VIOLIN (Validating Interactions Of Likely Importance to the Network) is a tool used to automatically classify and judge literature-extracted interactions curated from machine readers by comparing them to existing models. This comparison can help identify key interactions for model extension.

The BioRECIPE (Biological system Representation for Evaluation, Curation, Interoperability, Preserving, and Execution) representation format is introduced to facilitate seamless human-machine interaction when creating, verifying, evaluating, curating, and expanding executable models of intra- and intercellular signaling.

FIDDLE (Finding Interactions using Diagram Driven modeL Extension) is a tool to automatically assemble or extend models with the knowledge extracted from published literature. The two main methods developed as part of FIDDLE are called Breadth First Addition (BFA) and Depth First Addition (DFA), and they are based on network search algorithms.

FLUTE (The FiLter for Understanding True Events) - A tool for identifying high-confidence machine reading interactions through comparison to publicly available interaction databases.

CLARINET (CLARIfying NETworks) is a tool that equips modelers with a fast and reliable assistant to select the most relevant knowledge about the systems being modeled using graph-based approaches and literature occurrence metadata.

ACCORDION (ACCelerating and Optimizing model RecommenDatIONs) is a novel tool and methodology for rapid model assembly by automatically extending and evaluating dynamic network models with the information published in literature.

A placeholder repo to host the summary page of all tools' readthedocs, the readthedocs page of each tools will be a subproject to this repo. melodylab.readthedocs.io is registered.

The Dynamic System Explanation (DySE) Framework contains tools for building, simulating, and verifying qualitative models, built by the Mechanisms and Logic of Dynamics (MeLoDy) Lab at the University of Pittsburgh.