Model type
Constraint-based metabolic modelling software
Method
COBRApy
COBRApy supports constraint-based analysis of metabolic networks, including flux balance and gene-deletion analyses.
Sources
opencobra/cobrapy: README.rst · README.rst: What is COBRApy? and LicenseHow it worksCOBRApy workflow
Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation.
Sources
opencobra/cobrapy: README.rst · README.rst: What is COBRApy? and LicenseAt a glance
Inputs
A metabolic reconstruction, reaction constraints and an analysis objective.
Sources
opencobra/cobrapy: README.rst · README.rst: What is COBRApy? and LicenseOutputs
Flux solutions, feasible flux ranges and outputs of configured perturbation/essentiality analyses.
Sources
opencobra/cobrapy: README.rst · README.rst: What is COBRApy? and LicenseSource reviewed · Automated source review, 2026-09-16. All specifications and missing details
Evaluations and results
Release 2026-09-17-d277315f7d76 · 0 evaluations · 0 metric rows. Different protocols are not a single leaderboard.
No evaluations linked in this release.
How it works
How it works
COBRApy supports constraint-based analysis of metabolic networks, including flux balance and gene-deletion analyses. Metabolic network representation coupled to constrained optimization through a selected solver. The documented inputs are A metabolic reconstruction, reaction constraints and an analysis objective. The output consists of flux solutions, feasible flux ranges and outputs of configured perturbation/essentiality analyses.
Sources
opencobra/cobrapy: README.rst · README.rst: What is COBRApy? and LicenseVersions and reproducibility
COBRApy software and selected metabolic reconstruction must both be versioned. Network size and solver capacity; no sequence context.
Sources
opencobra/cobrapy: README.rst · README.rst: What is COBRApy? and LicenseStrengths and limitations
Strengths supported by sources
- One software framework exposes FBA, flux variability analysis and related methods over reusable metabolic models.
Sources
opencobra/cobrapy: README.rst · README.rst: What is COBRApy? and License
Limitations and conditions
- Results depend on the metabolic reconstruction, constraints, objective and solver; a library version alone does not define the biological model.
Sources
opencobra/cobrapy: README.rst · README.rst: What is COBRApy? and License
Profile review details
Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied.
Stable record: discovery-model-cobrapySpecifications
Inputs, training, access and other details
Explanatory profile: source reviewed · Automated source review, 2026-09-16. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.
| Property | Description and evidence |
|---|---|
| Model type | Constraint-based metabolic modelling softwareSourcesopencobra/cobrapy: README.rst · README.rst: What is COBRApy? and License |
| Architecture | Metabolic network representation coupled to constrained optimization through a selected solver.Sourcesopencobra/cobrapy: README.rst · README.rst: What is COBRApy? and License |
| Inputs | A metabolic reconstruction, reaction constraints and an analysis objective.Sourcesopencobra/cobrapy: README.rst · README.rst: What is COBRApy? and License |
| Outputs | Flux solutions, feasible flux ranges and outputs of configured perturbation/essentiality analyses.Sourcesopencobra/cobrapy: README.rst · README.rst: What is COBRApy? and License |
| Parameters | Inapplicable as a neural parameter count; reaction bounds and model constraints are scientific inputs. · Not applicableSourcesopencobra/cobrapy: README.rst · README.rst: What is COBRApy? and License |
| Known versions | COBRApy software and selected metabolic reconstruction must both be versioned.Sourcesopencobra/cobrapy: README.rst · README.rst: What is COBRApy? and License |
| Training data | No neural pretraining; the metabolic reconstruction and experimental constraints are supplied separately.Sourcesopencobra/cobrapy: README.rst · README.rst: What is COBRApy? and License |
| Training cutoff | Inapplicable to neural pretraining; reference-database and input-data dates must be recorded for each run. · Not applicableSourcesopencobra/cobrapy: README.rst · README.rst: What is COBRApy? and License |
| Context limits | Network size and solver capacity; no sequence context.Sourcesopencobra/cobrapy: README.rst · README.rst: What is COBRApy? and License |
| Weights licence | Inapplicable: no universal neural checkpoint. · Not applicableSourcesopencobra/cobrapy: README.rst · README.rst: What is COBRApy? and License |
| Access | Official project documentation and implementation: https://github.com/opencobra/cobrapySourcesopencobra/cobrapy: README.rst · README.rst: What is COBRApy? and License |
| Code licence | GPL-2.0-or-later or LGPL-2.0-or-later, at the user’s choice, as stated by the README.Sourcesopencobra/cobrapy: README.rst · README.rst: License |
| Assumptions | Not extracted or verified for this record. |
Evidence table
Inspect claims, sources and review details
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
20 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Diagram caption Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation. Individual claims | opencobra/cobrapy: README.rst README.rst: What is COBRApy? and License Version: 5aa19300fbf5dd632a9ac5c39ca28c1c621b943d | source checked automated source review · 2026-09-16 Audit detailsInspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Diagram steps ["Metabolic network","Constraints and objective","Optimization solver","Flux or perturbation analysis"] Individual claims | opencobra/cobrapy: README.rst README.rst: What is COBRApy? and License Version: 5aa19300fbf5dd632a9ac5c39ca28c1c621b943d | source checked automated source review · 2026-09-16 Audit detailsInspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Diagram title COBRApy workflow Individual claims | opencobra/cobrapy: README.rst README.rst: What is COBRApy? and License Version: 5aa19300fbf5dd632a9ac5c39ca28c1c621b943d | source checked automated source review · 2026-09-16 Audit detailsInspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Model type Constraint-based metabolic modelling software Individual claims | opencobra/cobrapy: README.rst README.rst: What is COBRApy? and License Version: 5aa19300fbf5dd632a9ac5c39ca28c1c621b943d | source checked automated source review · 2026-09-16 Audit detailsInspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Architecture Metabolic network representation coupled to constrained optimization through a selected solver. Individual claims | opencobra/cobrapy: README.rst README.rst: What is COBRApy? and License Version: 5aa19300fbf5dd632a9ac5c39ca28c1c621b943d | source checked automated source review · 2026-09-16 Audit detailsInspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Access Official project documentation and implementation: https://github.com/opencobra/cobrapy Individual claims | opencobra/cobrapy: README.rst README.rst: What is COBRApy? and License Version: 5aa19300fbf5dd632a9ac5c39ca28c1c621b943d | source checked automated source review · 2026-09-16 Audit detailsInspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Code licence GPL-2.0-or-later or LGPL-2.0-or-later, at the user’s choice, as stated by the README. Individual claims | opencobra/cobrapy: README.rst README.rst: License Version: 5aa19300fbf5dd632a9ac5c39ca28c1c621b943d | source checked automated source review · 2026-09-16 Audit detailsInspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Inputs A metabolic reconstruction, reaction constraints and an analysis objective. Individual claims | opencobra/cobrapy: README.rst README.rst: What is COBRApy? and License Version: 5aa19300fbf5dd632a9ac5c39ca28c1c621b943d | source checked automated source review · 2026-09-16 Audit detailsInspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Outputs Flux solutions, feasible flux ranges and outputs of configured perturbation/essentiality analyses. Individual claims | opencobra/cobrapy: README.rst README.rst: What is COBRApy? and License Version: 5aa19300fbf5dd632a9ac5c39ca28c1c621b943d | source checked automated source review · 2026-09-16 Audit detailsInspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Parameters Inapplicable as a neural parameter count; reaction bounds and model constraints are scientific inputs. Individual claims | opencobra/cobrapy: README.rst README.rst: What is COBRApy? and License Version: 5aa19300fbf5dd632a9ac5c39ca28c1c621b943d | inapplicable automated source review · 2026-09-16 Audit detailsInspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
Sources and history
Release 2026-09-17-d277315f7d76 · Record review: discovered
2 source records and release history
- opencobra/cobrapy official source · Original source · 5aa19300fbf5dd632a9ac5c39ca28c1c621b943d
- opencobra/cobrapy: README.rst · Original source · 5aa19300fbf5dd632a9ac5c39ca28c1c621b943d
Technical metadata and extraction receipts
Stable ID: discovery-model-cobrapy
- areas
- mechanistic-biology
- access
- official_source_linked
- benchmark applicability
- candidate; not evidence of a reported evaluation
- candidate benchmark ids
- None recorded
- entity level
- method
- reported name
- COBRApy
- version
- Not reported
- historical missing metadata
- checkpoint: unextracted; code licence: unextracted; parameters: unextracted; training cutoff: unextracted; training data: unextracted; version: unextracted; weights licence: unextracted
- metadata review scope
- historical_missing_metadata preserves the original discovery state. Current descriptive evidence and missingness are recorded in profile.facts; numerical-result review is separate.
- legacy kinds
- model
- entity classification
- review date: 2026-09-17; rationale: The cited architecture/procedure describes an algorithm, representation recipe or software toolkit, rather than a single released learned biological model. Fitted models, selected reference databases and concrete runs remain separate configurations.; source ids: evidence-official-eb328c1926fbe500f86b; source locator: README.rst: What is COBRApy? and License; ambiguities: None recorded
Related records
- model: Flux-balance prediction