Skip to content

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.

License

Notifications You must be signed in to change notification settings

pitt-miskov-zivanov-lab/FIDDLE

Repository files navigation

FIDDLE

Documentation Status Binder

(Finding Interactions using Diagram Driven modeL Extension)

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.

Contents

Installation

  1. Clone the FIDDLE repository to your computer.
    git clone https://github.com/pitt-miskov-zivanov-lab/FIDDLE.git
    
  2. Navigate into the directory, create a pythonvirtual environment, and install FIDDLE dependencies.
    cd FIDDLE
    python -m venv env
    pip install -e .
    
  3. Activate the python virtual environment.
    source env/bin/activate
    

Tutorial

See use_FIDDLE.ipynb, it is also available on Binder

This interactive jupyter notebook walks you though all of the pertinent code and functions to:

  1. Create a new Erdos-Renyi or Barabasi-Alberts Network.
  2. Remove edges from these networks in a consistent and systematic way.
  3. Extend a network with missing edges using the Breadth First Addition method (BFA).
  4. Extend a network with missing edges using the Depth First Addition method (BFA).

Citation

Using FIDDLE:

Butchy, Adam A., Cheryl A. Telmer, Natasa Miskov-Zivanov. "Automating Knowledge-Driven Model Recommendation: Methodology, Evaluation, and Key Challenges." arXiv preprint arXiv:2301.11397 (2023).

Using the DISH simulator:

Sayed K, Kuo Y-H, Kulkarni A, Miskov-Zivanov N. Dish simulator: capturing dynamics of cellular signaling with heterogeneous knowledge. Proceedings of the 2017 Winter Simulation Conference; Las Vegas, Nevada. 3242250: IEEE Press; 2017. p. 1-12.

Funding

This work was funded in part by DARPA Big Mechanism award, AIMCancer (W911NF-17-1-0135); and in part by the University of Pittsburgh, Swanson School of Engineering.

About

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.

Topics

Resources

License

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published

Languages