← Back to project catalogue
GP-BT-0YWYYI3BiotechnologyOpen for request

COBRApy metabolic flux simulator

A COBRApy constraint-based modelling study for analysing metabolic flux, nutrient conditions, flux variability, and gene-deletion scenarios in a public model organism.

  • COBRApy 0.32.1
  • Python
  • optlang
  • HiGHS
  • Docker

Software compatibility

COBRApy 0.32.1 only

The models and analysis scripts are delivered for a pinned COBRApy 0.32.1 environment. MATLAB COBRA Toolbox files and proprietary solver licences are not included.

Project definition

Problem statement

Flux-balance results depend on model quality, reaction direction, exchange bounds, medium, objective, and solver assumptions, and multiple flux distributions may produce the same objective value.

Project objectives

  • Import and validate a permitted public genome-scale or core metabolic model.
  • Define selected media and exchange conditions with clear units and bounds.
  • Run flux balance and flux variability analysis.
  • Compare selected nutrient, oxygen, objective, and gene-deletion scenarios.
  • Check mass balance, infeasibility, alternate optima, and biological plausibility.

System design

System modules

01

Model validator

Checks SBML import, metabolites, reactions, genes, compartments, bounds, and blocked reactions.

02

Medium manager

Defines exchange nutrients, uptake limits, oxygen state, and condition provenance.

03

Flux analyser

Runs FBA, parsimonious FBA, and FVA with saved objectives and solver settings.

04

Deletion module

Tests selected single-gene or reaction deletions and classifies growth effects.

05

Pathway viewer

Summarises objective, exchanges, key fluxes, ranges, shadow values, and condition differences.

Methodology

System workflow

  1. 01
    Validate model

    The public model is imported and structural and mass-balance checks are recorded.

  2. 02
    Reproduce reference

    A baseline medium and objective reproduce a documented growth result.

  3. 03
    Change conditions

    Nutrients, oxygen, and uptake limits are varied within the prepared scope.

  4. 04
    Analyse alternatives

    FVA identifies reactions with flexible and constrained flux.

  5. 05
    Screen deletions

    Selected gene or reaction deletions are compared with known or curated expectations.

Demonstration scenario

A public core metabolic model grows under aerobic glucose conditions. Oxygen and one nutrient are restricted, FVA reveals flexible pathways, and selected gene deletions identify essential and non-essential reactions under each medium.

Engineering

Technical architecture

Environment
Pinned COBRApy 0.32.1 with an open-source optlang-compatible solver.
Model format
Versioned SBML plus JSON exports and complete source provenance.
Optimisation
Linear flux balance, parsimonious objectives, variability ranges, and deletion workflows.
Verification
Mass-balance tests, reference growth, solver-status checks, and curated condition cases.

Testing

Evaluation

Evaluation measures

  • SBML import and model-structure validation
  • Mass-balanced reaction and blocked-reaction checks
  • Baseline objective agreement with the model reference
  • FVA range and alternate-optimum interpretation
  • Deletion classification agreement with prepared evidence
  • Runtime across reaction, condition, and deletion counts

System boundaries

  • Only the pinned COBRApy environment and public or explicitly permitted models are included.
  • Flux predictions are in-silico hypotheses and do not prove cellular behaviour.
  • The project does not design pathogens, virulence, toxins, or unsafe biological modifications.
  • Laboratory, clinical, industrial, or genetic decisions require qualified review and experimental validation.

Included

  1. 01Versioned public SBML metabolic model
  2. 02COBRApy FBA, FVA, medium, and deletion scripts
  3. 03Flux, growth, pathway, and sensitivity visualisations
  4. 04Prepared media conditions, checks, and simulation results
  5. 05Complete source code in a private GitHub repository
  6. 06Complete project documentation with synopsis, abstract, methodology, metabolic-network diagrams, simulation results, screenshots, and conclusion
  7. 07Setup and usage guide

Project record

No buyer information is collected on this page.

Permanent project ID
GP-BT-0YWYYI3
Catalogued
22 Aug 2026
Completed
Pending
Verified
Pending
Demonstration
Added when ready

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.