@pikaa-ai/pikaa 0.3.23 → 0.3.24

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (191) hide show
  1. package/assets/brand/orbit-logo-option4-whale.jpg +0 -0
  2. package/assets/brand/orbit-logo.jpg +0 -0
  3. package/assets/brand/orbit-logo.png +0 -0
  4. package/assets/brand/orbit-logo.svg +3 -0
  5. package/dist/cli.js +337 -162
  6. package/dist/index.js +1 -2
  7. package/package.json +1 -2
  8. package/skills/adaptyv/SKILL.md +0 -240
  9. package/skills/aeon/SKILL.md +0 -402
  10. package/skills/analytical-method-validation/SKILL.md +0 -299
  11. package/skills/anndata/SKILL.md +0 -431
  12. package/skills/arbor/SKILL.md +0 -152
  13. package/skills/arboreto/SKILL.md +0 -267
  14. package/skills/astropy/SKILL.md +0 -353
  15. package/skills/autoskill/SKILL.md +0 -233
  16. package/skills/benchling-integration/SKILL.md +0 -229
  17. package/skills/bgpt-paper-search/SKILL.md +0 -75
  18. package/skills/bids/SKILL.md +0 -237
  19. package/skills/biopython/SKILL.md +0 -472
  20. package/skills/bioservices/SKILL.md +0 -399
  21. package/skills/bulk-rnaseq/SKILL.md +0 -198
  22. package/skills/cellxgene-census/SKILL.md +0 -283
  23. package/skills/cirq/SKILL.md +0 -370
  24. package/skills/citation-management/SKILL.md +0 -329
  25. package/skills/clinical-decision-support/SKILL.md +0 -238
  26. package/skills/clinical-decision-support/references/README.md +0 -62
  27. package/skills/clinical-reports/SKILL.md +0 -248
  28. package/skills/clinical-reports/references/README.md +0 -34
  29. package/skills/cobrapy/SKILL.md +0 -496
  30. package/skills/consciousness-council/SKILL.md +0 -151
  31. package/skills/dask/SKILL.md +0 -482
  32. package/skills/database-lookup/SKILL.md +0 -386
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  34. package/skills/deepchem/SKILL.md +0 -244
  35. package/skills/deepspot-m/SKILL.md +0 -175
  36. package/skills/deeptools/SKILL.md +0 -412
  37. package/skills/depmap/SKILL.md +0 -301
  38. package/skills/dhdna-profiler/SKILL.md +0 -184
  39. package/skills/diffdock/SKILL.md +0 -488
  40. package/skills/dnanexus-integration/SKILL.md +0 -325
  41. package/skills/docx/SKILL.md +0 -99
  42. package/skills/esm/SKILL.md +0 -334
  43. package/skills/etetoolkit/SKILL.md +0 -327
  44. package/skills/exa-search/SKILL.md +0 -102
  45. package/skills/executing-plans/SKILL.md +0 -14
  46. package/skills/experimental-design/SKILL.md +0 -234
  47. package/skills/exploratory-data-analysis/SKILL.md +0 -280
  48. package/skills/flowio/SKILL.md +0 -310
  49. package/skills/fluidsim/SKILL.md +0 -279
  50. package/skills/frontend-design/SKILL.md +0 -100
  51. package/skills/generate-image/SKILL.md +0 -304
  52. package/skills/geniml/SKILL.md +0 -310
  53. package/skills/genomic-coordinates/SKILL.md +0 -189
  54. package/skills/genomic-intelligence/SKILL.md +0 -243
  55. package/skills/geomaster/README.md +0 -105
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  57. package/skills/geopandas/SKILL.md +0 -250
  58. package/skills/get-available-resources/SKILL.md +0 -260
  59. package/skills/gget/SKILL.md +0 -153
  60. package/skills/ginkgo-cloud-lab/SKILL.md +0 -106
  61. package/skills/glycoengineering/SKILL.md +0 -339
  62. package/skills/gtars/SKILL.md +0 -282
  63. package/skills/guardian-rails/SKILL.md +0 -54
  64. package/skills/histolab/SKILL.md +0 -243
  65. package/skills/hugging-science/SKILL.md +0 -132
  66. package/skills/hypogenic/SKILL.md +0 -290
  67. package/skills/hypothesis-generation/SKILL.md +0 -264
  68. package/skills/imaging-data-commons/SKILL.md +0 -496
  69. package/skills/infographics/SKILL.md +0 -315
  70. package/skills/iso-standards-readiness/SKILL.md +0 -352
  71. package/skills/lab-hardware-cad/SKILL.md +0 -372
  72. package/skills/labarchive-integration/SKILL.md +0 -216
  73. package/skills/lamindb/SKILL.md +0 -408
  74. package/skills/latchbio-integration/SKILL.md +0 -227
  75. package/skills/latex-posters/SKILL.md +0 -369
  76. package/skills/latex-posters/references/README.md +0 -439
  77. package/skills/liteparse/SKILL.md +0 -295
  78. package/skills/literature-review/SKILL.md +0 -263
  79. package/skills/markdown-mermaid-writing/SKILL.md +0 -322
  80. package/skills/market-research-reports/SKILL.md +0 -337
  81. package/skills/markitdown/SKILL.md +0 -264
  82. package/skills/matchms/SKILL.md +0 -276
  83. package/skills/matlab/SKILL.md +0 -274
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  85. package/skills/medchem/SKILL.md +0 -321
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  92. package/skills/neuropixels-analysis/SKILL.md +0 -412
  93. package/skills/nextflow/SKILL.md +0 -195
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  117. package/skills/pkpd-modeling/SKILL.md +0 -381
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  123. package/skills/pptx-posters/SKILL.md +0 -258
  124. package/skills/primekg/SKILL.md +0 -99
  125. package/skills/protocolsio-integration/SKILL.md +0 -236
  126. package/skills/pufferlib/SKILL.md +0 -328
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  130. package/skills/pylabrobot/SKILL.md +0 -216
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  142. package/skills/relsa-severity-assessment/SKILL.md +0 -354
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  156. package/skills/scikit-bio/SKILL.md +0 -470
  157. package/skills/scikit-learn/SKILL.md +0 -324
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  174. package/skills/timesfm-forecasting/SKILL.md +0 -408
  175. package/skills/timesfm-forecasting/examples/global-temperature/README.md +0 -178
  176. package/skills/torch-geometric/SKILL.md +0 -458
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  178. package/skills/transformers/SKILL.md +0 -195
  179. package/skills/treatment-plans/SKILL.md +0 -174
  180. package/skills/treatment-plans/references/README.md +0 -19
  181. package/skills/umap-learn/SKILL.md +0 -488
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  190. package/skills/xlsx/SKILL.md +0 -110
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@@ -1,439 +0,0 @@
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- # LaTeX Research Poster Generation Skill
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-
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- Create professional, publication-ready research posters for conferences and academic presentations using LaTeX.
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-
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- ## Overview
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-
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- This skill provides comprehensive guidance for creating research posters with three major LaTeX packages:
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- - **beamerposter**: Traditional academic posters, familiar Beamer syntax
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- - **tikzposter**: Modern, colorful designs with TikZ integration
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- - **baposter**: Structured multi-column layouts with automatic positioning
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-
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- ## Quick Start
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-
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- ### 1. Choose a Template
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-
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- Browse templates in `assets/`:
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- - `beamerposter_template.tex` - Classic academic style
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- - `tikzposter_template.tex` - Modern, colorful design
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- - `baposter_template.tex` - Structured multi-column layout
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-
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- ### 2. Customize Content
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-
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- Edit the template with your research:
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- - Title, authors, affiliations
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- - Introduction, methods, results, conclusions
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- - Replace placeholder figures with your images
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- - Update references and acknowledgments
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-
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- ### 3. Configure for Full Page
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- Posters should span the entire page with minimal margins:
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-
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- ```latex
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- % beamerposter - full page setup
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- \documentclass[final,t]{beamer}
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- \usepackage[size=a0,scale=1.4,orientation=portrait]{beamerposter}
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- \setbeamersize{text margin left=5mm, text margin right=5mm}
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- \usepackage[margin=10mm]{geometry}
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-
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- % tikzposter - full page setup
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- \documentclass[25pt,a0paper,portrait,margin=10mm,innermargin=15mm]{tikzposter}
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-
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- % baposter - full page setup
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- \documentclass[a0paper,portrait,fontscale=0.285]{baposter}
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- ```
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-
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- ### 4. Compile
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- ```bash
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- pdflatex poster.tex
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-
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- # Or for better font support:
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- lualatex poster.tex
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- xelatex poster.tex
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- ```
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-
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- ### 5. Review PDF Quality
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- **Essential before printing!**
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- ```bash
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- # Run automated checks
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- ./scripts/review_poster.sh poster.pdf
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-
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- # Manual verification (see checklist below)
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- ```
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-
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- ## Key Features
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-
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- ### Full Page Coverage
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- All templates configured to maximize content area:
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- - Minimal outer margins (5-15mm)
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- - Optimal spacing between columns (15-20mm)
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- - Proper block padding for readability
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- - No wasted white space
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-
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- ### PDF Quality Control
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- **Automated Checks** (`review_poster.sh`):
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- - Page size verification
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- - Font embedding check
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- - Image resolution analysis
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- - File size optimization
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-
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- **Manual Verification** (`assets/poster_quality_checklist.md`):
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- - Visual inspection at 100% zoom
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- - Reduced-scale print test (25%)
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- - Typography and spacing review
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- - Content completeness check
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-
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- ### Design Principles
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- All templates follow evidence-based poster design:
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- - **Typography**: 72pt+ title, 48-72pt headers, 24-36pt body text
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- - **Color**: High contrast (≥4.5:1), color-blind friendly palettes
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- - **Layout**: Clear visual hierarchy, logical flow
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- - **Content**: 300-800 words maximum, 40-50% visual content
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-
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- ## Common Poster Sizes
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- Templates support all standard sizes:
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- | Size | Dimensions | Configuration |
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- |------|------------|---------------|
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- | A0 | 841 × 1189 mm | `size=a0` or `a0paper` |
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- | A1 | 594 × 841 mm | `size=a1` or `a1paper` |
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- | 36×48" | 914 × 1219 mm | Custom page size |
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- | 42×56" | 1067 × 1422 mm | Custom page size |
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-
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- ## Documentation
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-
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- ### Reference Guides
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- **Comprehensive Documentation** (in `references/`):
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- 1. **`latex_poster_packages.md`** (746 lines)
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- - Detailed comparison of beamerposter, tikzposter, baposter
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- - Package-specific syntax and examples
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- - Strengths, limitations, best use cases
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- - Theme and color customization
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- - Compilation tips and troubleshooting
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- 2. **`poster_design_principles.md`** (807 lines)
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- - Visual hierarchy and white space
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- - Typography: font selection, sizing, readability
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- - Color theory: schemes, contrast, accessibility
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- - Color-blind friendly palettes
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- - Icons, graphics, and visual elements
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- - Common design mistakes to avoid
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- 3. **`poster_layout_design.md`** (650+ lines)
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- - Grid systems (2, 3, 4-column layouts)
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- - Visual flow and reading patterns
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- - Spatial organization strategies
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- - White space management
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- - Block and box design
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- - Layout patterns by research type
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- 4. **`poster_content_guide.md`** (900+ lines)
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- - Content strategy (3-5 minute rule)
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- - Word budgets by section
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- - Visual-to-text ratio (40-50% visual)
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- - Section-specific writing guidance
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- - Figure integration and captions
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- - From paper to poster adaptation
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- 5. **`ai_graphics_for_posters.md`**
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- - Hard limits on elements, words, white space, and font sizes
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- - Per-graphic-type content limits with worked before/after prompts
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- - The mandatory pre- and post-generation review gates
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- - Patterns that always fail, and how to split them
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- 6. **`latex_poster_reference.md`**
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- - Package selection, layout, and standard poster sizes
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- - Figure and image integration, QR codes
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- - Color schemes and typography
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- 7. **`compilation_and_quality_control.md`**
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- - Compilation engines and bibliography handling
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- - Page-size verification and overflow detection
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- - Reduced-scale test prints, font embedding, image DPI, file size
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- - Log-warning triage
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- 8. **`poster_patterns_and_presentation.md`**
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- - Reusable content patterns per poster section
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- - Accessibility and inclusive design
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- - Presentation-day guidance
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- ### Tools and Assets
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- **Scripts** (in `scripts/`):
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- - `review_poster.sh`: Automated PDF quality check
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- - Page size verification
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- - Font embedding check
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- - Image resolution analysis
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- - File size assessment
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- **Checklists** (in `assets/`):
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- - `poster_quality_checklist.md`: Comprehensive pre-printing checklist
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- - Pre-compilation checks
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- - PDF quality verification
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- - Visual inspection items
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- - Accessibility checks
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- - Peer review guidelines
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- - Final printing checklist
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- **Templates** (in `assets/`):
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- - `beamerposter_template.tex`: Full working template
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- - `tikzposter_template.tex`: Full working template
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- - `baposter_template.tex`: Full working template
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- ## Workflow
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- ### Recommended Poster Creation Process
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- **1. Planning** (before LaTeX)
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- - Determine conference requirements (size, orientation)
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- - Identify 3-5 key results to highlight
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- - Create figures (300+ DPI)
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- - Draft 300-800 word content outline
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- **2. Template Selection**
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- - Choose package based on needs:
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- - **beamerposter**: Traditional conferences, institutional branding
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- - **tikzposter**: Modern conferences, creative fields
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- - **baposter**: Multi-section posters, structured layouts
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- **3. Content Integration**
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- - Copy template and customize
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- - Replace placeholder text
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- - Add figures and ensure high resolution
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- - Configure colors to match branding
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- **4. Compilation & Review**
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- - Compile to PDF
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- - Run `review_poster.sh` for automated checks
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- - Review visually at 100% zoom
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- - Check against `poster_quality_checklist.md`
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- **5. Test Print**
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- - **Critical step!** Print at 25% scale
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- - A0 → A4 paper, 36×48" → Letter paper
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- - View from 2-3 feet (simulates 8-12 feet for full poster)
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- - Verify readability and colors
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- **6. Revisions**
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- - Fix any issues identified
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- - Proofread carefully (errors are magnified!)
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- - Get colleague feedback
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- - Final compilation
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- **7. Printing**
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- - Verify page size: `pdfinfo poster.pdf`
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- - Check fonts embedded: `pdffonts poster.pdf`
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- - Send to professional printer 2-3 days before deadline
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- - Keep backup copy
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- ## Troubleshooting
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- ### Large White Margins
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- **Problem**: Excessive white space around poster edges
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- **Solution**:
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- ```latex
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- % beamerposter
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- \setbeamersize{text margin left=5mm, text margin right=5mm}
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- \usepackage[margin=10mm]{geometry}
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- % tikzposter
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- \documentclass[..., margin=5mm, innermargin=10mm]{tikzposter}
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- % baposter
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- \documentclass[a0paper, margin=5mm]{baposter}
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- ```
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- ### Content Cut Off
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- **Problem**: Text or figures extending beyond page
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- **Solution**:
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- - Check total width: columns + spacing + margins = pagewidth
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- - Reduce column widths or spacing
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- - Debug with visible page boundary:
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- ```latex
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- \usepackage{eso-pic}
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- \AddToShipoutPictureBG{
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- \AtPageLowerLeft{
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- \put(0,0){\framebox(\LenToUnit{\paperwidth},\LenToUnit{\paperheight}){}}
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- }
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- }
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- ```
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- ### Blurry Images
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- **Problem**: Pixelated or low-quality figures
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- **Solution**:
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- - Use vector graphics (PDF, SVG) when possible
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- - Raster images: minimum 300 DPI at final print size
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- - For A0 width (33.1"): 300 DPI = 9930 pixels minimum
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- - Check with: `pdfimages -list poster.pdf`
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- ### Fonts Not Embedded
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- **Problem**: Printer rejects PDF due to missing fonts
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- **Solution**:
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- ```bash
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- # Recompile with embedded fonts
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- pdflatex -dEmbedAllFonts=true poster.tex
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-
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- # Verify embedding
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- pdffonts poster.pdf
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- # All fonts should show "yes" in "emb" column
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- ```
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-
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- ### File Too Large
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-
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- **Problem**: PDF exceeds email size limit (>50MB)
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-
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- **Solution**:
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- ```bash
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- # Compress for digital sharing
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- gs -sDEVICE=pdfwrite -dCompatibilityLevel=1.4 \
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- -dPDFSETTINGS=/printer -dNOPAUSE -dQUIET -dBATCH \
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- -sOutputFile=poster_compressed.pdf poster.pdf
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-
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- # Keep original uncompressed version for printing
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- ```
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-
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- ## Common Mistakes to Avoid
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-
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- ### Content
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- - ❌ Too much text (>1000 words)
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- - ❌ Font sizes too small (<24pt body text)
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- - ❌ No clear main message
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- - ✅ 300-800 words, 30pt+ body text, 1-3 key findings
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-
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- ### Design
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- - ❌ Poor color contrast (<4.5:1)
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- - ❌ Red-green color combinations (color-blind issue)
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- - ❌ Cluttered layout with no white space
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- - ✅ High contrast, accessible colors, generous spacing
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-
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- ### Technical
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- - ❌ Wrong poster dimensions
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- - ❌ Low resolution images (<300 DPI)
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- - ❌ Fonts not embedded
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- - ✅ Verify specs, high-res images, embedded fonts
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-
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- ## Package Comparison
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-
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- Quick reference for choosing the right package:
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-
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- | Feature | beamerposter | tikzposter | baposter |
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- |---------|--------------|------------|----------|
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- | **Learning Curve** | Easy (Beamer users) | Moderate | Moderate |
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- | **Aesthetics** | Traditional | Modern | Professional |
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- | **Customization** | Moderate | High (TikZ) | Structured |
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- | **Compilation Speed** | Fast | Slower | Fast-Medium |
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- | **Best For** | Academic conferences | Creative designs | Multi-column layouts |
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-
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- **Recommendation**:
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- - First-time poster makers: **beamerposter** (familiar, simple)
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- - Modern conferences: **tikzposter** (beautiful, flexible)
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- - Complex layouts: **baposter** (automatic positioning)
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-
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- ## Example Usage
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-
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- ### In Scientific Writer CLI
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-
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- ```
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- > Create a research poster for NeurIPS conference on transformer attention
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-
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- The assistant will:
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- 1. Ask about poster size and orientation
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- 2. Generate complete LaTeX poster with your content
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- 3. Configure for full page coverage
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- 4. Provide compilation instructions
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- 5. Run quality checks on generated PDF
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- ```
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-
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- ### Manual Creation
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-
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- ```bash
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- # 1. Copy template
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- cp assets/tikzposter_template.tex my_poster.tex
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-
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- # 2. Edit content
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- vim my_poster.tex
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-
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- # 3. Compile
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- pdflatex my_poster.tex
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-
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- # 4. Review
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- ./scripts/review_poster.sh my_poster.pdf
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-
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- # 5. Test print at 25% scale
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- # (A0 on A4 paper)
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-
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- # 6. Final printing
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- ```
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-
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- ## Tips for Success
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-
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- ### Content Strategy
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- 1. **One main message**: What's the one thing viewers should remember?
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- 2. **3-5 key figures**: Visual content dominates
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- 3. **300-800 words**: Less is more
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- 4. **Bullet points**: More scannable than paragraphs
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-
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- ### Design Strategy
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- 1. **High contrast**: Dark on light or light on dark
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- 2. **Large fonts**: 30pt+ body text for readability from distance
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- 3. **White space**: 30-40% of poster should be empty
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- 4. **Visual hierarchy**: Vary sizes significantly (title 3× body text)
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-
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- ### Technical Strategy
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- 1. **Test early**: Print at 25% scale before final printing
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- 2. **Vector graphics**: Use PDF/SVG when possible
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- 3. **Verify specs**: Check page size, fonts, resolution
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- 4. **Get feedback**: Ask colleague to review before printing
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-
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- ## Additional Resources
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-
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- ### Online Tools
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- - **Color contrast checker**: https://webaim.org/resources/contrastchecker/
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- - **Color blindness simulator**: https://www.color-blindness.com/coblis-color-blindness-simulator/
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- - **Color palette generator**: https://coolors.co/
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-
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- ### LaTeX Packages
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- - `beamerposter`: Extends Beamer for poster-sized documents
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- - `tikzposter`: Modern poster creation with TikZ
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- - `baposter`: Box-based automatic poster layout
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- - `qrcode`: Generate QR codes in LaTeX
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- - `graphicx`: Include images
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- - `tcolorbox`: Colored boxes and frames
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-
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- ### Further Reading
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- - All reference documents in `references/` directory
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- - Quality checklist in `assets/poster_quality_checklist.md`
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- - Package comparison in `references/latex_poster_packages.md`
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-
426
- ## Support
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-
428
- For issues or questions:
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- - Review reference documentation in `references/`
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- - Check troubleshooting section above
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- - Run automated review: `./scripts/review_poster.sh`
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- - Use quality checklist: `assets/poster_quality_checklist.md`
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-
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- ## Version
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-
436
- LaTeX Poster Skill v1.0
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- Compatible with: beamerposter, tikzposter, baposter
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- Last updated: January 2025
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-