Welcome to FIDDLE’s documentation!

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.

FIDDLE architecture

Contents

• Installation
  • To install this package via Github
  • To install this package via DockerHub
• Tutorial
  • Available on Binder
• FIDDLE Functions
  • BFA()
  • DFA()
  • add_direction_to_undirected_network()
  • add_regulation_to_directed_network()
  • create_extendable_models()
  • create_initial_values()
  • create_initial_values_random()
  • do_the_sub_stuff()
  • extend_model_file()
  • extend_unit_breadth_sing()
  • extension_network_to_excel()
  • find_element_locations()
  • get_model_edges()
  • get_model_expected_values()
  • get_score_between_expected_and_actual()
  • get_simulation_end_values()
  • graph_maker()
  • network_to_excel()
  • parallelize_get_diff()
  • plot_network()
  • recursive_addition_for_DFA()
  • return_extension_stats()
  • return_model_stats()
  • score_actual_against_expected_values()
  • sim_and_get_diff()
  • simulate_network()
  • update_network_file()
• License
• Funding
• Citation