scientific-writer 2.1.1__py3-none-any.whl → 2.2.2__py3-none-any.whl

scientific_writer/.claude/skills/latex-posters/references/poster_content_guide.md

@@ -0,0 +1,748 @@
+# Research Poster Content Guide
+
+## Overview
+
+Content is king in research posters. This guide covers writing strategies, section-specific guidance, visual-text balance, and best practices for communicating research effectively in poster format.
+
+## Core Content Principles
+
+### 1. The 3-5 Minute Rule
+
+**Reality**: Most viewers spend 3-5 minutes at your poster
+- **1 minute**: Scanning from distance (title, figures)
+- **2-4 minutes**: Reading key points up close
+- **5+ minutes**: Engaged conversation (if interested)
+
+**Design Implication**: Poster must work at three levels:
+1. **Distance view** (6-10 feet): Title and main figure visible
+2. **Browse view** (3-6 feet): Section headers and key results readable
+3. **Detail view** (1-3 feet): Full content accessible
+
+### 2. Tell a Story, Not a Paper
+
+**Poster ≠ Condensed Paper**
+
+**Paper approach** (❌):
+- Comprehensive literature review
+- Detailed methodology
+- All results presented
+- Lengthy discussion
+- 50+ references
+
+**Poster approach** (✅):
+- One sentence background
+- Visual methods diagram
+- 3-5 key results
+- 3-4 bullet point conclusions
+- 5-10 key references
+
+**Story Arc for Posters**:
+```
+Hook (Problem) → Approach → Discovery → Impact
+```
+
+**Example**:
+- **Hook**: "Antibiotic resistance threatens millions of lives annually"
+- **Approach**: "We developed an AI system to predict resistance patterns"
+- **Discovery**: "Our model achieves 87% accuracy, 20% better than existing methods"
+- **Impact**: "Could reduce treatment failures by identifying resistance earlier"
+
+### 3. The 800-Word Maximum
+
+**Word Count Guidelines**:
+- **Ideal**: 300-500 words
+- **Maximum**: 800 words
+- **Hard limit**: 1000 words (beyond this, poster is unreadable)
+
+**Word Budget by Section**:
+| Section | Word Count | % of Total |
+|---------|-----------|------------|
+| Introduction/Background | 50-100 | 15% |
+| Methods | 100-150 | 25% |
+| Results (text) | 100-200 | 25% |
+| Discussion/Conclusions | 100-150 | 25% |
+| References/Acknowledgments | 50-100 | 10% |
+
+**Counting Tool**:
+```latex
+% Add word count to poster (remove for final)
+\usepackage{texcount}
+% Compile with: texcount -inc poster.tex
+```
+
+### 4. Visual-to-Text Ratio
+
+**Optimal Balance**: 40-50% visual content, 50-60% text+white space
+
+**Visual Content Includes**:
+- Figures and graphs
+- Photos and images
+- Diagrams and flowcharts
+- Icons and symbols
+- Color blocks and design elements
+
+**Too Text-Heavy** (❌):
+- Wall of text
+- Small figures
+- Intimidating to viewers
+- Low engagement
+
+**Well-Balanced** (✅):
+- Clear figures dominate
+- Text supports visuals
+- Easy to scan
+- Inviting appearance
+
+## Section-Specific Content Guidance
+
+### Title
+
+**Purpose**: Capture attention, convey topic, establish credibility
+
+**Characteristics of Effective Titles**:
+- **Concise**: 10-15 words maximum
+- **Descriptive**: Clearly states research topic
+- **Active**: Uses strong verbs when possible
+- **Specific**: Avoids vague terms
+- **Jargon-aware**: Balances field-specific terms with accessibility
+
+**Title Formulas**:
+
+**1. Descriptive**:
+```
+[Method/Approach] for [Problem/Application]
+
+Example: "Deep Learning for Early Detection of Alzheimer's Disease"
+```
+
+**2. Question**:
+```
+[Research Question]?
+
+Example: "Can Microbiome Diversity Predict Treatment Response?"
+```
+
+**3. Assertion**:
+```
+[Finding] in [Context]
+
+Example: "Novel Mechanism Identified in Drug Resistance Pathways"
+```
+
+**4. Colon Format**:
+```
+[Topic]: [Specific Approach/Finding]
+
+Example: "Urban Heat Islands: A Machine Learning Framework for Mitigation"
+```
+
+**Avoid**:
+- ❌ Generic titles: "A Study of X"
+- ❌ Overly cute or clever wordplay (confuses message)
+- ❌ Excessive jargon: "Utilization of CRISPR-Cas9..."
+- ❌ Unnecessarily long: "Investigation of the potential role of..."
+
+**LaTeX Title Formatting**:
+```latex
+% Emphasize key words with bold
+\title{Deep Learning for \textbf{Early Detection} of Alzheimer's Disease}
+
+% Two-line titles for long names
+\title{Machine Learning Framework for\\Urban Heat Island Mitigation}
+
+% Avoid ALL CAPS (harder to read)
+```
+
+### Authors and Affiliations
+
+**Best Practices**:
+- **Presenting author**: Bold, underline, or asterisk
+- **Corresponding author**: Include email
+- **Affiliations**: Superscript numbers or symbols
+- **Institutional logos**: 2-4 maximum
+
+**Format Examples**:
+```latex
+% Simple format
+\author{\textbf{Jane Smith}\textsuperscript{1}, John Doe\textsuperscript{2}}
+\institute{
+  \textsuperscript{1}University of Example, 
+  \textsuperscript{2}Research Institute
+}
+
+% With contact
+\author{Jane Smith\textsuperscript{1,*}}
+\institute{
+  \textsuperscript{1}Department, University\\
+  \textsuperscript{*}jane.smith@university.edu
+}
+```
+
+### Introduction/Background
+
+**Purpose**: Establish context, motivate research, state objective
+
+**Structure** (50-100 words):
+1. **Problem statement** (1-2 sentences): What's the issue?
+2. **Knowledge gap** (1-2 sentences): What's unknown/unsolved?
+3. **Research objective** (1 sentence): What did you do?
+
+**Example** (95 words):
+```
+Antibiotic resistance causes 700,000 deaths annually, projected to reach 
+10 million by 2050. Current diagnostic methods require 48-72 hours, 
+delaying appropriate treatment. Machine learning offers potential for 
+rapid resistance prediction, but existing models lack generalizability 
+across bacterial species. 
+
+We developed a transformer-based deep learning model to predict antibiotic 
+resistance from genomic sequences across multiple pathogen species. Our 
+approach integrates evolutionary information and protein structure to 
+improve cross-species accuracy.
+```
+
+**Visual Support**:
+- Conceptual diagram showing problem
+- Infographic with statistics
+- Image of application context
+
+**Common Mistakes**:
+- ❌ Extensive literature review
+- ❌ Too much background detail
+- ❌ Undefined acronyms at first use
+- ❌ Missing clear objective statement
+
+### Methods
+
+**Purpose**: Describe approach sufficiently for understanding (not replication)
+
+**Key Question**: "How did you do it?" not "How could someone else replicate it?"
+
+**Content Strategy**:
+- **Prioritize**: Visual methods diagram > text description
+- **Include**: Study design, key procedures, analysis approach
+- **Omit**: Detailed protocols, routine procedures, specific reagent details
+
+**Visual Methods (Highly Recommended)**:
+```latex
+% Flowchart of study design
+\begin{tikzpicture}[node distance=2cm]
+  \node (start) [box] {Data Collection\\n=1,000 samples};
+  \node (process) [box, below of=start] {Preprocessing\\Quality Control};
+  \node (analysis) [box, below of=process] {Statistical Analysis\\Mixed Models};
+  \node (end) [box, below of=analysis] {Validation\\Independent Cohort};
+  
+  \draw [arrow] (start) -- (process);
+  \draw [arrow] (process) -- (analysis);
+  \draw [arrow] (analysis) -- (end);
+\end{tikzpicture}
+```
+
+**Text Methods** (50-150 words):
+
+**For Experimental Studies**:
+```
+Methods
+• Study design: Randomized controlled trial (n=200)
+• Participants: Adults aged 18-65 with Type 2 diabetes
+• Intervention: 12-week exercise program vs. standard care
+• Outcomes: HbA1c (primary), insulin sensitivity (secondary)
+• Analysis: Linear mixed models, intention-to-treat
+```
+
+**For Computational Studies**:
+```
+Methods
+• Dataset: 10,000 labeled images from ImageNet
+• Architecture: ResNet-50 with custom attention mechanism
+• Training: 100 epochs, Adam optimizer, learning rate 0.001
+• Validation: 5-fold cross-validation
+• Comparison: Baseline CNN, VGG-16, Inception-v3
+```
+
+**Format Options**:
+- **Bullet points**: Quick scanning (recommended)
+- **Numbered list**: Sequential procedures
+- **Diagram + brief text**: Ideal combination
+- **Table**: Multiple conditions or parameters
+
+### Results
+
+**Purpose**: Present key findings visually and clearly
+
+**Golden Rule**: Show, don't tell
+
+**Content Allocation**:
+- **Figures**: 70-80% of Results section
+- **Text**: 20-30% (brief descriptions, statistics)
+
+**How Many Results**:
+- **Ideal**: 3-5 main findings
+- **Maximum**: 6-7 distinct results
+- **Focus**: Primary outcomes, most impactful findings
+
+**Figure Selection Criteria**:
+1. Does it support the main message?
+2. Is it self-explanatory with caption?
+3. Can it be understood in 10 seconds?
+4. Does it add information beyond text?
+
+**Figure Captions**:
+- **Descriptive**: Explain what is shown
+- **Standalone**: Understandable without reading full poster
+- **Statistical**: Include significance indicators, sample sizes
+- **Concise**: 1-3 sentences
+
+**Example Caption**:
+```latex
+\caption{Treatment significantly improved outcomes. 
+Mean±SD shown for control (blue, n=45) and treatment (orange, n=47) groups. 
+**p<0.01, ***p<0.001 (two-tailed t-test).}
+```
+
+**Text Support for Results** (100-200 words):
+- State main finding per figure
+- Include key statistics
+- Note trends or patterns
+- Avoid detailed interpretation (save for Discussion)
+
+**Example Results Text**:
+```
+Key Findings
+• Model achieved 87% accuracy on test set (vs. 73% baseline)
+• Performance consistent across 5 bacterial species (p<0.001)
+• Prediction speed: <30 seconds per isolate
+• Feature importance: protein structure (42%), sequence (35%), 
+  evolutionary conservation (23%)
+```
+
+**Data Presentation Formats**:
+
+**1. Bar Charts**: Comparing categories
+```latex
+\begin{tikzpicture}
+  \begin{axis}[
+    ybar,
+    ylabel=Accuracy (\%),
+    symbolic x coords={Baseline, Model A, Our Method},
+    xtick=data,
+    nodes near coords
+  ]
+  \addplot coordinates {(Baseline,73) (Model A,81) (Our Method,87)};
+  \end{axis}
+\end{tikzpicture}
+```
+
+**2. Line Graphs**: Trends over time
+**3. Scatter Plots**: Correlations
+**4. Heatmaps**: Matrix data, clustering
+**5. Box Plots**: Distributions, comparisons
+**6. ROC Curves**: Classification performance
+
+### Discussion/Conclusions
+
+**Purpose**: Interpret findings, state implications, acknowledge limitations
+
+**Structure** (100-150 words):
+
+**1. Main Conclusions** (50-75 words):
+- 3-5 bullet points
+- Clear, specific takeaways
+- Linked to research objectives
+
+**Example**:
+```
+Conclusions
+• First cross-species model for antibiotic resistance prediction 
+  achieving >85% accuracy
+• Protein structure integration critical for generalizability 
+  (improved accuracy by 14%)
+• Prediction speed enables clinical decision support within 
+  consultation timeframe
+• Potential to reduce inappropriate antibiotic use by 20-30%
+```
+
+**2. Limitations** (25-50 words, optional but recommended):
+- Acknowledge key constraints
+- Brief, honest
+- Shows scientific rigor
+
+**Example**:
+```
+Limitations
+• Training data limited to 5 bacterial species
+• Requires genomic sequencing (not widely available)
+• Validation needed in prospective clinical trials
+```
+
+**3. Future Directions** (25-50 words, optional):
+- Next steps
+- Broader implications
+- Call to action
+
+**Example**:
+```
+Next Steps
+• Expand to 20+ additional species
+• Develop point-of-care sequencing integration
+• Launch multi-center clinical validation study (2025)
+```
+
+**Avoid**:
+- ❌ Overstating findings: "This revolutionary breakthrough..."
+- ❌ Extensive comparison to other work
+- ❌ New results in Discussion
+- ❌ Vague conclusions: "Further research is needed"
+
+### References
+
+**How Many**: 5-10 key citations
+
+**Selection Criteria**:
+- Include seminal work in the field
+- Recent relevant studies (last 5 years)
+- Methods cited in your poster
+- Controversial claims that need support
+
+**Format**: Abbreviated, consistent style
+
+**Examples**:
+
+**Numbered (Vancouver)**:
+```
+References
+1. Smith et al. (2023). Nature. 615:234-240.
+2. Jones & Lee (2024). Science. 383:112-118.
+3. Chen et al. (2022). Cell. 185:456-470.
+```
+
+**Author-Year (APA)**:
+```
+References
+Smith, J. et al. (2023). Title. Nature, 615, 234-240.
+Jones, A., & Lee, B. (2024). Title. Science, 383, 112-118.
+```
+
+**Minimal (For Space Constraints)**:
+```
+Key References: Smith (Nature 2023), Jones (Science 2024), 
+Chen (Cell 2022). Full bibliography: [QR Code]
+```
+
+**Alternative**: QR code linking to full reference list
+
+### Acknowledgments
+
+**Include**:
+- Funding sources (with grant numbers)
+- Major collaborators
+- Core facilities used
+- Dataset sources
+
+**Format** (25-50 words):
+```
+Acknowledgments
+Funded by NIH Grant R01-123456 and NSF Award 7890123. 
+We thank Dr. X for data access, the Y Core Facility for 
+sequencing, and Z for helpful discussions.
+```
+
+### Contact Information
+
+**Essential Elements**:
+- Name of presenting/corresponding author
+- Email address
+- Optional: Lab website, Twitter/X, LinkedIn, ORCID
+
+**Format**:
+```
+Contact: Jane Smith, jane.smith@university.edu
+Lab: smithlab.university.edu | Twitter: @smithlab
+```
+
+**QR Code Alternative**:
+- Link to personal/lab website
+- Link to paper preprint/publication
+- Link to code repository (GitHub)
+- Link to supplementary materials
+
+## Writing Style for Posters
+
+### Active vs. Passive Voice
+
+**Prefer Active Voice** (more engaging, clearer):
+- ✅ "We developed a model..."
+- ✅ "The treatment reduced symptoms..."
+
+**Passive Voice** (when appropriate):
+- ✅ "Samples were collected from..."
+- ✅ "Data were analyzed using..."
+
+### Sentence Length
+
+**Keep Sentences Short**:
+- **Ideal**: 10-15 words per sentence
+- **Maximum**: 20-25 words
+- **Avoid**: >30 words (hard to follow)
+
+**Example Revision**:
+- ❌ Long: "We performed a comprehensive analysis of gene expression data from 500 patients with colorectal cancer using RNA sequencing and identified 47 differentially expressed genes associated with treatment response." (31 words)
+- ✅ Short: "We analyzed RNA sequencing data from 500 colorectal cancer patients. We identified 47 genes associated with treatment response." (19 words total, two sentences)
+
+### Bullet Points vs. Paragraphs
+
+**Use Bullet Points For**:
+- ✅ Lists of items or findings
+- ✅ Key conclusions
+- ✅ Methods steps
+- ✅ Study characteristics
+
+**Use Short Paragraphs For**:
+- ✅ Narrative flow (Introduction)
+- ✅ Complex explanations
+- ✅ Connected ideas
+
+**Bullet Point Best Practices**:
+- Start with action verbs or nouns
+- Parallel structure throughout list
+- 3-7 bullets per list (not too many)
+- Brief (1-2 lines each)
+
+**Example**:
+```
+Methods
+• Participants: 200 adults (18-65 years)
+• Design: Double-blind RCT (12 weeks)
+• Intervention: Daily 30-min exercise
+• Control: Standard care
+• Analysis: Mixed models (SPSS v.28)
+```
+
+### Acronyms and Jargon
+
+**First Use Rule**: Define at first appearance
+```
+We used machine learning (ML) to analyze... Later, ML predicted...
+```
+
+**Common Acronyms**: May not need definition if universal to field
+- DNA, RNA, MRI, CT, PCR (in biomedical context)
+- AI, ML, CNN (in computer science context)
+
+**Avoid Excessive Jargon**:
+- ❌ "Utilized" → ✅ "Used"
+- ❌ "Implement utilization of" → ✅ "Use"
+- ❌ "A majority of" → ✅ "Most"
+
+### Numbers and Statistics
+
+**Present Statistics Clearly**:
+- Always include measure of variability (SD, SE, CI)
+- Report sample sizes: n=50
+- Indicate significance: p<0.05, p<0.01, p<0.001
+- Use symbols consistently: * for p<0.05, ** for p<0.01
+
+**Format Numbers**:
+- Round appropriately (avoid false precision)
+- Use consistent decimal places
+- Include units: 25 mg/dL, 37°C
+- Large numbers: 1,000 or 1000 (be consistent)
+
+**Example**:
+```
+Treatment increased response by 23.5% (95% CI: 18.2-28.8%, p<0.001, n=150)
+```
+
+## Visual-Text Integration
+
+### Figure-Text Relationship
+
+**Figure First, Text Second**:
+1. Design poster around key figures
+2. Add text to support and explain visuals
+3. Ensure figures can stand alone
+
+**Text Placement Relative to Figures**:
+- **Above**: Context, "What you're about to see"
+- **Below**: Explanation, statistics, caption
+- **Beside**: Comparison, interpretation
+
+### Callouts and Annotations
+
+**On-Figure Annotations**:
+```latex
+\begin{tikzpicture}
+  \node[inner sep=0] (img) {\includegraphics[width=10cm]{figure.pdf}};
+  \draw[->, thick, red] (8,5) -- (6,3) node[left] {Key region};
+  \draw[red, thick] (3,2) circle (1cm) node[above=1.2cm] {Anomaly};
+\end{tikzpicture}
+```
+
+**Callout Boxes**:
+```latex
+\begin{tcolorbox}[colback=yellow!10, colframe=orange!80, 
+                  title=Key Finding]
+Our method reduces errors by 34\% compared to state-of-the-art.
+\end{tcolorbox}
+```
+
+### Icons for Section Headers
+
+**Visual Section Markers**:
+```latex
+\usepackage{fontawesome5}
+
+\block{\faFlask~Introduction}{...}
+\block{\faCog~Methods}{...}
+\block{\faChartBar~Results}{...}
+\block{\faLightbulb~Conclusions}{...}
+```
+
+## Content Adaptation Strategies
+
+### From Paper to Poster
+
+**Condensation Process**:
+
+**1. Identify Core Message** (The Elevator Pitch):
+- What's the one thing you want people to remember?
+- If you had 30 seconds, what would you say?
+
+**2. Select Key Results**:
+- Choose 3-5 most impactful findings
+- Omit supporting/secondary results
+- Focus on figures with strong visual impact
+
+**3. Simplify Methods**:
+- Visual flowchart > text description
+- Omit routine procedures
+- Include only essential parameters
+
+**4. Trim Literature Review**:
+- One sentence background
+- One sentence gap/motivation
+- One sentence your contribution
+
+**5. Condense Discussion**:
+- Main conclusions only
+- Brief limitations
+- One sentence future direction
+
+### For Different Audiences
+
+**Specialist Audience** (Same Field):
+- Can use field-specific jargon
+- Less background needed
+- Focus on novel methodology
+- Emphasize nuanced findings
+
+**General Scientific Audience**:
+- Define key terms
+- More context/background
+- Broader implications
+- Visual metaphors helpful
+
+**Public/Lay Audience**:
+- Minimal jargon, all defined
+- Extensive context
+- Real-world applications
+- Analogies and simple language
+
+**Example Adaptation**:
+
+**Specialist**: "CRISPR-Cas9 knockout of BRCA1 induced synthetic lethality with PARP inhibitors"
+
+**General**: "We used gene editing to make cancer cells vulnerable to existing drugs"
+
+**Public**: "We found a way to make cancer treatments work better by targeting specific genetic weaknesses"
+
+## Quality Control Checklist
+
+### Content Review
+
+**Clarity**:
+- [ ] Main message immediately clear
+- [ ] All acronyms defined
+- [ ] Sentences short and direct
+- [ ] No unnecessary jargon
+
+**Completeness**:
+- [ ] Research question/objective stated
+- [ ] Methods sufficiently described
+- [ ] Key results presented
+- [ ] Conclusions drawn
+- [ ] Limitations acknowledged
+
+**Accuracy**:
+- [ ] All statistics correct
+- [ ] Figure captions accurate
+- [ ] References properly cited
+- [ ] No overstated claims
+
+**Engagement**:
+- [ ] Compelling title
+- [ ] Visual interest
+- [ ] Clear take-home message
+- [ ] Conversation starters
+
+### Readability Testing
+
+**Distance Test**:
+- Print at 25% scale
+- View from 2-3 feet (simulates 8-12 feet for full poster)
+- Can you read: Title? Section headers? Body text?
+
+**Scan Test**:
+- Give poster to colleague for 30 seconds
+- Ask: "What is this poster about?"
+- They should identify: Topic, approach, main finding
+
+**Detail Test**:
+- Ask colleague to read poster thoroughly (5 min)
+- Ask: "What are the key conclusions?"
+- Verify understanding matches your intent
+
+## Common Content Mistakes
+
+**1. Too Much Text**
+- ❌ >1000 words
+- ❌ Long paragraphs
+- ❌ Full paper condensed
+- ✅ 300-800 words, bullet points, key findings only
+
+**2. Unclear Message**
+- ❌ Multiple unrelated findings
+- ❌ No clear conclusion
+- ❌ Vague implications
+- ✅ 1-3 main points, explicit conclusions
+
+**3. Methods Overkill**
+- ❌ Detailed protocols
+- ❌ All parameters listed
+- ❌ Routine procedures described
+- ✅ Visual flowchart, key details only
+
+**4. Poor Figure Integration**
+- ❌ Figures without context
+- ❌ Unclear captions
+- ❌ Text doesn't reference figures
+- ✅ Figures central, well-captioned, text integrated
+
+**5. Missing Context**
+- ❌ No background
+- ❌ Undefined acronyms
+- ❌ Assumes expert knowledge
+- ✅ Brief context, definitions, accessible to broader audience
+
+## Conclusion
+
+Effective poster content:
+- **Concise**: 300-800 words maximum
+- **Visual**: 40-50% figures and graphics
+- **Clear**: One main message, 3-5 key findings
+- **Engaging**: Compelling story, not just facts
+- **Accessible**: Appropriate for target audience
+- **Actionable**: Clear implications and next steps
+
+Remember: Your poster is a conversation starter, not a comprehensive treatise. Design content to intrigue, engage, and invite discussion.
+