This repository provides metabolic models for the earthworm species Lumbricus rubellus and Lumbricus terrestris.

The models are generated from custom BioCyc Pathway/Genome Databases (PGDBs) built with PathwayTools v29.0. The repository contains the final SBML models as well as the complete workflow required to replicate their creation, from initial PGDB setup to final annotation and compartmentalization.

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Quick Access: Final Models & PGDBs

For users who want to use the completed models or databases directly:

• Final Models: The fully compartmentalized models are available in this repository:

  • L. rubellus: lumbricus_rubellus/metabolic_model/LRU1.sbml
  • L. terrestris: lumbricus_terrestris/metabolic_model/LRT1.sbml

• Pathway/Genome Databases (PGDBs): The earthworm PGDBs can be accessed through the following sources:

  • Web Portal: LumbriCyc
  • Download: Zenodo
  • PathwayTools: Via the PathwayTools Registry

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Installation

To replicate the model-building workflow, you must install the required dependencies:

1. PathwayTools: Install PathwayTools v29.0 as described on its homepage.
2. PythonCyc: Install PythonCyc.
3. Repository: Clone this repository.
4. Python Environment: Navigate into the cloned earthworm-models directory and install the necessary Python packages into your environment:

   pip install .
   

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Model Replication Workflow

This workflow describes the process of generating the final models from scratch.

Step 1: Create Pathway Tools PGDBs

• Notebook: create_biocyc_input.ipynb
• Action: This notebook generates the necessary input files for the PathoLogic component of PathwayTools.
• Note: This process cannot be fully automated and requires several manual user actions within PathwayTools. Experience with PathwayTools is highly recommended.

Step 2: Generate Initial SBML Models

• Tool: MetaFlux component of PathwayTools.
• Action: Use the MetaFlux component to create the initial metabolic models based on the provided FBA (Flux Balance Analysis) files:
  • lumbricus_rubellus/MetaFlux/SBML_export.fba
  • lumbricus_terrestris/MetaFlux/SBML_export.fba

Step 3: Get Metabolite Annotations from MetaNetX

• Notebook: get_MetaNetX_annotations.ipynb
• Action: This notebook must be executed to gather metabolite annotations from MetaNetX.

Step 4: Integrate Annotations

• Notebook: preprocess_MetaFlux_SBML.ipynb
• Action: This notebook integrates the metabolite annotations from Step 3 into the SBML models generated in Step 2.

Step 5: Final Compartmentalization

• Notebook: use_icel_compartments_for_metabolic_model.ipynb
• Action: This final notebook applies compartmentalization rules to the models, resulting in the fully compartmentalized LRU1.sbml and LRT1.sbml models.