PlantSimLab - a modeling and simulation web tool for plant biologists

S Ha,D Altarawy,J Glazebrook,B M Tyler,R Laubenbacher,S Hoops,D Deb,F Katagiri,M Megraw,J Mcdowell,H Shahin,J Setubal,M Ansariola,R Hillmer,E Dimitrova

doi:10.1186/s12859-019-3094-9

Abstract

BackgroundAt the molecular level, nonlinear networks of heterogeneous molecules control many biological processes, so that systems biology provides a valuable approach in this field, building on the integration of experimental biology with mathematical modeling. One of the biggest challenges to making this integration a reality is that many life scientists do not possess the mathematical expertise needed to build and manipulate mathematical models well enough to use them as tools for hypothesis generation. Available modeling software packages often assume some modeling expertise. There is a need for software tools that are easy to use and intuitive for experimentalists.ResultsThis paper introduces PlantSimLab, a web-based application developed to allow plant biologists to construct dynamic mathematical models of molecular networks, interrogate them in a manner similar to what is done in the laboratory, and use them as a tool for biological hypothesis generation. It is designed to be used by experimentalists, without direct assistance from mathematical modelers.ConclusionsMathematical modeling techniques are a useful tool for analyzing complex biological systems, and there is a need for accessible, efficient analysis tools within the biological community. PlantSimLab enables users to build, validate, and use intuitive qualitative dynamic computer models, with a graphical user interface that does not require mathematical modeling expertise. It makes analysis of complex models accessible to a larger community, as it is platform-independent and does not require extensive mathematical expertise.

Highlights

At the molecular level, nonlinear networks of heterogeneous molecules control many biological processes, so that systems biology provides a valuable approach in this field, building on the integration of experimental biology with mathematical modeling
The magnitudes of the node states in the attractor are presented by their numerical values as well as in a heat-map-style color scheme to enable a quick grasp of the information about the attractor
Software components We developed PlantSimLab as a client-server-based web application running on Apache2 on a dedicated server and supporting most modern web browsers on any platform

Summary

Introduction

Nonlinear networks of heterogeneous molecules control many biological processes, so that systems biology provides a valuable approach in this field, building on the integration of experimental biology with mathematical modeling. If the interest is in studying dynamic effects, one needs to build and analyze dynamic computer models of networks In both cases, two approaches are used: the so-called “bottom-up” approach, which builds a model of the network from available information about its components, and the “top-down” approach, which extracts network links from experimental, typically highdimensional, data. The goal is to provide biologists with an usable, virtual laboratory tool to integrate available information and data for the purpose of hypothesis generation. These constraints require a mathematically simple way of constructing models and interpreting model output, making modeling frameworks such as differential equations less well-suited. They have been used successfully to capture a wide range of molecular networks in recent years; see, e.g., [3,4,5,6]

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