Agent Claude Code
FBA simulation agent. Runs standard FBA, parsimonious FBA, Flux Variability Analysis, and gene/reaction knockout simulations using COBRApy. Use after a validated metabolic model is available and the user wants to compute growth rates, flux distributions, or knockout phenotypes.
Agent Claude Code
Metabolic flux analysis agent. Performs gene essentiality analysis, phenotypic phase plane construction, flux sampling, and subsystem-level pathway analysis. Use after FBA simulations are complete and the user wants deeper phenotypic characterisation or to identify metabolic engineering targets.
Agent Claude Code
Metabolic phenotype interpretation and publication figure agent. Compares wild-type vs. mutant flux distributions, predicts maximum theoretical product yields, identifies metabolic bottlenecks, and generates publication-quality metabolic maps and charts. Use after flux analysis is complete and the user needs…
Agent Claude Code
Genome-scale metabolic model builder. Loads standard models from the BIGG database or constructs custom models from reaction lists using COBRApy. Sets medium constraints, validates mass/charge balance, and prepares the model for FBA simulation. Use when the user specifies an organism, BIGG model ID, or a custom set of…
Skill Claude CodeCodex
Run Flux Balance Analysis (FBA) and related constraint-based simulations using COBRApy. Covers standard FBA, parsimonious FBA (pFBA), Flux Variability Analysis (FVA), loopless FBA, gene/reaction knockouts, and carbon source swapping. Outputs flux distributions and CSV files.
Skill Claude CodeCodex
Analyse FBA flux distributions to extract biological insights. Covers gene essentiality, phenotypic phase planes, flux sampling, pathway-level aggregation, secretion product prediction, and production of publication- quality figures.
Skill Claude CodeCodex
Build or load a genome-scale metabolic model (GSMM) using COBRApy. Covers loading from BIGG, constructing minimal models from scratch, setting medium constraints, and exporting validated .json model files.
Skill Claude CodeCodex
Validate a COBRApy genome-scale metabolic model for mass/charge balance, stoichiometric consistency, biomass producibility, dead-end metabolites, thermodynamic loops, and GPR rule formatting. Outputs a structured validation report with errors and warnings.
Skill Claude CodeCodex
Plan publishable constraint-based metabolic modelling studies when the user has a broad biological or metabolic-engineering topic but no concrete dataset, organism, model, or hypothesis. Selects feasible BiGG/COBRA models, objectives, perturbations, analyses, metrics, figures, and risk controls before FBA code is…
Skill Claude CodeCodex
Orchestrate the full metabolic flux analysis pipeline from model loading to phenotype prediction and publication figures. Triggers when the user provides an organism name, BIGG model ID, or custom reaction list and wants end-to-end metabolic modelling run automatically.
Agent Claude Code
Statistical comparison agent. Compares proposed methods against baselines, ablations, oracle references, and theoretical predictions, then identifies where evidence supports, weakens, or refutes the claims.
Agent Claude Code
Statistical experiment designer and executor. Designs simulations, empirical studies, perturbations, diagnostics, and evaluation protocols that test the formulation, method proposal, and theoretical predictions.
Agent Claude Code
Statistical method proposal agent. Proposes candidate methods, baselines, variants, diagnostics, and ablations that directly address the formal problem formulation.
Agent Claude Code
Statistical problem formulation agent. Converts a prompt, topic file, paper idea, or dataset description into a rigorous mathematical/statistical problem statement with notation, data model, estimand, assumptions, hypotheses, evaluation criteria, and theory targets.
Agent Claude Code
Statistical research quality auditor. Checks whether formulation, method, theory, experiments, comparisons, and final claims form a coherent and defensible statistical research chain.
Agent Claude Code
Statistical result synthesis agent. Writes the final research narrative, combining formulation, proposed method, theory, experiments, comparisons, and limitations into a coherent report.
Agent Claude Code
Statistical theory analysis agent. Derives or sketches theoretical properties of the proposed methods, including identifiability, bias, variance, consistency, asymptotic behavior, coverage, error bounds, robustness, and limitations under stated assumptions.
Skill Claude CodeCodex
Orchestrate a statistical research pipeline centered on formal problem formulation, method proposal, theoretical analysis, experimental evaluation, comparison, and final result synthesis.
Skill Claude CodeCodex
Validate statistical research outputs for formulation quality, method-to- problem alignment, theory presence, experimental evidence, fair comparison, artifact completeness, and final-claim consistency.
Skill Claude CodeCodex
Design and run statistical experiments that test the formal problem, proposed methods, theoretical predictions, baselines, and ablations.
Skill Claude CodeCodex
Design statistical methods, baselines, diagnostics, variants, and ablations that directly address a formal problem formulation.
Skill Claude CodeCodex
Formulate statistical research problems with formal notation, target parameters, assumptions, hypotheses, evaluation criteria, and theory targets.
Skill Claude CodeCodex
Analyze theoretical properties of statistical methods under the formal formulation: identifiability, bias, variance, consistency, asymptotics, coverage, error bounds, robustness, and limitations.
Skill Claude CodeCodex
Best practices for image classification tasks. Use when working on CIFAR, ImageNet, or other classification benchmarks.
At most 3 mods per repository are shown here, and a mod shipped inside a plugin is left to that plugin's page — the rest are on their repository pages: