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This approach is more complex to use and larger ODE models (above 130 nodes) are more difficult to build and manage, and may also require dedicated computational facilities. Others employ Ordinary Differential Equations (ODE) as their mathematical method of modeling.
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Many of these tools also lack features that would enable interactive and dynamic ways for pathway visualization and simulation. These tools are primarily used by trained modelers and are not suited for biologists who do not have rigorous training in mathematics and computation, thus leaving the most numerous group of scientists without adequate computational biology tools to aid their bench work.
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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. 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. This does not alter the authors' adherence to all PLOS ONE policies on sharing data and materials. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Ĭompeting interests: JS, GEW, and PS are employees of Visinets, Inc., and received salary from them.
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The code for CMAP modeling engine has been deposited for free use at: under open source MIT license.įunding: Visinets, Inc., provided support in the form of salaries for this study.
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This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are creditedĭata Availability: Software availability: Visinets software is freely available as an online resource at with full user documentation and a list of executable signaling pathways with datasets, including those described in this report ( ). Received: AugAccepted: FebruPublished: May 28, 2015Ĭopyright: © 2015 Spychala et al. PLoS ONE 10(5):Īcademic Editor: Byung-Jun Yoon, Texas A&M University, UNITED STATES 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.Ĭitation: Spychala J, Spychala P, Gomez S, Weinreb GE (2015) Visinets: A Web-Based Pathway Modeling and Dynamic Visualization Tool. 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. 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. 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. Such integration allows for fully graphical and interactive process of modeling, from building the network to simulation of the finished model. The Visinets mathematical approach is based on causal mapping (CMAP) that has been fully integrated with graphical interface. 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.