Using the Unified Modelling Language (UML) to guide the systemic description of biological processes and systems

Roux-Rouquié, Magali; Caritey, Nicolas; Gaubert, Laurent; Rosenthal‐Sabroux, Camille

doi:10.1016/j.biosystems.2004.03.009

Cited by 21 publications

(15 citation statements)

References 13 publications

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“…Object-oriented programming (OOP) is attracting more modelers' attention and has been increasingly used in biomedical computational projects [56,57,78]. We applied OOP concepts to describe a complex biological system which encompasses biological components and processes from the molecular level to the tissue level.…”

Section: Discussionmentioning

confidence: 99%

“…Alternatively, the object-oriented modeling methodology provides a strategy to describe the biological organizations and flexible solution to integrate currently available models. For example, universal modeling language (UML) [56,57] and other meta-languages such as E-cell [58] have been proposed. However, the robustness of the integration of external models is dependent on the interface of these meta-languages.…”

Section: Introductionmentioning

confidence: 99%

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Module-based multiscale simulation of angiogenesis in skeletal muscle

Liu

Qutub

Vempati

et al. 2011

Theor Biol Med Model

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BackgroundMathematical modeling of angiogenesis has been gaining momentum as a means to shed new light on the biological complexity underlying blood vessel growth. A variety of computational models have been developed, each focusing on different aspects of the angiogenesis process and occurring at different biological scales, ranging from the molecular to the tissue levels. Integration of models at different scales is a challenging and currently unsolved problem.ResultsWe present an object-oriented module-based computational integration strategy to build a multiscale model of angiogenesis that links currently available models. As an example case, we use this approach to integrate modules representing microvascular blood flow, oxygen transport, vascular endothelial growth factor transport and endothelial cell behavior (sensing, migration and proliferation). Modeling methodologies in these modules include algebraic equations, partial differential equations and agent-based models with complex logical rules. We apply this integrated model to simulate exercise-induced angiogenesis in skeletal muscle. The simulation results compare capillary growth patterns between different exercise conditions for a single bout of exercise. Results demonstrate how the computational infrastructure can effectively integrate multiple modules by coordinating their connectivity and data exchange. Model parameterization offers simulation flexibility and a platform for performing sensitivity analysis.ConclusionsThis systems biology strategy can be applied to larger scale integration of computational models of angiogenesis in skeletal muscle, or other complex processes in other tissues under physiological and pathological conditions.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Module-based multiscale simulation of angiogenesis in skeletal muscle

Liu

Qutub

Vempati

et al. 2011

Theor Biol Med Model

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“…Kohn and coworkers [23,76], for example, have developed a formalization of diagrammatic interaction maps, which are commonly used ad hoc to describe the interactions of a system of proteins or the effects of protein interactions. Others have introduced tools of computer science, such as process algebra for representing con-current processes, in an attempt to develop a formal language of molecular biology [77][78][79]. Notably, graphs have been used to represent biological systems in the frameworks of rewriting logic [80,81] and process algebra [82,83].…”

Section: Discussionmentioning

confidence: 99%

Rule‐based modeling of biochemical networks

Faeder¹,

Blinov²,

Goldstein³

et al. 2005

Complexity

120

136

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We present a method for generating a biochemical reaction network from a description of the interactions of components of biomolecules. The interactions are specified in the form of reaction rules, each of which defines a class of reaction associated with a type of interaction. Reactants within a class have shared properties, which are specified in the rule defining the class. A rule also provides a rate law, which governs each reaction in a class, and a template for transforming reactants into products. A set of reaction rules can be applied to a seed set of

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“…Software engineering uses to deal with these issues putting the ideas in the UML world (or in domain specific modeling language) to perform model transformation, for example from UML statecharts to Picalculus [20]. In this perspective, we [21] and others [8] have shown that the dynamics of biological systems can be captured using statecharts.…”

Section: Capturing the System Dynamics (Linking Structure To Behavior)mentioning

confidence: 99%

“…Taking advantage of the UML language [21], work is in progress to delineate a profile for systems biology that will combine these two major requirements to achieve a process view of biological entities [22].…”

Section: Capturing the System Dynamics (Linking Structure To Behavior)mentioning

confidence: 99%

Ten top reasons for systems biology to get into model-driven engineering

Roux-Rouquié

Rosa

2006

Proceedings of the 2006 International Workshop on Global Integrated Model Management

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Recent progresses in post-genomic biology allow addressing issues at the system level through the coupling of experimental and modeling approaches that constitute the core of Systems Biology (SB). The challenge for researchers is to integrate disparate data into models to infer useful biological knowledge. Problems which are questioning Model-Driven Engineering (MDE) deal with complexity, systems modeling (including modularity and structure/behavior relationships), models networking and integration, domain-specific language, etc. Among these issues, ten arguments are presented to consider the conceptual convergence and cross-fertilization of SB with MDE. Current models in SB are reviewed and the main requirements to conduct models integration are identified. Some perspectives are provided towards the translation of high-level SB descriptions into formal languages for performing static and dynamic analyses.

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Using the Unified Modelling Language (UML) to guide the systemic description of biological processes and systems

Cited by 21 publications

References 13 publications

Module-based multiscale simulation of angiogenesis in skeletal muscle

Module-based multiscale simulation of angiogenesis in skeletal muscle

Rule‐based modeling of biochemical networks

Ten top reasons for systems biology to get into model-driven engineering

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