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GP-BT-0YWYYI3BiotechnologyReady

COBRApy metabolic flux simulator

A COBRApy 0.31.1 biotechnology study of E. coli core metabolism, covering nutrient response, pathway flux, succinate production, flux variability, and gene essentiality.

COBRApy metabolic flux simulator project visual
GP-BT-0YWYYI3 · Biotechnology
  • COBRApy 0.31.1
  • Python 3.11
  • GLPK
  • NumPy
  • Pandas
  • Matplotlib

Software compatibility

COBRApy 0.31.1 only

The model, solver, scripts, and reference results use the pinned COBRApy 0.31.1 environment with GLPK. MATLAB COBRA Toolbox files and proprietary solver licences are not included.

Project definition

Problem statement

Microbial growth and product formation change with nutrient supply, oxygen, reaction constraints, and gene loss. One optimal growth value cannot show pathway flexibility, production limits, or condition-dependent gene importance.

Project objectives

  • Validate the public E. coli core model and its biological inventory.
  • Compare aerobic, microaerobic, and anaerobic growth across glucose levels.
  • Run pFBA and FVA to study reference pathway use and alternate feasible fluxes.
  • Measure the anaerobic trade-off between succinate production and growth.
  • Compare complete aerobic and anaerobic single-gene deletion screens.

Project structure

Project components

01

Model loader

Loads the versioned 95-reaction model, selects GLPK, and applies glucose and oxygen limits.

02

Growth analysis

Runs FBA and pFBA for the reference state, nine named conditions, and fifty nutrient combinations.

03

Flux variability

Calculates minimum and maximum flux for all 95 reactions at 90 percent of optimum growth.

04

Succinate study

Maximises anaerobic succinate at eleven increasing minimum-growth requirements.

05

Gene deletion

Screens all 137 genes under aerobic and anaerobic conditions and classifies the growth effect.

06

Verification

Checks model counts, balance, reference growth, biological trends, documents, evidence counts, and repository safety.

Methodology

Project workflow

  1. 01
    Load

    The same versioned JSON model is loaded for every analysis.

  2. 02
    Validate

    Reaction, metabolite, gene, formula, and internal mass-balance checks are completed.

  3. 03
    Simulate

    Growth, nutrient response, pFBA, FVA, succinate, and deletion studies run with saved solver status.

  4. 04
    Compare

    Processed tables and figures show nutrient, product, pathway, and genetic differences.

  5. 05
    Verify

    Six tests, the Docker smoke test, and repository validation check the completed delivery.

Demonstration scenario

The E. coli core model is solved under aerobic, microaerobic, and anaerobic glucose conditions. The study then maps flux flexibility, measures the growth and succinate frontier, and compares the effect of deleting every modelled gene under two oxygen states.

Engineering

Tools and method

Tools
The project uses COBRApy 0.31.1, Python 3.11, GLPK, NumPy, Pandas, Matplotlib for subject analysis, simulation, and results.
Environment
Pinned COBRApy 0.31.1, Python 3.11, GLPK, and numerical packages in a digest-pinned Docker image.
Model format
The public E. coli core model is included in JSON and SBML formats with source and licence records.
Optimisation
Linear FBA, parsimonious FBA, 90 percent FVA, product optimisation, and gene-protein-reaction deletion logic.
Evidence
Seven processed tables and 345 raw JSON records preserve every reference condition and deletion case.

Testing

Evaluation

Evaluation measures

  • Reference aerobic growth rate of 0.8326 per hour
  • Forty-nine optimal nutrient states and one retained infeasible low-glucose anaerobic state
  • Maximum anaerobic succinate flux of 13.9058 mmol/gDW/h
  • Maximum predicted succinate yield of 1.3906 mol/mol glucose
  • Five aerobic and three anaerobic essential-gene predictions
  • Thirty-four genes with a changed deletion class between oxygen conditions
  • FRD7 and SUCDi cycle limitation identified from 1000-unit FVA ranges

Project boundaries

  • Only the pinned COBRApy 0.31.1 model and generated result files are delivered.
  • The E. coli core model is a compact educational reconstruction and does not include regulation, kinetics, enzyme capacity, or strain variation.
  • All flux, growth, yield, and deletion values are computational predictions, not laboratory measurements.
  • Laboratory, clinical, manufacturing, genetic, or biosafety decisions require qualified review and experimental validation.

Included

  1. 01Versioned E. coli core model in JSON and SBML formats
  2. 02FBA, pFBA, FVA, nutrient response, succinate trade-off, and gene deletion analyses
  3. 0350 nutrient states and 274 paired gene deletion cases
  4. 04345 raw JSON evidence files with CSV, PNG, and SVG results
  5. 05Complete project files, models, calculations, and analysis material in a private GitHub repository
  6. 0680-page project documentation in PDF and editable Word formats
  7. 079-page setup and usage guide

Project record

No information is collected on this page.

Permanent project ID
GP-BT-0YWYYI3
Catalogued
22 Aug 2026
Completed
23 Aug 2026
Verified
23 Aug 2026
Demonstration
Included in repository

Handover

After purchase

  1. 01
    Payment is confirmed

    The project is marked unavailable and cannot be purchased again.

  2. 02
    Repository access is granted

    The buyer's submitted GitHub account receives access to the private repository.

  3. 03
    The purchase record is delivered

    The certification sheet is prepared from the reviewed buyer details and sent privately by email.