Tool Catalogue (auto-generated)
This file is generated by scripts/generate_tool_catalogue.py. Do not edit manually.
| Tool | Description | Module |
|---|---|---|
analyze_essentiality |
Analyze gene and reaction essentiality to identify critical components required for model growth and viability. | src.tools.cobra.essentiality.EssentialityAnalysisTool |
analyze_media_compatibility |
Analyze compatibility between media and models. Identifies mapping issues and suggests media modifications for better compatibility. | src.tools.cobra.media_tools.MediaCompatibilityTool |
analyze_metabolic_model |
Analyze structural properties of a metabolic model including reaction connectivity, pathway completeness, and potential gaps. | src.tools.cobra.analysis.ModelAnalysisTool |
analyze_pathway |
Analyze specific metabolic pathways including flux distributions, gene associations, and regulatory features. | src.tools.cobra.analysis.PathwayAnalysisTool |
analyze_reaction_expression |
Analyze reaction expression levels using pFBA to obtain realistic flux distributions. | src.tools.cobra.reaction_expression.ReactionExpressionTool |
annotate_genome_rast |
Annotate a genome or protein FASTA using the RAST (Rapid Annotation using Subsystem Technology) service. Provides functional annotation of protein-coding genes from genomes or protein sequences. | src.tools.modelseed.annotation.RastAnnotationTool |
build_metabolic_model |
Build a metabolic model from genome annotations using ModelSEED with MSGenome support. Can use RAST annotations, MSGenome objects, or other supported annotation formats. | src.tools.modelseed.builder.ModelBuildTool |
check_missing_media |
Identify missing media components in a metabolic model using FBA. | src.tools.cobra.missing_media.MissingMediaTool |
compare_media_performance |
Compare how a model performs across different media conditions. Provides detailed growth analysis and identifies optimal conditions. | src.tools.cobra.media_tools.MediaComparatorTool |
find_minimal_media |
Determine the minimal set of media components required for growth by iteratively removing nutrients using FBA. | src.tools.cobra.minimal_media.MinimalMediaTool |
gapfill_model |
Perform gap filling on metabolic models to resolve network gaps and enable model growth using ModelSEED. | src.tools.modelseed.gapfill.GapFillTool |
identify_auxotrophies |
Identify potential auxotrophies by testing the removal of candidate nutrients using FBA. | src.tools.cobra.auxotrophy.AuxotrophyTool |
manipulate_media_composition |
Modify media compositions using AI-driven natural language commands. Examples: 'make anaerobic', 'add vitamins', 'increase glucose uptake', 'remove amino acids'. | src.tools.cobra.media_tools.MediaManipulatorTool |
optimize_media_composition |
Optimize media composition using AI to achieve specific growth targets. Uses iterative optimization with pathway analysis to minimize media complexity while meeting growth requirements. | src.tools.cobra.advanced_media_ai.MediaOptimizationTool |
predict_auxotrophies |
Predict potential auxotrophies by analyzing metabolic gaps and testing compound removal. Uses AI to identify essential nutrients and predict growth requirements. | src.tools.cobra.advanced_media_ai.AuxotrophyPredictionTool |
resolve_biochem_entity |
Resolve biochemistry entity IDs (compounds/reactions) to human-readable names and aliases | src.tools.biochem.resolver.BiochemEntityResolverTool |
run_flux_sampling |
Sample the feasible flux space to understand flux distributions and variability across the metabolic network. | src.tools.cobra.flux_sampling.FluxSamplingTool |
run_flux_variability_analysis |
Run Flux Variability Analysis (FVA) to determine minimum and maximum flux values for each reaction in the model while maintaining a specified fraction of the optimal objective. | src.tools.cobra.flux_variability.FluxVariabilityTool |
run_gene_deletion_analysis |
Run gene deletion analysis to predict the effect of gene knockouts on model growth and identify essential genes. | src.tools.cobra.gene_deletion.GeneDeletionTool |
run_metabolic_fba |
Run Flux Balance Analysis (FBA) on a metabolic model using a configurable simulation method. | src.tools.cobra.fba.FBATool |
run_production_envelope |
Calculate production envelope to analyze the relationship between growth rate and product formation, useful for metabolic engineering design. | src.tools.cobra.production_envelope.ProductionEnvelopeTool |
search_biochem |
Search the biochemistry database for compounds and reactions by name or alias | src.tools.biochem.resolver.BiochemSearchTool |
select_optimal_media |
Select the most appropriate media type for a metabolic model. Analyzes model characteristics and suggests compatible media with growth predictions. | src.tools.cobra.media_tools.MediaSelectorTool |
test_modelseed_cobra_compatibility |
Test compatibility between ModelSEED models and COBRApy through SBML round-trip verification and growth rate comparison. | src.tools.modelseed.compatibility.ModelCompatibilityTool |
validate_ai_audit |
Validates the AI audit system functionality including: - AI reasoning step capture - Workflow tracking and coherence analysis - Decision verification and confidence scoring - Multi-step reasoning chain validation | src.tools.system.audit_tools.AIAuditTool |
validate_realtime_verification |
Validates the real-time verification system functionality including: - Real-time alert generation and processing - Live metrics calculation and tracking - Anomaly detection and pattern analysis - Verification threshold management | src.tools.system.audit_tools.RealtimeVerificationTool |
validate_tool_audit |
Validates the tool audit system functionality including: - Audit record creation and storage - Console output capture - File tracking and verification - Execution metadata collection | src.tools.system.audit_tools.ToolAuditTool |
Total tools: 24 – last updated: 2025-06-18