biochemical networks for the ACR property. ACRE has a user-friendly interface, and it can facilitate efficient analysis of key structural features that guarantee the presence and the absence of the ACR property from combinatorial networks. Such analysis is expected to be useful in synthetic biology as it can increase our understanding of how to design molecular mechanisms to tightly control the concentration of molecular species. ACRE is freely available at https://github.com/ramzan1990/ACRE.

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JSBML: a flexible Java library for working with SBML

Cited by 72 publications

References 10 publications

Cyrface: An interface from Cytoscape to R that provides a user interface to R packages

Cyrface: An interface from Cytoscape to R that provides a user interface to R packages

SBMLSimulator: A Java Tool for Model Simulation and Parameter Estimation in Systems Biology

ACRE: Absolute concentration robustness exploration in module-based combinatorial networks

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