Abstract
BackgroundSoftware tools that model and simulate the dynamics of biological processes and systems are becoming increasingly important. Some of these tools offer sophisticated graphical user interfaces (GUIs), which greatly enhance their acceptance by users. Such GUIs are based on symbolic or graphical notations used to describe, interact and communicate the developed models. Typically, these graphical notations are geared towards conventional biochemical pathway diagrams. They permit the user to represent the transport and transformation of chemical species and to define inhibitory and stimulatory dependencies. A critical weakness of existing tools is their lack of supporting an integrative representation of transport, transformation as well as biological information processing.ResultsNarrator is a software tool facilitating the development and simulation of biological systems as Co-dependence models. The Co-dependence Methodology complements the representation of species transport and transformation together with an explicit mechanism to express biological information processing. Thus, Co-dependence models explicitly capture, for instance, signal processing structures and the influence of exogenous factors or events affecting certain parts of a biological system or process. This combined set of features provides the system biologist with a powerful tool to describe and explore the dynamics of life phenomena. Narrator's GUI is based on an expressive graphical notation which forms an integral part of the Co-dependence Methodology. Behind the user-friendly GUI, Narrator hides a flexible feature which makes it relatively easy to map models defined via the graphical notation to mathematical formalisms and languages such as ordinary differential equations, the Systems Biology Markup Language or Gillespie's direct method. This powerful feature facilitates reuse, interoperability and conceptual model development.ConclusionNarrator is a flexible and intuitive systems biology tool. It is specifically intended for users aiming to construct and simulate dynamic models of biology without recourse to extensive mathematical detail. Its design facilitates mappings to different formal languages and frameworks. The combined set of features makes Narrator unique among tools of its kind. Narrator is implemented as Java software program and available as open-source from .
Highlights
Software tools that model and simulate the dynamics of biological processes and systems are becoming increasingly important
The Systems Biology Markup Language (SBML) Web site [1] lists more than 100 such tools, all of which adhere to the SBML standard, facilitating the exchange of biochemical reaction network models
To evaluate Narrator, we described and simulated a model of the protein kinase C (PKC) pathway taken from Pettinen et al [26] which used this pathway model as a test case for comparing and evaluating different simulation tools for biochemical networks
Summary
Software tools that model and simulate the dynamics of biological processes and systems are becoming increasingly important Some of these tools offer sophisticated graphical user interfaces (GUIs), which greatly enhance their acceptance by users. Such GUIs are based on symbolic or graphical notations used to describe, interact and communicate the developed models. These graphical notations are geared towards conventional biochemical pathway diagrams. Several excellent tools have been developed for modeling and simulating biochemical networks, some of which provide sophisticated, GUI-based design tools for visual model development Most of these tools are freely available as software packages or as online tools. Examples include Copasi [34], Virtual Cell [9], JDesigner [10], CellWare [12] and CellDesigner [11,33], which are well developed and widely used in the systems biology community
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
