Construction, visualization, and analysis of biological network models in Dynetica

Abstract

Mathematical modeling has become an increasingly important aspect of biological research. Computer simulations help to improve our understanding of complex systems by testing the validity of proposed mechanisms and generating experimentally testable hypotheses. However, significant overhead is generated by the creation, debugging, and perturbation of these computational models and their parameters, especially for researchers who are unfamiliar with programming or numerical methods. Dynetica 2.0 is a user-friendly dynamic network simulator designed to expedite this process. Models are created and visualized in an easy-to-use graphical interface, which displays all of the species and reactions involved in a graph layout. System inputs and outputs, indicators, and intermediate expressions may be incorporated into the model via the versatile “expression variable” entity. Models can also be modular, allowing for the quick construction of complex systems from simpler components. Dynetica 2.0 supports a number of deterministic and stochastic algorithms for performing time-course simulations. Additionally, Dynetica 2.0 provides built-in tools for performing sensitivity or dose response analysis for a number of different metrics. Its parameter searching tools can optimize specific objectives of the time course or dose response of the system. Systems can be translated from Dynetica 2.0 into MATLAB code or the Systems Biology Markup Language (SBML) format for further analysis or publication. Finally, since it is written in Java, Dynetica 2.0 is platform independent, allowing for easy sharing and collaboration between researchers.

Graphical abstract

Keywords

mathematical modeling / systems biology / synthetic biology / quantitative biology / gene circuits

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SUPPLEMENTARY MATERIALS

The supplementary materials can be found with this article at DOI 10.1007/s40484-014-0036-4.

ACKNOWLEDGMENTS

The work is partially funded by the National Institutes of Health, the National Science Foundation, the Army Research Office, and the David and Lucile Packard Foundation. DE acknowledges the support for a Pratt Fellowship.

COMPLIANCE WITH ETHICS GUIDELINES

The authors Derek Eidum, Kanishk Asthana, Samir Unni, Michael Deng and Lingchong You declare that they have no conflict of interests.

This article does not contain any studies with human or animal subjects performed by any of the authors.

RIGHTS & PERMISSIONS

2014 Higher Education Press and Springer-Verlag Berlin Heidelberg