scientific-writer 2.3.1__py3-none-any.whl

scientific_writer/.claude/skills/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.

scientific_writer/.claude/skills/research-grants/README.md

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+# Research Grants Skill
+
+## Overview
+
+Comprehensive skill for writing competitive research grant proposals focused on four major U.S. funding agencies:
+- **NSF** (National Science Foundation)
+- **NIH** (National Institutes of Health)
+- **DOE** (Department of Energy)
+- **DARPA** (Defense Advanced Research Projects Agency)
+
+## What This Skill Provides
+
+### Agency-Specific Guidance
+
+Detailed reference materials for each funding agency including:
+- Mission and priorities
+- Review criteria and scoring
+- Proposal structure and page limits
+- Budget requirements
+- Submission processes
+- Tips for competitive applications
+
+### Core Components
+
+- **Specific Aims Pages** (NIH): Template and detailed guide for the critical 1-page aims page
+- **Project Summaries** (NSF): Template for the required Overview, Intellectual Merit, and Broader Impacts
+- **Broader Impacts**: Comprehensive strategies for NSF's equally-weighted review criterion
+- **Budget Justification**: Templates and examples for personnel, equipment, travel, and supplies
+- **Review Criteria**: Understanding what reviewers look for at each agency
+
+### Templates
+
+Ready-to-use templates for:
+- NSF Project Summary
+- NIH Specific Aims Page
+- Budget Justifications
+- (Additional templates in development)
+
+## How to Use This Skill
+
+### Quick Start
+
+When writing a grant proposal, specify the agency and grant type:
+
+```
+> Help me write an NSF proposal for computational biology research
+> I need to draft NIH R01 Specific Aims for my cancer research project
+> What should I include in a DOE ARPA-E concept paper?
+> I'm applying for a DARPA program - help me structure the proposal
+```
+
+### Detailed Guidance
+
+For in-depth help on specific components:
+
+```
+> Help me write compelling broader impacts for my NSF proposal
+> Review my NIH Specific Aims page
+> What should I include in my budget justification?
+> How do I respond to reviewer comments in an NIH resubmission?
+```
+
+### Agency Comparison
+
+```
+> What are the key differences between NSF and NIH proposals?
+> Should I apply to DOE or DARPA for my energy technology project?
+```
+
+## Key Features
+
+### NSF Proposals
+
+- **Intellectual Merit + Broader Impacts** (equally weighted)
+- Strategies for substantive, measurable broader impacts
+- Integration of research and education
+- Broadening participation in STEM
+- 15-page project description limits (most programs)
+
+### NIH Proposals
+
+- **Specific Aims Page**: The most critical page (detailed 1-page guide included)
+- **Research Strategy**: Significance, Innovation, Approach sections
+- **Preliminary Data**: Essential for R01 applications
+- Rigor and reproducibility requirements
+- Modular vs. detailed budgets
+- Resubmission strategies (A1 applications)
+
+### DOE Proposals
+
+- **Energy relevance** and alignment with DOE mission
+- **Technology readiness levels** (TRLs)
+- National laboratory collaborations
+- Cost sharing requirements (especially ARPA-E)
+- Commercialization pathways
+- User facilities access
+
+### DARPA Proposals
+
+- **DARPA-hard problems**: High-risk, high-reward
+- **Heilmeier Catechism**: The 8 critical questions
+- Program Manager engagement (critical!)
+- Phase-based structure with milestones
+- Technology transition planning
+- Demonstration and prototypes
+
+## Reference Materials
+
+### Agency Guidelines
+- `references/nsf_guidelines.md` - Comprehensive NSF guidance
+- `references/nih_guidelines.md` - NIH mechanisms and review criteria
+- `references/doe_guidelines.md` - DOE offices and programs
+- `references/darpa_guidelines.md` - DARPA structure and strategy
+
+### Specialized Guides
+- `references/broader_impacts.md` - NSF broader impacts strategies
+- `references/specific_aims_guide.md` - NIH Specific Aims page mastery
+- `references/budget_preparation.md` - Budget development (coming soon)
+- `references/review_criteria.md` - Comparative review criteria (coming soon)
+- `references/timeline_planning.md` - Project management (coming soon)
+
+### Templates
+- `assets/nsf_project_summary_template.md`
+- `assets/nih_specific_aims_template.md`
+- `assets/budget_justification_template.md`
+
+## Success Metrics
+
+Typical success rates by agency:
+- **NSF**: 15-30% (varies by program)
+- **NIH R01**: ~20% overall (~27% for Early Stage Investigators)
+- **DOE Office of Science**: 20-40% (varies by program)
+- **ARPA-E**: 2-5% (concept papers to awards)
+- **DARPA**: Highly variable by program
+
+## Common Use Cases
+
+### First-Time Applicants
+```
+> I've never written a grant before. Help me understand NSF proposal structure.
+> What are the most common mistakes in first NIH R01 applications?
+```
+
+### Experienced Investigators
+```
+> Help me strengthen the innovation section for my NIH resubmission
+> I need to address broader impacts more substantively for NSF
+> What's the best way to show technology transition for DARPA?
+```
+
+### Career Development
+```
+> Help me write a competitive NSF CAREER proposal
+> What should I emphasize in an NIH K99/R00 application?
+```
+
+### Multi-Agency Strategy
+```
+> Should I submit this to NSF or NIH?
+> Can I submit similar proposals to DOE and DARPA?
+```
+
+## Best Practices
+
+### Start Early
+- NSF/NIH proposals: Start 3-6 months before deadline
+- DOE/DARPA proposals: 4-6 months (especially if involving national labs)
+
+### Get Feedback
+- Mock review sessions
+- Colleagues in and outside your field
+- Institutional grant support offices
+- Program officers (when appropriate)
+
+### Understand Review Criteria
+- NSF: Intellectual Merit + Broader Impacts (equal weight)
+- NIH: Significance, Investigator, Innovation, Approach, Environment (scored 1-9)
+- DOE: Technical merit, qualifications, budget, relevance
+- DARPA: Innovation, impact, team, feasibility, transition
+
+### Common Success Factors
+
+✅ Clear, compelling significance and innovation
+✅ Strong preliminary data (NIH, DOE)
+✅ Detailed, rigorous methodology
+✅ Realistic timeline and budget
+✅ Specific, measurable outcomes
+✅ Strong team with relevant expertise
+✅ Integration of broader impacts (NSF)
+✅ Technology transition plan (DOE, DARPA)
+
+## Integration with Other Skills
+
+This skill works well with:
+- **Scientific Writing**: For clear, compelling prose
+- **Literature Review**: For background sections
+- **Research Lookup**: For finding relevant citations
+- **Peer Review**: For self-assessment before submission
+
+## Updates and Additions
+
+This skill is continuously updated with:
+- Current agency priorities
+- Recent policy changes
+- New funding mechanisms
+- Additional templates and examples
+
+### Coming Soon
+- More budget examples
+- Timeline templates
+- Collaboration letter templates
+- Data management plan templates
+- Facilities and equipment description templates
+
+## Tips for Maximum Effectiveness
+
+### For NSF Proposals
+1. Start with Specific Aims/Objectives (even though not required)
+2. Develop broader impacts with same rigor as research plan
+3. Use figures and diagrams liberally (make it skimmable)
+4. Address both review criteria explicitly
+5. Get feedback from outside your immediate field
+
+### For NIH Proposals
+1. Perfect your Specific Aims page first (10+ drafts)
+2. Include substantial preliminary data
+3. Address rigor and reproducibility explicitly
+4. Identify potential problems proactively with alternatives
+5. Make sure your aims are independent but synergistic
+
+### For DOE Proposals
+1. Emphasize energy relevance and impact
+2. Include quantitative metrics (cost, efficiency, emissions)
+3. Develop pathway to deployment or commercialization
+4. Consider national laboratory partnerships
+5. Address technology readiness levels
+
+### For DARPA Proposals
+1. Contact the Program Manager early (essential!)
+2. Attend Proposers Day events
+3. Focus on breakthrough innovation (10x, not 10%)
+4. Answer the Heilmeier Catechism explicitly
+5. Develop clear transition strategy
+
+## Resources Beyond This Skill
+
+### Official Resources
+- NSF: https://www.nsf.gov/funding/
+- NIH: https://grants.nih.gov/
+- DOE: https://science.osti.gov/grants/
+- DARPA: https://www.darpa.mil/work-with-us/opportunities
+
+### Institutional Resources
+- Your institution's Office of Sponsored Research
+- Grant writing workshops
+- Internal review programs
+- Successful proposal archives
+
+### Professional Development
+- Grant writing courses and webinars
+- Agency-specific guidance documents
+- Professional society resources
+- Mentoring networks
+
+## Questions or Issues?
+
+This skill is designed to be comprehensive but may not cover every specific situation. When using this skill:
+
+1. **Be specific** about your agency, program, and grant type
+2. **Provide context** about your research area and career stage
+3. **Ask follow-up questions** for clarification
+4. **Request examples** for specific sections you're working on
+
+## Version History
+
+- **v1.0** (January 2025): Initial release with NSF, NIH, DOE, DARPA guidance
+- Comprehensive reference materials for all four agencies
+- Templates for key proposal components
+- Specific Aims and Broader Impacts detailed guides
+
+---
+
+**Remember**: Grant writing is both an art and a science. This skill provides the frameworks, strategies, and best practices—but your unique research vision, preliminary data, and team expertise are what will ultimately win funding. Start early, seek feedback, revise extensively, and don't be discouraged by rejection. Even the most successful scientists face many declined proposals before achieving funding success.
+
+Good luck with your proposals! 🎯