wotann 0.5.0 → 0.5.39

package/skills/scientific/peer-review/references/reporting_standards.md

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+# Scientific Reporting Standards and Guidelines
+
+This document catalogs major reporting standards and guidelines across scientific disciplines. When reviewing manuscripts, verify that authors have followed the appropriate guidelines for their study type and discipline.
+
+## Clinical Trials and Medical Research
+
+### CONSORT (Consolidated Standards of Reporting Trials)
+**Purpose:** Randomized controlled trials (RCTs)
+**Key Requirements:**
+- Trial design, participants, and interventions clearly described
+- Primary and secondary outcomes specified
+- Sample size calculation and statistical methods
+- Participant flow through trial (enrollment, allocation, follow-up, analysis)
+- Baseline characteristics of participants
+- Numbers analyzed in each group
+- Outcomes and estimation with confidence intervals
+- Adverse events
+- Trial registration number and protocol access
+
+**Reference:** http://www.consort-statement.org/
+
+### STROBE (Strengthening the Reporting of Observational Studies in Epidemiology)
+**Purpose:** Observational studies (cohort, case-control, cross-sectional)
+**Key Requirements:**
+- Study design clearly stated
+- Setting, eligibility criteria, and participant sources
+- Variables clearly defined
+- Data sources and measurement methods
+- Bias assessment
+- Sample size justification
+- Statistical methods including handling of missing data
+- Participant flow and characteristics
+- Main results with confidence intervals
+- Limitations discussed
+
+**Reference:** https://www.strobe-statement.org/
+
+### PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses)
+**Purpose:** Systematic reviews and meta-analyses
+**Key Requirements:**
+- Protocol registration
+- Systematic search strategy across multiple databases
+- Inclusion/exclusion criteria
+- Study selection process
+- Data extraction methods
+- Quality assessment of included studies
+- Statistical methods for meta-analysis
+- Assessment of publication bias
+- Heterogeneity assessment
+- PRISMA flow diagram showing study selection
+- Summary of findings tables
+
+**Reference:** http://www.prisma-statement.org/
+
+### SPIRIT (Standard Protocol Items: Recommendations for Interventional Trials)
+**Purpose:** Clinical trial protocols
+**Key Requirements:**
+- Administrative information (title, registration, funding)
+- Introduction (rationale, objectives)
+- Methods (design, participants, interventions, outcomes, sample size)
+- Ethics and dissemination
+- Trial schedule and assessments
+
+**Reference:** https://www.spirit-statement.org/
+
+### CARE (CAse REport guidelines)
+**Purpose:** Case reports
+**Key Requirements:**
+- Patient information and demographics
+- Clinical findings
+- Timeline of events
+- Diagnostic assessment
+- Therapeutic interventions
+- Follow-up and outcomes
+- Patient perspective
+- Informed consent
+
+**Reference:** https://www.care-statement.org/
+
+## Animal Research
+
+### ARRIVE (Animal Research: Reporting of In Vivo Experiments)
+**Purpose:** Studies involving animal research
+**Key Requirements:**
+- Title indicates study involves animals
+- Abstract provides accurate summary
+- Background and objectives clearly stated
+- Ethical statement and approval
+- Housing and husbandry details
+- Animal details (species, strain, sex, age, weight)
+- Experimental procedures in detail
+- Experimental animals (number, allocation, welfare assessment)
+- Statistical methods appropriate
+- Exclusion criteria stated
+- Sample size determination
+- Randomization and blinding described
+- Outcome measures defined
+- Adverse events reported
+
+**Reference:** https://arriveguidelines.org/
+
+## Genomics and Molecular Biology
+
+### MIAME (Minimum Information About a Microarray Experiment)
+**Purpose:** Microarray experiments
+**Key Requirements:**
+- Experimental design clearly described
+- Array design information
+- Samples (origin, preparation, labeling)
+- Hybridization procedures and parameters
+- Image acquisition and quantification
+- Normalization and data transformation
+- Raw and processed data availability
+- Database accession numbers
+
+**Reference:** http://fged.org/projects/miame/
+
+### MINSEQE (Minimum Information about a high-throughput Nucleotide Sequencing Experiment)
+**Purpose:** High-throughput sequencing (RNA-seq, ChIP-seq, etc.)
+**Key Requirements:**
+- Experimental design and biological context
+- Sample information (source, preparation, QC)
+- Library preparation (protocol, adapters, size selection)
+- Sequencing platform and parameters
+- Data processing pipeline (alignment, quantification, normalization)
+- Quality control metrics
+- Raw data deposition (SRA, GEO, ENA)
+- Processed data and analysis code availability
+
+### MIGS/MIMS (Minimum Information about a Genome/Metagenome Sequence)
+**Purpose:** Genome and metagenome sequencing
+**Key Requirements:**
+- Sample origin and environmental context
+- Sequencing methods and coverage
+- Assembly methods and quality metrics
+- Annotation approach
+- Quality control and contamination screening
+- Data deposition in INSDC databases
+
+**Reference:** https://gensc.org/
+
+## Structural Biology
+
+### PDB (Protein Data Bank) Deposition Requirements
+**Purpose:** Macromolecular structure determination
+**Key Requirements:**
+- Atomic coordinates deposited
+- Structure factors for X-ray structures
+- Restraints and experimental data for NMR
+- EM maps and metadata for cryo-EM
+- Model quality validation metrics
+- Experimental conditions (crystallization, sample preparation)
+- Data collection parameters
+- Refinement statistics
+
+**Reference:** https://www.wwpdb.org/
+
+## Proteomics and Mass Spectrometry
+
+### MIAPE (Minimum Information About a Proteomics Experiment)
+**Purpose:** Proteomics experiments
+**Key Requirements:**
+- Sample processing and fractionation
+- Separation methods (2D gel, LC)
+- Mass spectrometry parameters (instrument, acquisition)
+- Database search and validation parameters
+- Peptide and protein identification criteria
+- Quantification methods
+- Statistical analysis
+- Data deposition (PRIDE, PeptideAtlas)
+
+**Reference:** http://www.psidev.info/
+
+## Neuroscience
+
+### COBIDAS (Committee on Best Practices in Data Analysis and Sharing)
+**Purpose:** MRI and fMRI studies
+**Key Requirements:**
+- Scanner and sequence parameters
+- Preprocessing pipeline details
+- Software versions and parameters
+- Statistical analysis approach
+- Multiple comparison correction
+- ROI definitions
+- Data sharing (raw data, analysis scripts)
+
+**Reference:** https://www.humanbrainmapping.org/cobidas
+
+## Flow Cytometry
+
+### MIFlowCyt (Minimum Information about a Flow Cytometry Experiment)
+**Purpose:** Flow cytometry experiments
+**Key Requirements:**
+- Experimental overview and purpose
+- Sample characteristics and preparation
+- Instrument information and settings
+- Reagents (antibodies, fluorophores, concentrations)
+- Compensation and controls
+- Gating strategy
+- Data analysis approach
+- Data availability
+
+**Reference:** http://flowcyt.org/
+
+## Ecology and Environmental Science
+
+### MIAPPE (Minimum Information About a Plant Phenotyping Experiment)
+**Purpose:** Plant phenotyping studies
+**Key Requirements:**
+- Investigation and study metadata
+- Biological material information
+- Environmental parameters
+- Experimental design and factors
+- Phenotypic measurements and methods
+- Data file descriptions
+
+**Reference:** https://www.miappe.org/
+
+## Chemistry and Chemical Biology
+
+### MIRIBEL (Minimum Information Reporting in Bio-Nano Experimental Literature)
+**Purpose:** Nanomaterial characterization
+**Key Requirements:**
+- Nanomaterial composition and structure
+- Size, shape, and morphology characterization
+- Surface chemistry and functionalization
+- Purity and stability
+- Experimental conditions
+- Characterization methods
+
+## Quality Assessment and Bias
+
+### CAMARADES (Collaborative Approach to Meta-Analysis and Review of Animal Data from Experimental Studies)
+**Purpose:** Quality assessment for animal studies in systematic reviews
+**Key Items:**
+- Publication in peer-reviewed journal
+- Statement of temperature control
+- Randomization to treatment
+- Blinded assessment of outcome
+- Avoidance of anesthetic with marked intrinsic properties
+- Use of appropriate animal model
+- Sample size calculation
+- Compliance with regulatory requirements
+- Statement of conflict of interest
+- Study pre-registration
+
+### SYRCLE's Risk of Bias Tool
+**Purpose:** Assessing risk of bias in animal intervention studies
+**Domains:**
+- Selection bias (sequence generation, baseline characteristics, allocation concealment)
+- Performance bias (random housing, blinding of personnel)
+- Detection bias (random outcome assessment, blinding of assessors)
+- Attrition bias (incomplete outcome data)
+- Reporting bias (selective outcome reporting)
+- Other sources of bias
+
+## General Principles Across Guidelines
+
+### Common Requirements
+1. **Transparency:** All methods, materials, and analyses fully described
+2. **Reproducibility:** Sufficient detail for independent replication
+3. **Data Availability:** Raw data and analysis code shared or deposited
+4. **Registration:** Studies pre-registered where applicable
+5. **Ethics:** Appropriate approvals and consent documented
+6. **Conflicts of Interest:** Disclosed for all authors
+7. **Statistical Rigor:** Methods appropriate and fully described
+8. **Completeness:** All outcomes reported, including negative results
+
+### Red Flags for Non-Compliance
+- Methods section lacks critical details
+- No mention of following reporting guidelines
+- Data availability statement missing or vague
+- No database accession numbers for omics data
+- No trial registration for clinical studies
+- Sample size not justified
+- Statistical methods inadequately described
+- Missing flow diagrams (CONSORT, PRISMA)
+- Selective reporting of outcomes
+
+## How to Use This Reference
+
+When reviewing a manuscript:
+1. Identify the study type and discipline
+2. Find the relevant reporting guideline(s)
+3. Check if authors mention following the guideline
+4. Verify that key requirements are addressed
+5. Note any missing elements in your review
+6. Suggest the appropriate guideline if not mentioned
+
+Many journals require authors to complete reporting checklists at submission. Reviewers should verify compliance even if a checklist was submitted.

package/skills/scientific/peer-review/scripts/generate_schematic.py

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+#!/usr/bin/env python3
+"""
+Scientific schematic generation using Nano Banana 2.
+
+Generate any scientific diagram by describing it in natural language.
+Nano Banana 2 handles everything automatically with smart iterative refinement.
+
+Smart iteration: Only regenerates if quality is below threshold for your document type.
+Quality review: Uses Gemini 3.1 Pro Preview for professional scientific evaluation.
+
+Usage:
+    # Generate for journal paper (highest quality threshold)
+    python generate_schematic.py "CONSORT flowchart" -o flowchart.png --doc-type journal
+    
+    # Generate for presentation (lower threshold, faster)
+    python generate_schematic.py "Transformer architecture" -o transformer.png --doc-type presentation
+    
+    # Generate for poster
+    python generate_schematic.py "MAPK signaling pathway" -o pathway.png --doc-type poster
+"""
+
+import argparse
+import os
+import subprocess
+import sys
+from pathlib import Path
+
+
+def main():
+    """Command-line interface."""
+    parser = argparse.ArgumentParser(
+        description="Generate scientific schematics using AI with smart iterative refinement",
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+        epilog="""
+How it works:
+  Simply describe your diagram in natural language
+  Nano Banana 2 generates it automatically with:
+  - Smart iteration (only regenerates if quality is below threshold)
+  - Quality review by Gemini 3.1 Pro Preview
+  - Document-type aware quality thresholds
+  - Publication-ready output
+
+Document Types (quality thresholds):
+  journal      8.5/10  - Nature, Science, peer-reviewed journals
+  conference   8.0/10  - Conference papers
+  thesis       8.0/10  - Dissertations, theses
+  grant        8.0/10  - Grant proposals
+  preprint     7.5/10  - arXiv, bioRxiv, etc.
+  report       7.5/10  - Technical reports
+  poster       7.0/10  - Academic posters
+  presentation 6.5/10  - Slides, talks
+  default      7.5/10  - General purpose
+
+Examples:
+  # Generate for journal paper (strict quality)
+  python generate_schematic.py "CONSORT participant flow" -o flowchart.png --doc-type journal
+  
+  # Generate for poster (moderate quality)
+  python generate_schematic.py "Transformer architecture" -o arch.png --doc-type poster
+  
+  # Generate for slides (faster, lower threshold)
+  python generate_schematic.py "System diagram" -o system.png --doc-type presentation
+  
+  # Custom max iterations
+  python generate_schematic.py "Complex pathway" -o pathway.png --iterations 2
+  
+  # Verbose output
+  python generate_schematic.py "Circuit diagram" -o circuit.png -v
+
+Environment Variables:
+  OPENROUTER_API_KEY    Required for AI generation
+        """
+    )
+    
+    parser.add_argument("prompt", 
+                       help="Description of the diagram to generate")
+    parser.add_argument("-o", "--output", required=True,
+                       help="Output file path")
+    parser.add_argument("--doc-type", default="default",
+                       choices=["journal", "conference", "poster", "presentation",
+                               "report", "grant", "thesis", "preprint", "default"],
+                       help="Document type for quality threshold (default: default)")
+    parser.add_argument("--iterations", type=int, default=2,
+                       help="Maximum refinement iterations (default: 2, max: 2)")
+    parser.add_argument("--api-key", 
+                       help="OpenRouter API key (or use OPENROUTER_API_KEY env var)")
+    parser.add_argument("-v", "--verbose", action="store_true",
+                       help="Verbose output")
+    
+    args = parser.parse_args()
+    
+    # Check for API key
+    api_key = args.api_key or os.getenv("OPENROUTER_API_KEY")
+    if not api_key:
+        print("Error: OPENROUTER_API_KEY environment variable not set")
+        print("\nFor AI generation, you need an OpenRouter API key.")
+        print("Get one at: https://openrouter.ai/keys")
+        print("\nSet it with:")
+        print("  export OPENROUTER_API_KEY='your_api_key'")
+        print("\nOr use --api-key flag")
+        sys.exit(1)
+    
+    # Find AI generation script
+    script_dir = Path(__file__).parent
+    ai_script = script_dir / "generate_schematic_ai.py"
+    
+    if not ai_script.exists():
+        print(f"Error: AI generation script not found: {ai_script}")
+        sys.exit(1)
+    
+    # Build command
+    cmd = [sys.executable, str(ai_script), args.prompt, "-o", args.output]
+    
+    if args.doc_type != "default":
+        cmd.extend(["--doc-type", args.doc_type])
+    
+    # Enforce max 2 iterations
+    iterations = min(args.iterations, 2)
+    if iterations != 2:
+        cmd.extend(["--iterations", str(iterations)])
+    
+    if args.verbose:
+        cmd.append("-v")
+    
+    # Execute — pass API key via environment to avoid exposure in process listings
+    try:
+        env = os.environ.copy()
+        if api_key:
+            env["OPENROUTER_API_KEY"] = api_key
+        result = subprocess.run(cmd, check=False, env=env)
+        sys.exit(result.returncode)
+    except Exception as e:
+        print(f"Error executing AI generation: {e}")
+        sys.exit(1)
+
+
+if __name__ == "__main__":
+    main()
+