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Showing 1 to 5 of 5 for “"JigCell"”.
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JigCell Model Connector: Building Large Molecular Network Models from Components
… can seem nearly impossible. We present the JigCell Model Connector, a software tool that supports large-scale molecular network modeling. Our approach to developing large models is to combine together smaller models, making the result easier to comprehend. At the base, the smaller models …
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Extending Regulatory Network Modeling with Multistate Species
… In this work, we have extended JCMB (the JigCell Model Builder) to comply with multistate species and reactions modeling and presented a proposal for enhancing SBML (the Systems Biology Markup Language) standards to support multistate models.
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Bridging the Gap between Deterministic and Stochastic Modeling with Automatic Scaling and Conversion
… converting are introduced and implemented in the JigCell modeling environment. Our tool makes it easier for the modeler to include complete details as well as to convert the model. Stochastic simulations are known for being computationally intensive, and thus require high performance computing …
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Computational Software for Building Biochemical Reaction Network Models with Differential Equations
The cell is a highly ordered and intricate machine within which a wide variety of chemical processes take place. The full scientific understanding of cellular physiology requires accurate mathematical models that depict the temporal dynamics of these chemical processes. Modelers build mathematical …
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Model Composition and Aggregation in Macromolecular Regulatory Networks
Mathematical models of regulatory networks become more difficult to construct and understand as they grow in size and complexity. Large regulatory network models can be built up from smaller models, representing subsets of reactions within the larger network. This dissertation focuses on novel …