# LimbNET: collaborative platform for simulating spatial patterns of gene networks in limb development

## TL;DR

LimbNET is a web-based platform that allows researchers to model, simulate, and share gene regulatory networks involved in limb development using a user-friendly interface.

## Contribution

LimbNET introduces a collaborative, web-accessible platform for simulating and comparing gene regulatory networks in limb development with integrated image-based data.

## Key findings

- LimbNET enables users to define and simulate gene regulatory networks in a standardized computational framework.
- The platform integrates spatiotemporal gene expression data with simulations, enabling direct comparisons between data and models.
- LimbNET lowers the barrier for non-experts to engage in computational modelling of developmental processes.

## Abstract

Successful computational modelling of complex biological phenomena will depend on the seamless sharing of models and hypotheses between researchers of all backgrounds—experimental and theoretical. LimbNET, a new online tool for modelling, simulating and visualising spatiotemporal patterning in limb development, aims to facilitate this process within the limb development community. LimbNET enables remote users to define and simulate arbitrary gene regulatory network (GRN) models of 2D spatiotemporal developmental patterning processes. Researchers can test and compare each others’ hypotheses within a common framework. A database of previously created models empowers users to simulate, explore, and extend each others’ work. Spatiotemporally varying gene expression intensities, derived from image-based data, are mapped into a standardised computational description of limb growth, integrated within our modelling framework. This enables direct comparison not only between datasets but between data and simulation outputs, closing the feedback loop between experiments and simulation via parameter optimisation. All functionality is accessible through a web browser (https://limbnet.embl.es), requiring no special software, and opening the field of image-driven modelling to the full scientific community.

LimbNET is a new web application that provides a user-friendly GUI for biologists to share, compare and create hypotheses and dynamic simulations of the gene regulatory networks (GRNs) that control spatial patterning during limb development.

A web-based platform was developed for computational modelling of spatiotemporal patterning by gene regulatory networks, in growing limb buds, via an easy-to-use Graphical User Interface.Users can share ideas/hypotheses as computational models, directly integrated with the simulation tools to run them.By providing a straightforward interface for definition and simulation of models, the platform lowers the energy barrier for model development and streamline the modelling process, especially for non-experts.Models are integrated with image-based data in a common platform: an atlas of 2D spatiotemporal gene expression patterns and a repository of models/simulations.

A web-based platform was developed for computational modelling of spatiotemporal patterning by gene regulatory networks, in growing limb buds, via an easy-to-use Graphical User Interface.

Users can share ideas/hypotheses as computational models, directly integrated with the simulation tools to run them.

By providing a straightforward interface for definition and simulation of models, the platform lowers the energy barrier for model development and streamline the modelling process, especially for non-experts.

Models are integrated with image-based data in a common platform: an atlas of 2D spatiotemporal gene expression patterns and a repository of models/simulations.

LimbNET is a new web application that provides a user-friendly GUI for biologists to share, compare and create hypotheses and dynamic simulations of the gene regulatory networks (GRNs) that control spatial patterning during limb development.