A Transformation Tool for ODE Based Models

Barbosa, C. B.; Santos, Rodrigo Weber dos; Amorim, Ronan; Ciuffo, Leandro; Manfroi, Fairus; Oliveira, Rafael Sachetto; Campos, Fernanda

doi:10.1007/11758501_14

Cited by 14 publications

(14 citation statements)

References 2 publications

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“…These modifications were performed on the Web via a CellML editor which is one of the applications of a Web-based computational framework that provides support for cardiac electrophysiology modeling [7,8]. In addition, all simulations and the visualization of results were performed on the web with the support of our computational framework.…”

Section: Methodsmentioning

confidence: 99%

“…Due to the multi-scale and multi-physics nature of these biological models, their development becomes particularly challenging, not only from a biological or biophysical viewpoint, but also from a mathematical and computational perspective. A Web-based computational framework that provides support for cardiac electrophysiology modeling is under development [7,8]. Such framework integrates different tools and allows one to bypass many complex steps during the development and use of cardiac models that are based on systems of ordinary differential equations.…”

Section: Introductionmentioning

confidence: 99%

“…Such framework integrates different tools and allows one to bypass many complex steps during the development and use of cardiac models that are based on systems of ordinary differential equations. The implementation of cardiac cell models is supported by a code generator named AGOS [7] that generates C++ code by translating models described in the CellML language [9], a recently emerged international open standard for the description of biological models. The generated code allows one to manipulate and solve the mathematical models numerically.…”

Section: Introductionmentioning

confidence: 99%

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Web Applications Supporting the Development of Models of Chagas’ Disease for Left Ventricular Myocytes of Adult Rats

Costa

Campos

et al. 2008

Computational Science – ICCS 2008

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Abstract. Chagas' Disease is an endemic infection in many areas of South and Central America that may cause a fatal type of myocarditis. In the acute phase of the disease, ventricular extrasystoles and tachycardia have been reported. Experiments with cardiac myocytes in the acute stage of Chagas' Disease have suggested a depression of Ito, the Ca 2+ -independent K + Transient Outward current. In this work we use computational models of left ventricular myocytes of adult rats to qualify the effects of Ito reduction that appear during the acute phase of Chagas' Disease. The simulations are carried out by Web applications based on the CellML language, a recently emerged international standard for the description of biological models. The computational framework supports the development of mathematical models, simulations and visualization of the results. Our preliminary simulation results suggest that the reduction of Ito density elicits modifications of electrophysiological mechanisms that are strongly related to the phenomena of arrhythmia.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Web Applications Supporting the Development of Models of Chagas’ Disease for Left Ventricular Myocytes of Adult Rats

Costa

Campos

et al. 2008

Computational Science – ICCS 2008

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“…If a new structure or even a new language in the output is needed, all that is required is to modify the last step, i.e. the grammar and/or the template (Barbosa et al 2006). …”

Section: (D ) Code Generatorsmentioning

confidence: 99%

CellML and associated tools and techniques

Garny

Nickerson

Cooper

et al. 2008

Phil. Trans. R. Soc. A.

127

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We have, in the last few years, witnessed the development and availability of an ever increasing number of computer models that describe complex biological structures and processes. The multi-scale and multi-physics nature of these models makes their development particularly challenging, not only from a biological or biophysical viewpoint but also from a mathematical and computational perspective. In addition, the issue of sharing and reusing such models has proved to be particularly problematic, with the published models often lacking information that is required to accurately reproduce the published results.The International Union of Physiological Sciences Physiome Project was launched in 1997 with the aim of tackling the aforementioned issues by providing a framework for the modelling of the human body. As part of this initiative, the specifications of the CellML mark-up language were released in 2001. Now, more than 7 years later, the time has come to assess the situation, in particular with regard to the tools and techniques that are now available to the modelling community. Thus, after introducing CellML, we review and discuss existing editors, validators, online repository, code generators and simulation environments, as well as the CellML Application Program Interface. We also address possible future directions including the need for additional mark-up languages.

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“…The use of the semantic to express the intrinsic model knowledge aims to improve its validation, reuse other models components, automate the processes of models composition and construct Web repositories with semantic queries. The structure of the ontology aims its integration with simulations of CellML models, using tools as AGOS [8] and PCEnv [9].…”

Section: Cell Component Ontology -Celomentioning

confidence: 99%

CelOWS: A Service Oriented Architecture to Define, Query and Reuse Biological Models

Matos¹,

Campos

Braga

et al. 2009

Lecture Notes in Computer Science

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Abstract. The amount of information generated by biological research has lead to an intensive use of models. Mathematical and computational modeling needs accurate description to share, reuse and simulate models as formulated by original authors. In this paper, we introduce the Cell Component Ontology -CelO, expressed in OWL-DL. This ontology captures both the structure of a cell model and the properties of functional components. We use this ontology in a Web project -CelOWS -to describe, query and compose CellML models. It aims to improve reuse and composition of existent components and allow semantic validation of new models.

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A Transformation Tool for ODE Based Models

Cited by 14 publications

References 2 publications

Web Applications Supporting the Development of Models of Chagas’ Disease for Left Ventricular Myocytes of Adult Rats

Web Applications Supporting the Development of Models of Chagas’ Disease for Left Ventricular Myocytes of Adult Rats

CellML and associated tools and techniques

CelOWS: A Service Oriented Architecture to Define, Query and Reuse Biological Models

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