Skill Claude CodeCodex
Apply A-Evolve's agentic evolution methodology to improve AI agent performance across runs. Use when the user wants to diagnose agent failures, generate targeted skills from error patterns, evolve system prompts, or accumulate episodic knowledge. Works standalone or inside AutoResearchClaw pipelines. Triggers on…
Skill Claude CodeCodex
Bioinformatics with Biopython for sequence manipulation, file parsing, BLAST, and phylogenetics. Use when working with DNA/RNA/protein sequences or biological databases.
Skill Claude CodeCodex
Computational chemistry with RDKit for molecular analysis, descriptors, fingerprints, and substructure search. Use when working with SMILES, drug discovery, or cheminformatics tasks.
Skill Claude CodeCodex
Structured scientific hypothesis generation from observations. Use when formulating testable hypotheses, competing explanations, or experimental predictions.
Skill Claude CodeCodex
Systematic literature review methodology including search strategy, screening, and synthesis. Use when conducting literature reviews or writing background sections.
Skill Claude CodeCodex
Run the ResearchClaw autonomous research pipeline from a topic, config, and output directory.
Skill Claude CodeCodex
Publication-ready scientific figure design with matplotlib and seaborn. Use when creating journal submission figures with proper formatting, accessibility, and statistical annotations.
Skill Claude CodeCodex
Academic manuscript writing with IMRAD structure, citation formatting, and reporting guidelines. Use when drafting or revising research papers.
Skill Claude CodeCodex
Statistical test selection, assumption checking, and APA-formatted reporting. Use when analyzing experimental results or writing results sections.
Agent
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
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
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
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
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
Statistical experiment designer and executor. Designs simulations, empirical studies, perturbations, diagnostics, and evaluation protocols that test the formulation, method proposal, and theoretical predictions.
Agent
Statistical method proposal agent. Proposes candidate methods, baselines, variants, diagnostics, and ablations that directly address the formal problem formulation.
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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.
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Statistical research quality auditor. Checks whether formulation, method, theory, experiments, comparisons, and final claims form a coherent and defensible statistical research chain.