Model type
Microbial community simulation software
Pipeline
CAMISIM
CAMISIM creates simulated microbial communities and corresponding shotgun metagenomic datasets.
Sources
CAMI-challenge/CAMISIM: README.md · README.md: overview and CAMISIM 2.0How it worksCAMISIM workflow
Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation.
Sources
CAMI-challenge/CAMISIM: README.md · README.md: overview and CAMISIM 2.0At a glance
Inputs
Chosen genomes, community-abundance settings and simulation configuration.
Sources
CAMI-challenge/CAMISIM: README.md · README.md: overview and CAMISIM 2.0Outputs
Simulated shotgun metagenomic datasets with known generating communities.
Sources
CAMI-challenge/CAMISIM: README.md · README.md: overview and CAMISIM 2.0Source 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
CAMISIM creates simulated microbial communities and corresponding shotgun metagenomic datasets. Community-abundance simulation followed by metagenomic read generation; CAMISIM 2 uses a Nextflow workflow. The documented inputs are chosen genomes, community-abundance settings and simulation configuration. The output consists of simulated shotgun metagenomic datasets with known generating communities.
Sources
CAMI-challenge/CAMISIM: README.md · README.md: overview and CAMISIM 2.0Versions and reproducibility
CAMISIM 2.0 Nextflow workflow; legacy Python version retained as 1.31-final. Simulation size and read-generation configuration, not a neural token window.
Sources
CAMI-challenge/CAMISIM: README.md · README.md: overview and CAMISIM 2.0Strengths and limitations
Strengths supported by sources
- Provides controlled synthetic data useful for evaluating metagenomic analysis methods.
Sources
CAMI-challenge/CAMISIM: README.md · README.md: overview and CAMISIM 2.0
Limitations and conditions
- Simulation realism depends on its inputs and configuration. The authors advise checking converted CAMISIM 1 configurations rather than assuming automatic compatibility.
Sources
CAMI-challenge/CAMISIM: README.md · README.md: overview and CAMISIM 2.0
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-camisimSpecifications
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 | Microbial community simulation softwareSourcesCAMI-challenge/CAMISIM: README.md · README.md: overview and CAMISIM 2.0 |
| Architecture | Community-abundance simulation followed by metagenomic read generation; CAMISIM 2 uses a Nextflow workflow.SourcesCAMI-challenge/CAMISIM: README.md · README.md: overview and CAMISIM 2.0 |
| Inputs | Chosen genomes, community-abundance settings and simulation configuration.SourcesCAMI-challenge/CAMISIM: README.md · README.md: overview and CAMISIM 2.0 |
| Outputs | Simulated shotgun metagenomic datasets with known generating communities.SourcesCAMI-challenge/CAMISIM: README.md · README.md: overview and CAMISIM 2.0 |
| Parameters | Inapplicable as a neural parameter count; simulation settings must be pinned. · Not applicableSourcesCAMI-challenge/CAMISIM: README.md · README.md: overview and CAMISIM 2.0 |
| Known versions | CAMISIM 2.0 Nextflow workflow; legacy Python version retained as 1.31-final.SourcesCAMI-challenge/CAMISIM: README.md · README.md: overview and CAMISIM 2.0 |
| Training data | No neural pretraining; selected input genomes determine the simulation source material.SourcesCAMI-challenge/CAMISIM: README.md · README.md: overview and CAMISIM 2.0 |
| Training cutoff | Inapplicable to neural pretraining; reference-database and input-data dates must be recorded for each run. · Not applicableSourcesCAMI-challenge/CAMISIM: README.md · README.md: overview and CAMISIM 2.0 |
| Context limits | Simulation size and read-generation configuration, not a neural token window.SourcesCAMI-challenge/CAMISIM: README.md · README.md: overview and CAMISIM 2.0 |
| Weights licence | Inapplicable: simulator rather than a pretrained predictor. · Not applicableSourcesCAMI-challenge/CAMISIM: README.md · README.md: overview and CAMISIM 2.0 |
| Access | Official project documentation and implementation: https://github.com/CAMI-challenge/CAMISIMSourcesCAMI-challenge/CAMISIM: README.md · README.md: overview and CAMISIM 2.0 |
| Code licence | Apache-2.0SourcesCAMI-challenge/CAMISIM: LICENSE.txt · LICENSE.txt: licence text |
Applicable tests and references
Applicability is distinct from a completed evaluation.
- CAMI · Proposed association
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 | CAMI-challenge/CAMISIM: README.md README.md: overview and CAMISIM 2.0 Version: 7ce6013c6d5a0fac8ba8a80e52a03560d3546fa6 | 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 ["Reference genomes","Community abundance model","Read simulation","Synthetic metagenome"] Individual claims | CAMI-challenge/CAMISIM: README.md README.md: overview and CAMISIM 2.0 Version: 7ce6013c6d5a0fac8ba8a80e52a03560d3546fa6 | 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 CAMISIM workflow Individual claims | CAMI-challenge/CAMISIM: README.md README.md: overview and CAMISIM 2.0 Version: 7ce6013c6d5a0fac8ba8a80e52a03560d3546fa6 | 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 Microbial community simulation software Individual claims | CAMI-challenge/CAMISIM: README.md README.md: overview and CAMISIM 2.0 Version: 7ce6013c6d5a0fac8ba8a80e52a03560d3546fa6 | 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 Community-abundance simulation followed by metagenomic read generation; CAMISIM 2 uses a Nextflow workflow. Individual claims | CAMI-challenge/CAMISIM: README.md README.md: overview and CAMISIM 2.0 Version: 7ce6013c6d5a0fac8ba8a80e52a03560d3546fa6 | 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/CAMI-challenge/CAMISIM Individual claims | CAMI-challenge/CAMISIM: README.md README.md: overview and CAMISIM 2.0 Version: 7ce6013c6d5a0fac8ba8a80e52a03560d3546fa6 | 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 Apache-2.0 Individual claims | CAMI-challenge/CAMISIM: LICENSE.txt LICENSE.txt: licence text Version: 7ce6013c6d5a0fac8ba8a80e52a03560d3546fa6 | 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 Chosen genomes, community-abundance settings and simulation configuration. Individual claims | CAMI-challenge/CAMISIM: README.md README.md: overview and CAMISIM 2.0 Version: 7ce6013c6d5a0fac8ba8a80e52a03560d3546fa6 | 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 Simulated shotgun metagenomic datasets with known generating communities. Individual claims | CAMI-challenge/CAMISIM: README.md README.md: overview and CAMISIM 2.0 Version: 7ce6013c6d5a0fac8ba8a80e52a03560d3546fa6 | 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; simulation settings must be pinned. Individual claims | CAMI-challenge/CAMISIM: README.md README.md: overview and CAMISIM 2.0 Version: 7ce6013c6d5a0fac8ba8a80e52a03560d3546fa6 | 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
3 source records and release history
- CAMI-challenge/CAMISIM official source · Original source · 7ce6013c6d5a0fac8ba8a80e52a03560d3546fa6
- CAMI-challenge/CAMISIM: README.md · Original source · 7ce6013c6d5a0fac8ba8a80e52a03560d3546fa6
- CAMI-challenge/CAMISIM: LICENSE.txt · Original source · 7ce6013c6d5a0fac8ba8a80e52a03560d3546fa6
Technical metadata and extraction receipts
Stable ID: discovery-model-camisim
- areas
- microbiome
- access
- official_source_linked
- benchmark applicability
- candidate; not evidence of a reported evaluation
- candidate benchmark ids
- discovery-benchmark-cami
- entity level
- method
- reported name
- CAMISIM
- 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: This record identifies a composed analysis workflow with separately identifiable upstream models, representations or tools and a downstream prediction/scoring procedure. Results belong to that complete composition rather than to an upstream model alone.; source ids: evidence-official-e604b144dfbd97bf8917; source locator: README.md: overview and CAMISIM 2.0; ambiguities: None recorded
Related records
- applicable to: CAMI