Welcome to coralME documentation!

Description

The COmprehensive Reconstruction ALgorithm for ME-models (coralME) is an automatic pipeline for the reconstruction of ME-models. coralME integrates existing ME-modeling packages COBRAme, ECOLIme, and solveME, generalizes their functions for implementation on any prokaryote, and processes readily available organism-specific inputs for the automatic generation of a working ME-model.

coralME has four main objectives:

1. Synchronize input files to remove contradictory entries.

2. Complement input files from homology with a template organism to complete the E-matrix.

3. Build a working ME-model

4. Inform the user about necessary steps to curate the ME-model.

This resource is intended to:

1. Describe basic inputs required for ME-model reconstruction.

2. Describe the architecture of coralME.

3. Demonstrate how to build a ME-model with coralME.

4. Describe how to perform manual curation guided by coralME’s curation notes.

Content

• 1. Getting started
  • 1.1. Reconstruct with coralME
  • 1.2. Understanding the file structure
  • 1.3. Curate manually
• 2. Description of Inputs
  • 2.1. Types of inputs
  • 2.2. Description
• 3. Adding annotation from a BioCyc Database
  • 3.1. Download files from BioCyc
  • 3.2. Initialize the folder for your organism
• 4. Architecture of coralME
  • 4.1. Organism()
  • 4.2. MEBuilder()
  • 4.3. MEReconstruction()
  • 4.4. Homology()
  • 4.5. Curation()
• 5. Reconstructing with BioCyc information and curated files
  • 5.1. Import libraries
  • 5.2. Path to configuration files
  • 5.3. Create MEBuilder instance
  • 5.4. Generate files
  • 5.5. Build ME-model
  • 5.6. Troubleshoot ME-model
  • 5.7. Save as a JSON
• 6. Reconstructing a ME-model from the OSM
  • 6.1. Import libraries
  • 6.2. Path to configuration files
  • 6.3. Create MEBuilder instance
  • 6.4. Build ME-model
  • 6.5. Troubleshoot ME-model
• 7. Loading and inspecting ME-models
  • 7.1. Import libraries
  • 7.2. Load as a JSON
  • 7.3. Load as a pickle
  • 7.4. Inspecting ME-model properties
• 8. Inspecting predicted fluxes
  • 8.1. Import libraries
  • 8.2. Load
  • 8.3. Solve
  • 8.4. Inspecting fluxes
  • 8.5. Biomass profile
• 9. Memory- and time-efficient solving of ME-models
  • 9.1. Import libraries
  • 9.2. Load
  • 9.3. Convert to NLP problem
  • 9.4. Retrieve metabolite and reaction indexes
  • 9.5. Solving the MEModel vs. NLP
  • 9.6. Re-using the basis for even more speed-up
  • 9.7. Modifying the NLP
  • 9.8. Modifying the NLP from a dictionary of new bounds
  • 9.9. Inspecting the solution
• 10. Frequently Asked Questions
  • 10.1. My gene identifiers are not consistent, what should I do?

Indices and tables

• Index

• Module Index

• Search Page