Pitt - Miskov-Zivanov Lab
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BioRECIPE
PublicThe 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.CELESTA
PublicVIOLIN
PublicVIOLIN (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.FIDDLE
PublicFIDDLE (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.DiSH
PublicFLUTE
PublicFLUTE (The FiLter for Understanding True Events) - A tool for identifying high-confidence machine reading interactions through comparison to publicly available interaction databases.CLARINET
PublicCLARINET (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
PublicACCORDION (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.TernaryBody
Publicmelodylab
Publicdyse_wm
Public