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

Jozef Spychala,Pawel Spychala,Gabriel E Weinreb,Shawn Gomez,Byung-Jun Yoon

doi:10.1371/journal.pone.0123773

Jozef Spychala, Pawel Spychala + Show 3 more

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https://doi.org/10.1371/journal.pone.0123773

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Journal: PloS one	Publication Date: May 28, 2015
Citations: 14	License type: CC BY 4.0

Affiliation: University of North Carolina at Chapel Hill

Abstract

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.

Highlights

One of the persistent challenges in today’s biomedical research is the development of easy to use modeling software tools for biological networks, which would be widely accessible for bench scientists
In this report we describe our attempt to create such a software tool based on a standardized approach using causal mapping (CMAP)
The core pathway consists of 2 initial branches of EGFR signaling, Grb2-PTP1B and Shc-Grb2-Sos1 (MAPK pathway)

Summary

Introduction

One of the persistent challenges in today’s biomedical research is the development of easy to use modeling software tools for biological networks, which would be widely accessible for bench scientists. There are a number of advanced software packages for pathway display, analysis and simulation, including: Cytoscape, Ingenuity, CellDesigner, KEGG, SymBiology in Matlab, just to name a few. These tools are primarily used by trained modelers and are not suited for biologists who do not have rigorous training in mathematics and computation, leaving the most numerous group of scientists without adequate computational biology tools to aid their bench work. Many of these tools lack features that would enable interactive.

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