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GP-BT-0TTUU9QBiotechnologyReady

Data-Calibrated Microbial Cross-Feeding and Coexistence Robustness Study

A completed biotechnology study of four-species microbial persistence, carbon-source niches, spent-medium effects, chemostat occupancy, and consumer-resource model robustness.

Data-Calibrated Microbial Cross-Feeding and Coexistence Robustness Study project visual
GP-BT-0TTUU9Q · Biotechnology
  • Python 3.12
  • NumPy
  • Pandas
  • SciPy
  • NetworkX
  • Matplotlib

Project definition

Problem statement

A microbial community can persist even when individual members cannot use every supplied carbon source, but persistence alone does not identify the exchanges or conditions that support coexistence.

The biotechnology problem is to combine released phenotype, community, spent-medium, and chemostat evidence with a transparent consumer-resource model while keeping measured observations separate from model scenarios.

Project objectives

  • Validate and retain the seven released source tables with exact checksums.
  • Measure carbon-source breadth and identify direct-growth gaps across four organisms.
  • Summarise community persistence, diversity, culturable abundance, and chemostat occupancy.
  • Classify significant positive and negative spent-medium effects without assigning unmeasured metabolites.
  • Build a declared consumer-resource model and test leakage, dilution, member dropout, and parameter uncertainty.
  • Retain complete tables, figures, tests, references, documents, and scientific claim boundaries.

Project structure

Project components

01

Evidence validation

Checks retained file hashes, schemas, condition counts, species labels, and reproducible summaries.

02

Phenotype and assembly analysis

Measures resource breadth, fitted growth-rate patterns, four-member persistence, diversity, and culturable abundance.

03

Interaction analysis

Classifies adjusted-significant spent-medium effects and builds a directed evidence network without naming unmeasured compounds.

04

Consumer-resource model

Simulates Monod uptake, maintenance, dilution, leakage, secretion, biomass, and secondary-resource dynamics.

05

Robustness experiments

Runs leakage and dilution sweeps, four member-dropout scenarios, and 160 seeded parameter draws.

06

Evidence and verification

Retains source checksums, fourteen result tables, sixteen figures, tests, references, documents, and a Docker gate.

Methodology

Project workflow

  1. 01
    Verify public evidence

    Confirm the seven retained tables and reproduce phenotype, assembly, interaction, and chemostat summaries.

  2. 02
    Construct the model

    Load the declared four-species parameterisation and initialise biomass and resource states.

  3. 03
    Run the baseline

    Integrate the deterministic model and compare final richness with the retained coexistence evidence.

  4. 04
    Test robustness

    Vary leakage and dilution, remove each member, and perturb uptake, leakage, and dilution under a fixed seed.

  5. 05
    Interpret the study

    Use the retained evidence and scenario results while preserving the biological validation boundary.

Demonstration scenario

All four organisms remain detected across all sixty-four retained assembly conditions and all four final chemostat observations. The baseline model also retains four members with total biomass 5.5985 model units, while the dilution sweep, member removal, and parameter uncertainty show that coexistence is conditional rather than guaranteed.

Engineering

Tools and method

Tools
The project uses Python 3.12, NumPy, Pandas, SciPy, NetworkX, Matplotlib for subject analysis, simulation, and results.
Data preparation
Pandas validates and summarises the retained public CSV evidence.
Dynamic model
SciPy integrates a declared consumer-resource system with Monod uptake, maintenance, washout, leakage, and secretion.
Network analysis
NetworkX represents adjusted-significant directed spent-medium evidence.
Scenario experiments
NumPy and deterministic seeds support parameter sweeps, dropout experiments, and uncertainty samples.
Evidence
CSV, JSON, PNG, PDF, and Word files preserve source identity, calculations, figures, interpretation, and report content.
Verification
Tests, linting, dependency audits, checksums, accessibility checks, repository validation, and non-root Docker execution verify the handover.

Testing

Evaluation

Evaluation measures

  • Carbon-source growth breadth across thirty-three tested conditions
  • Four-member detection across sixty-four assembly conditions and four chemostats
  • Positive and negative adjusted-significant spent-medium effects
  • Baseline richness, final composition, and resource trajectories
  • Richness and total biomass across leakage and dilution scenarios
  • Member-dropout response and richness under 160 uncertainty draws
  • Automated tests, dependency audit, document checks, and non-root Docker execution

Project boundaries

  • The project is a secondary analysis of released public data and does not claim original wet-lab experimentation.
  • Spent-medium responses do not identify the exchanged molecules or prove a universal interaction sign.
  • The secretion tensor and several model parameters are declared scenario assumptions rather than fitted biochemical measurements.
  • The results do not establish application safety, industrial performance, environmental behavior, or clinical relevance.
  • Stronger validation requires metabolomics, isotope tracing, replicated leave-one-out communities, and application-specific experiments.

Included

  1. 01Complete microbial cross-feeding analysis and modelling source code
  2. 02Seven retained public source tables with exact checksums
  3. 03Fourteen generated result tables and sixteen analytical figures
  4. 04Assembly, spent-medium, chemostat, model-sweep, dropout, and uncertainty evidence
  5. 05Twenty-four automated tests with 99.24 percent branch-aware coverage
  6. 06Complete project files, calculations, results, and analysis material in a private GitHub repository
  7. 0771-page project documentation in PDF and editable Word formats
  8. 0814-page setup and usage guide in PDF and editable Word formats
  9. 09Forty-five annotated references

Project record

No information is collected on this page.

Permanent project ID
GP-BT-0TTUU9Q
Catalogued
21 Aug 2026
Completed
27 Aug 2026
Verified
27 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.