Visinets

In this report we describe a novel graphically oriented method for pathway
modeling and a software package that allows for both modeling and visualization
of biological networks in a user-friendly format. The Visinets mathematical
approach is based on causal mapping (CMAP) that has been fully integrated with
graphical interface. Such integration allows for fully graphical and interactive
process of modeling, from building the network to simulation of the finished
model. To test the performance of Visinets software we have applied it to: a)
create executable EGFR-MAPK pathway model using an intuitive graphical way of
modeling based on biological data, and b) translate existing ordinary
differential equation (ODE) based insulin signaling model into CMAP formalism and
compare the results. Our testing fully confirmed the potential of the CMAP method
for broad application for pathway modeling and visualization and, additionally,
showed significant advantage in computational efficiency. Furthermore, we showed
that Visinets web-based graphical platform, along with standardized method of
pathway analysis, may offer a novel and attractive alternative for dynamic
simulation in real time for broader use in biomedical research. Since Visinets
uses graphical elements with mathematical formulas hidden from the users, we
believe that this tool may be particularly suited for those who are new to
pathway modeling and without the in-depth modeling skills often required when
using other software packages.

Visinets: a web-based pathway modeling and dynamic visualization tool.

Visinets is a software tool to model and visualize biological networks and pathways graphically. The Visinets algorithm uses causal mapping (CMAP).

Visinets

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