MoCha is a software tool for finding unknown proteins and their pathways interacting with a given set of proteins. Due to its highly optimized pre-processing, MoCha can search within seconds through more than a billion interactions from over 2,000 organisms in the STRING database. This tool is useful for working on network models by hand or as an integrated software pipeline and can readily aid in the reverse-engineering of regulatory models.
Planform is a database and user-friendly application for the design, storage, and search of formally-encoded planarian regenerative experiments, manipulations, and morphologies. It contains more than 1,000 different experiments curated from the literature and provides a graphical user interface that allows any scientist to query, extend, and search in this large dataset.
Limbform is a database and software tool that centralizes with a mathematical ontology the details of more than 800 experiments of limb regeneration curated from the literature and comprising many model organisms, including salamanders, frogs, insects, crustaceans and arachnids. The user-friendly software tool can be used for mining the curated experiments, as well as for formalizing new ones.
We have created a computational method that can reverse-engineer dynamic regulatory networks directly from experimental results. A software application is available to visualize and interact with the discovered models of planarian regeneration. You can download the application and simulate planarian regeneration experiments with the inferred models in your own computer.