Open AccessConstruction, visualization, and analysis of biological network models in Dynetica
Author(s) -
Eidum Derek,
Asthana Kanishk,
Unni Samir,
Deng Michael,
You Lingchong
Publication year - 2015
Publication title -
quantitative biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.707
H-Index - 15
eISSN - 2095-4697
pISSN - 2095-4689
DOI - 10.1007/s40484-014-0036-4
Subject(s) - sbml , computer science , modular design , debugging , visualization , graphical user interface , programming language , theoretical computer science , biological network , java , matlab , process (computing) , markup language , distributed computing , data mining , xml , bioinformatics , biology , operating system
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.