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Documentation
Methodology Generation
Generate comprehensive research methodology frameworks based on your evidence base. BioSkepsis synthesizes experimental approaches from your selected papers to create structured methodology recommendations, with every element grounded in published research.
Methodology Components
Generated methodologies include structured recommendations for each key aspect of experimental design:
- Study Design: Study type, arms, timeline, randomization/blinding strategy, preregistration recommendations
- Model System Justification: Recommended cell/animal models with species, sex, age, passage details and scientific rationale
- Sample Size and Power: Alpha level, statistical power, effect size estimates, replicate numbers based on published studies
- Interventions and Assays: Experimental perturbations and key assays with brand names where relevant
- Controls and Replicates: Positive, negative, and sham controls with technical and biological replicate recommendations
- Endpoints and Go/No-Go Criteria: Primary metrics with thresholds, secondary endpoints, success and futility rules
- Statistical Analysis: Recommended statistical tests, assumptions, effect sizes, confidence intervals, and multiplicity corrections
- Confounders and Handling: Identified confounding factors and mitigation strategies
Evidence Grounding
Every methodology recommendation is tied to source publications:
- Direct Evidence: The PMID explicitly reports the methodological approach
- Derived Reasoning: The recommendation is synthesized from methodological details in cited papers
Each component ends with a citation marker indicating the evidence type and source PMID(s), for example: (Direct; PMID:12345678) or (Derived; PMID:12345678, PMID:87654321)
Methodology Modes
Different modes optimize recommendations for your research context:
Fundamental Methodology
Focused on basic science experiments: mechanistic studies, pathway analysis, in vitro and in vivo model systems, molecular assays.
Applied Methodology
Focused on translational and clinical research: clinical trial design, patient selection, therapeutic endpoints, regulatory considerations.
Using Generated Methodologies
Generated methodologies serve as evidence-based starting points:
- Grant proposals: Use as a framework for methods sections, with citations to support each approach
- Study planning: Start with evidence-based parameters and adjust for your specific context
- Protocol development: Build on successful approaches from published research
- Literature reviews: Synthesize methodological trends across your evidence base
- Verify and adapt: Always verify source papers and adapt recommendations to your specific experimental needs