scientific-writer 2.2.1__py3-none-any.whl → 2.2.3__py3-none-any.whl

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  1. scientific_writer/.claude/WRITER.md +748 -0
  2. scientific_writer/.claude/settings.local.json +30 -0
  3. scientific_writer/.claude/skills/citation-management/SKILL.md +1046 -0
  4. scientific_writer/.claude/skills/citation-management/assets/bibtex_template.bib +264 -0
  5. scientific_writer/.claude/skills/citation-management/assets/citation_checklist.md +386 -0
  6. scientific_writer/.claude/skills/citation-management/references/bibtex_formatting.md +908 -0
  7. scientific_writer/.claude/skills/citation-management/references/citation_validation.md +794 -0
  8. scientific_writer/.claude/skills/citation-management/references/google_scholar_search.md +725 -0
  9. scientific_writer/.claude/skills/citation-management/references/metadata_extraction.md +870 -0
  10. scientific_writer/.claude/skills/citation-management/references/pubmed_search.md +839 -0
  11. scientific_writer/.claude/skills/citation-management/scripts/doi_to_bibtex.py +204 -0
  12. scientific_writer/.claude/skills/citation-management/scripts/extract_metadata.py +569 -0
  13. scientific_writer/.claude/skills/citation-management/scripts/format_bibtex.py +349 -0
  14. scientific_writer/.claude/skills/citation-management/scripts/search_google_scholar.py +282 -0
  15. scientific_writer/.claude/skills/citation-management/scripts/search_pubmed.py +398 -0
  16. scientific_writer/.claude/skills/citation-management/scripts/validate_citations.py +497 -0
  17. scientific_writer/.claude/skills/clinical-reports/IMPLEMENTATION_SUMMARY.md +641 -0
  18. scientific_writer/.claude/skills/clinical-reports/README.md +236 -0
  19. scientific_writer/.claude/skills/clinical-reports/SKILL.md +1088 -0
  20. scientific_writer/.claude/skills/clinical-reports/assets/case_report_template.md +352 -0
  21. scientific_writer/.claude/skills/clinical-reports/assets/clinical_trial_csr_template.md +353 -0
  22. scientific_writer/.claude/skills/clinical-reports/assets/clinical_trial_sae_template.md +359 -0
  23. scientific_writer/.claude/skills/clinical-reports/assets/consult_note_template.md +305 -0
  24. scientific_writer/.claude/skills/clinical-reports/assets/discharge_summary_template.md +453 -0
  25. scientific_writer/.claude/skills/clinical-reports/assets/hipaa_compliance_checklist.md +395 -0
  26. scientific_writer/.claude/skills/clinical-reports/assets/history_physical_template.md +305 -0
  27. scientific_writer/.claude/skills/clinical-reports/assets/lab_report_template.md +309 -0
  28. scientific_writer/.claude/skills/clinical-reports/assets/pathology_report_template.md +249 -0
  29. scientific_writer/.claude/skills/clinical-reports/assets/quality_checklist.md +338 -0
  30. scientific_writer/.claude/skills/clinical-reports/assets/radiology_report_template.md +318 -0
  31. scientific_writer/.claude/skills/clinical-reports/assets/soap_note_template.md +253 -0
  32. scientific_writer/.claude/skills/clinical-reports/references/case_report_guidelines.md +570 -0
  33. scientific_writer/.claude/skills/clinical-reports/references/clinical_trial_reporting.md +693 -0
  34. scientific_writer/.claude/skills/clinical-reports/references/data_presentation.md +530 -0
  35. scientific_writer/.claude/skills/clinical-reports/references/diagnostic_reports_standards.md +629 -0
  36. scientific_writer/.claude/skills/clinical-reports/references/medical_terminology.md +588 -0
  37. scientific_writer/.claude/skills/clinical-reports/references/patient_documentation.md +744 -0
  38. scientific_writer/.claude/skills/clinical-reports/references/peer_review_standards.md +585 -0
  39. scientific_writer/.claude/skills/clinical-reports/references/regulatory_compliance.md +577 -0
  40. scientific_writer/.claude/skills/clinical-reports/scripts/check_deidentification.py +346 -0
  41. scientific_writer/.claude/skills/clinical-reports/scripts/compliance_checker.py +78 -0
  42. scientific_writer/.claude/skills/clinical-reports/scripts/extract_clinical_data.py +102 -0
  43. scientific_writer/.claude/skills/clinical-reports/scripts/format_adverse_events.py +103 -0
  44. scientific_writer/.claude/skills/clinical-reports/scripts/generate_report_template.py +163 -0
  45. scientific_writer/.claude/skills/clinical-reports/scripts/terminology_validator.py +133 -0
  46. scientific_writer/.claude/skills/clinical-reports/scripts/validate_case_report.py +334 -0
  47. scientific_writer/.claude/skills/clinical-reports/scripts/validate_trial_report.py +89 -0
  48. scientific_writer/.claude/skills/document-skills/docx/LICENSE.txt +30 -0
  49. scientific_writer/.claude/skills/document-skills/docx/SKILL.md +197 -0
  50. scientific_writer/.claude/skills/document-skills/docx/docx-js.md +350 -0
  51. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
  52. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
  53. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
  54. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
  55. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
  56. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
  57. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
  58. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
  59. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
  60. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
  61. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
  62. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
  63. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
  64. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
  65. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
  66. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
  67. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
  68. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
  69. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
  70. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
  71. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
  72. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
  73. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
  74. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
  75. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
  76. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
  77. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
  78. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
  79. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
  80. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
  81. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
  82. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/mce/mc.xsd +75 -0
  83. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2010.xsd +560 -0
  84. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2012.xsd +67 -0
  85. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2018.xsd +14 -0
  86. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-cex-2018.xsd +20 -0
  87. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-cid-2016.xsd +13 -0
  88. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
  89. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-symex-2015.xsd +8 -0
  90. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/pack.py +159 -0
  91. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/unpack.py +29 -0
  92. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validate.py +69 -0
  93. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/__init__.py +15 -0
  94. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/base.py +951 -0
  95. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/docx.py +274 -0
  96. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/pptx.py +315 -0
  97. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/redlining.py +279 -0
  98. scientific_writer/.claude/skills/document-skills/docx/ooxml.md +610 -0
  99. scientific_writer/.claude/skills/document-skills/docx/scripts/__init__.py +1 -0
  100. scientific_writer/.claude/skills/document-skills/docx/scripts/document.py +1276 -0
  101. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/comments.xml +3 -0
  102. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/commentsExtended.xml +3 -0
  103. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/commentsExtensible.xml +3 -0
  104. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/commentsIds.xml +3 -0
  105. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/people.xml +3 -0
  106. scientific_writer/.claude/skills/document-skills/docx/scripts/utilities.py +374 -0
  107. scientific_writer/.claude/skills/document-skills/pdf/LICENSE.txt +30 -0
  108. scientific_writer/.claude/skills/document-skills/pdf/SKILL.md +294 -0
  109. scientific_writer/.claude/skills/document-skills/pdf/forms.md +205 -0
  110. scientific_writer/.claude/skills/document-skills/pdf/reference.md +612 -0
  111. scientific_writer/.claude/skills/document-skills/pdf/scripts/check_bounding_boxes.py +70 -0
  112. scientific_writer/.claude/skills/document-skills/pdf/scripts/check_bounding_boxes_test.py +226 -0
  113. scientific_writer/.claude/skills/document-skills/pdf/scripts/check_fillable_fields.py +12 -0
  114. scientific_writer/.claude/skills/document-skills/pdf/scripts/convert_pdf_to_images.py +35 -0
  115. scientific_writer/.claude/skills/document-skills/pdf/scripts/create_validation_image.py +41 -0
  116. scientific_writer/.claude/skills/document-skills/pdf/scripts/extract_form_field_info.py +152 -0
  117. scientific_writer/.claude/skills/document-skills/pdf/scripts/fill_fillable_fields.py +114 -0
  118. scientific_writer/.claude/skills/document-skills/pdf/scripts/fill_pdf_form_with_annotations.py +108 -0
  119. scientific_writer/.claude/skills/document-skills/pptx/LICENSE.txt +30 -0
  120. scientific_writer/.claude/skills/document-skills/pptx/SKILL.md +484 -0
  121. scientific_writer/.claude/skills/document-skills/pptx/html2pptx.md +625 -0
  122. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
  123. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
  124. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
  125. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
  126. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
  127. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
  128. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
  129. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
  130. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
  131. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
  132. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
  133. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
  134. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
  135. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
  136. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
  137. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
  138. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
  139. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
  140. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
  141. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
  142. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
  143. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
  144. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
  145. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
  146. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
  147. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
  148. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
  149. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
  150. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
  151. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
  152. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
  153. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/mce/mc.xsd +75 -0
  154. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2010.xsd +560 -0
  155. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2012.xsd +67 -0
  156. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2018.xsd +14 -0
  157. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-cex-2018.xsd +20 -0
  158. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-cid-2016.xsd +13 -0
  159. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
  160. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-symex-2015.xsd +8 -0
  161. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/pack.py +159 -0
  162. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/unpack.py +29 -0
  163. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validate.py +69 -0
  164. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/__init__.py +15 -0
  165. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/base.py +951 -0
  166. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/docx.py +274 -0
  167. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/pptx.py +315 -0
  168. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/redlining.py +279 -0
  169. scientific_writer/.claude/skills/document-skills/pptx/ooxml.md +427 -0
  170. scientific_writer/.claude/skills/document-skills/pptx/scripts/html2pptx.js +979 -0
  171. scientific_writer/.claude/skills/document-skills/pptx/scripts/inventory.py +1020 -0
  172. scientific_writer/.claude/skills/document-skills/pptx/scripts/rearrange.py +231 -0
  173. scientific_writer/.claude/skills/document-skills/pptx/scripts/replace.py +385 -0
  174. scientific_writer/.claude/skills/document-skills/pptx/scripts/thumbnail.py +450 -0
  175. scientific_writer/.claude/skills/document-skills/xlsx/LICENSE.txt +30 -0
  176. scientific_writer/.claude/skills/document-skills/xlsx/SKILL.md +289 -0
  177. scientific_writer/.claude/skills/document-skills/xlsx/recalc.py +178 -0
  178. scientific_writer/.claude/skills/hypothesis-generation/SKILL.md +155 -0
  179. scientific_writer/.claude/skills/hypothesis-generation/assets/hypothesis_output_template.md +302 -0
  180. scientific_writer/.claude/skills/hypothesis-generation/references/experimental_design_patterns.md +327 -0
  181. scientific_writer/.claude/skills/hypothesis-generation/references/hypothesis_quality_criteria.md +196 -0
  182. scientific_writer/.claude/skills/hypothesis-generation/references/literature_search_strategies.md +505 -0
  183. scientific_writer/.claude/skills/latex-posters/README.md +417 -0
  184. scientific_writer/.claude/skills/latex-posters/SKILL.md +919 -0
  185. scientific_writer/.claude/skills/latex-posters/assets/baposter_template.tex +257 -0
  186. scientific_writer/.claude/skills/latex-posters/assets/beamerposter_template.tex +244 -0
  187. scientific_writer/.claude/skills/latex-posters/assets/poster_quality_checklist.md +358 -0
  188. scientific_writer/.claude/skills/latex-posters/assets/tikzposter_template.tex +251 -0
  189. scientific_writer/.claude/skills/latex-posters/references/latex_poster_packages.md +745 -0
  190. scientific_writer/.claude/skills/latex-posters/references/poster_content_guide.md +748 -0
  191. scientific_writer/.claude/skills/latex-posters/references/poster_design_principles.md +806 -0
  192. scientific_writer/.claude/skills/latex-posters/references/poster_layout_design.md +900 -0
  193. scientific_writer/.claude/skills/latex-posters/scripts/review_poster.sh +214 -0
  194. scientific_writer/.claude/skills/literature-review/SKILL.md +546 -0
  195. scientific_writer/.claude/skills/literature-review/assets/review_template.md +412 -0
  196. scientific_writer/.claude/skills/literature-review/references/citation_styles.md +166 -0
  197. scientific_writer/.claude/skills/literature-review/references/database_strategies.md +381 -0
  198. scientific_writer/.claude/skills/literature-review/scripts/generate_pdf.py +176 -0
  199. scientific_writer/.claude/skills/literature-review/scripts/search_databases.py +303 -0
  200. scientific_writer/.claude/skills/literature-review/scripts/verify_citations.py +222 -0
  201. scientific_writer/.claude/skills/markitdown/INSTALLATION_GUIDE.md +318 -0
  202. scientific_writer/.claude/skills/markitdown/LICENSE.txt +22 -0
  203. scientific_writer/.claude/skills/markitdown/OPENROUTER_INTEGRATION.md +359 -0
  204. scientific_writer/.claude/skills/markitdown/QUICK_REFERENCE.md +309 -0
  205. scientific_writer/.claude/skills/markitdown/README.md +184 -0
  206. scientific_writer/.claude/skills/markitdown/SKILL.md +450 -0
  207. scientific_writer/.claude/skills/markitdown/SKILL_SUMMARY.md +307 -0
  208. scientific_writer/.claude/skills/markitdown/assets/example_usage.md +463 -0
  209. scientific_writer/.claude/skills/markitdown/references/api_reference.md +399 -0
  210. scientific_writer/.claude/skills/markitdown/references/file_formats.md +542 -0
  211. scientific_writer/.claude/skills/markitdown/scripts/batch_convert.py +228 -0
  212. scientific_writer/.claude/skills/markitdown/scripts/convert_literature.py +283 -0
  213. scientific_writer/.claude/skills/markitdown/scripts/convert_with_ai.py +243 -0
  214. scientific_writer/.claude/skills/paper-2-web/SKILL.md +455 -0
  215. scientific_writer/.claude/skills/paper-2-web/references/installation.md +141 -0
  216. scientific_writer/.claude/skills/paper-2-web/references/paper2poster.md +346 -0
  217. scientific_writer/.claude/skills/paper-2-web/references/paper2video.md +305 -0
  218. scientific_writer/.claude/skills/paper-2-web/references/paper2web.md +187 -0
  219. scientific_writer/.claude/skills/paper-2-web/references/usage_examples.md +436 -0
  220. scientific_writer/.claude/skills/peer-review/SKILL.md +375 -0
  221. scientific_writer/.claude/skills/peer-review/references/common_issues.md +552 -0
  222. scientific_writer/.claude/skills/peer-review/references/reporting_standards.md +290 -0
  223. scientific_writer/.claude/skills/research-grants/README.md +285 -0
  224. scientific_writer/.claude/skills/research-grants/SKILL.md +896 -0
  225. scientific_writer/.claude/skills/research-grants/assets/budget_justification_template.md +453 -0
  226. scientific_writer/.claude/skills/research-grants/assets/nih_specific_aims_template.md +166 -0
  227. scientific_writer/.claude/skills/research-grants/assets/nsf_project_summary_template.md +92 -0
  228. scientific_writer/.claude/skills/research-grants/references/broader_impacts.md +392 -0
  229. scientific_writer/.claude/skills/research-grants/references/darpa_guidelines.md +636 -0
  230. scientific_writer/.claude/skills/research-grants/references/doe_guidelines.md +586 -0
  231. scientific_writer/.claude/skills/research-grants/references/nih_guidelines.md +851 -0
  232. scientific_writer/.claude/skills/research-grants/references/nsf_guidelines.md +570 -0
  233. scientific_writer/.claude/skills/research-grants/references/specific_aims_guide.md +458 -0
  234. scientific_writer/.claude/skills/research-lookup/README.md +116 -0
  235. scientific_writer/.claude/skills/research-lookup/SKILL.md +443 -0
  236. scientific_writer/.claude/skills/research-lookup/examples.py +174 -0
  237. scientific_writer/.claude/skills/research-lookup/lookup.py +93 -0
  238. scientific_writer/.claude/skills/research-lookup/research_lookup.py +335 -0
  239. scientific_writer/.claude/skills/research-lookup/scripts/research_lookup.py +261 -0
  240. scientific_writer/.claude/skills/scholar-evaluation/SKILL.md +254 -0
  241. scientific_writer/.claude/skills/scholar-evaluation/references/evaluation_framework.md +663 -0
  242. scientific_writer/.claude/skills/scholar-evaluation/scripts/calculate_scores.py +378 -0
  243. scientific_writer/.claude/skills/scientific-critical-thinking/SKILL.md +530 -0
  244. scientific_writer/.claude/skills/scientific-critical-thinking/references/common_biases.md +364 -0
  245. scientific_writer/.claude/skills/scientific-critical-thinking/references/evidence_hierarchy.md +484 -0
  246. scientific_writer/.claude/skills/scientific-critical-thinking/references/experimental_design.md +496 -0
  247. scientific_writer/.claude/skills/scientific-critical-thinking/references/logical_fallacies.md +478 -0
  248. scientific_writer/.claude/skills/scientific-critical-thinking/references/scientific_method.md +169 -0
  249. scientific_writer/.claude/skills/scientific-critical-thinking/references/statistical_pitfalls.md +506 -0
  250. scientific_writer/.claude/skills/scientific-schematics/SKILL.md +2035 -0
  251. scientific_writer/.claude/skills/scientific-schematics/assets/block_diagram_template.tex +199 -0
  252. scientific_writer/.claude/skills/scientific-schematics/assets/circuit_template.tex +159 -0
  253. scientific_writer/.claude/skills/scientific-schematics/assets/flowchart_template.tex +161 -0
  254. scientific_writer/.claude/skills/scientific-schematics/assets/pathway_template.tex +162 -0
  255. scientific_writer/.claude/skills/scientific-schematics/assets/tikz_styles.tex +422 -0
  256. scientific_writer/.claude/skills/scientific-schematics/references/best_practices.md +562 -0
  257. scientific_writer/.claude/skills/scientific-schematics/references/diagram_types.md +637 -0
  258. scientific_writer/.claude/skills/scientific-schematics/references/python_libraries.md +791 -0
  259. scientific_writer/.claude/skills/scientific-schematics/references/tikz_guide.md +734 -0
  260. scientific_writer/.claude/skills/scientific-schematics/scripts/circuit_generator.py +307 -0
  261. scientific_writer/.claude/skills/scientific-schematics/scripts/compile_tikz.py +292 -0
  262. scientific_writer/.claude/skills/scientific-schematics/scripts/generate_flowchart.py +281 -0
  263. scientific_writer/.claude/skills/scientific-schematics/scripts/pathway_diagram.py +406 -0
  264. scientific_writer/.claude/skills/scientific-writing/SKILL.md +443 -0
  265. scientific_writer/.claude/skills/scientific-writing/references/citation_styles.md +720 -0
  266. scientific_writer/.claude/skills/scientific-writing/references/figures_tables.md +806 -0
  267. scientific_writer/.claude/skills/scientific-writing/references/imrad_structure.md +658 -0
  268. scientific_writer/.claude/skills/scientific-writing/references/reporting_guidelines.md +748 -0
  269. scientific_writer/.claude/skills/scientific-writing/references/writing_principles.md +824 -0
  270. scientific_writer/.claude/skills/treatment-plans/README.md +483 -0
  271. scientific_writer/.claude/skills/treatment-plans/SKILL.md +817 -0
  272. scientific_writer/.claude/skills/treatment-plans/assets/chronic_disease_management_plan.tex +636 -0
  273. scientific_writer/.claude/skills/treatment-plans/assets/general_medical_treatment_plan.tex +616 -0
  274. scientific_writer/.claude/skills/treatment-plans/assets/mental_health_treatment_plan.tex +745 -0
  275. scientific_writer/.claude/skills/treatment-plans/assets/pain_management_plan.tex +770 -0
  276. scientific_writer/.claude/skills/treatment-plans/assets/perioperative_care_plan.tex +724 -0
  277. scientific_writer/.claude/skills/treatment-plans/assets/quality_checklist.md +471 -0
  278. scientific_writer/.claude/skills/treatment-plans/assets/rehabilitation_treatment_plan.tex +727 -0
  279. scientific_writer/.claude/skills/treatment-plans/references/goal_setting_frameworks.md +411 -0
  280. scientific_writer/.claude/skills/treatment-plans/references/intervention_guidelines.md +507 -0
  281. scientific_writer/.claude/skills/treatment-plans/references/regulatory_compliance.md +476 -0
  282. scientific_writer/.claude/skills/treatment-plans/references/specialty_specific_guidelines.md +607 -0
  283. scientific_writer/.claude/skills/treatment-plans/references/treatment_plan_standards.md +456 -0
  284. scientific_writer/.claude/skills/treatment-plans/scripts/check_completeness.py +318 -0
  285. scientific_writer/.claude/skills/treatment-plans/scripts/generate_template.py +244 -0
  286. scientific_writer/.claude/skills/treatment-plans/scripts/timeline_generator.py +369 -0
  287. scientific_writer/.claude/skills/treatment-plans/scripts/validate_treatment_plan.py +367 -0
  288. scientific_writer/.claude/skills/venue-templates/SKILL.md +590 -0
  289. scientific_writer/.claude/skills/venue-templates/assets/grants/nih_specific_aims.tex +235 -0
  290. scientific_writer/.claude/skills/venue-templates/assets/grants/nsf_proposal_template.tex +375 -0
  291. scientific_writer/.claude/skills/venue-templates/assets/journals/nature_article.tex +171 -0
  292. scientific_writer/.claude/skills/venue-templates/assets/journals/neurips_article.tex +283 -0
  293. scientific_writer/.claude/skills/venue-templates/assets/journals/plos_one.tex +317 -0
  294. scientific_writer/.claude/skills/venue-templates/assets/posters/beamerposter_academic.tex +311 -0
  295. scientific_writer/.claude/skills/venue-templates/references/conferences_formatting.md +564 -0
  296. scientific_writer/.claude/skills/venue-templates/references/grants_requirements.md +787 -0
  297. scientific_writer/.claude/skills/venue-templates/references/journals_formatting.md +486 -0
  298. scientific_writer/.claude/skills/venue-templates/references/posters_guidelines.md +628 -0
  299. scientific_writer/.claude/skills/venue-templates/scripts/customize_template.py +206 -0
  300. scientific_writer/.claude/skills/venue-templates/scripts/query_template.py +260 -0
  301. scientific_writer/.claude/skills/venue-templates/scripts/validate_format.py +255 -0
  302. scientific_writer/__init__.py +1 -1
  303. scientific_writer/api.py +9 -5
  304. scientific_writer/cli.py +9 -5
  305. scientific_writer/core.py +28 -5
  306. {scientific_writer-2.2.1.dist-info → scientific_writer-2.2.3.dist-info}/METADATA +1 -1
  307. scientific_writer-2.2.3.dist-info/RECORD +312 -0
  308. scientific_writer-2.2.1.dist-info/RECORD +0 -11
  309. {scientific_writer-2.2.1.dist-info → scientific_writer-2.2.3.dist-info}/WHEEL +0 -0
  310. {scientific_writer-2.2.1.dist-info → scientific_writer-2.2.3.dist-info}/entry_points.txt +0 -0
  311. {scientific_writer-2.2.1.dist-info → scientific_writer-2.2.3.dist-info}/licenses/LICENSE +0 -0
@@ -0,0 +1,900 @@
1
+ # Poster Layout and Design Guide
2
+
3
+ ## Overview
4
+
5
+ Effective poster layout organizes content for maximum impact and comprehension. This guide covers grid systems, spatial organization, visual flow, and layout patterns for research posters.
6
+
7
+ ## Grid Systems and Column Layouts
8
+
9
+ ### Common Grid Patterns
10
+
11
+ #### 1. Two-Column Layout
12
+
13
+ **Characteristics**:
14
+ - Simple, traditional structure
15
+ - Easy to design and execute
16
+ - Clear narrative flow
17
+ - Good for text-heavy content
18
+ - Best for A1 size or smaller
19
+
20
+ **Content Organization**:
21
+ ```
22
+ +-------------------------+
23
+ | Title/Header |
24
+ +-------------------------+
25
+ | Column 1 | Column 2 |
26
+ | | |
27
+ | Intro | Results |
28
+ | | |
29
+ | Methods | Discussion |
30
+ | | |
31
+ | | Conclusions |
32
+ +-------------------------+
33
+ | References/Contact |
34
+ +-------------------------+
35
+ ```
36
+
37
+ **LaTeX Implementation (beamerposter)**:
38
+ ```latex
39
+ \begin{columns}[t]
40
+ \begin{column}{.48\linewidth}
41
+ \begin{block}{Introduction}
42
+ % Content
43
+ \end{block}
44
+ \begin{block}{Methods}
45
+ % Content
46
+ \end{block}
47
+ \end{column}
48
+
49
+ \begin{column}{.48\linewidth}
50
+ \begin{block}{Results}
51
+ % Content
52
+ \end{block}
53
+ \begin{block}{Conclusions}
54
+ % Content
55
+ \end{block}
56
+ \end{column}
57
+ \end{columns}
58
+ ```
59
+
60
+ **Best For**:
61
+ - Small posters (A1, A2)
62
+ - Narrative-heavy content
63
+ - Simple comparisons (before/after, control/treatment)
64
+ - Linear storytelling
65
+
66
+ **Limitations**:
67
+ - Limited space for multiple results
68
+ - Can appear basic or dated
69
+ - Less visual variety
70
+
71
+ #### 2. Three-Column Layout (Most Popular)
72
+
73
+ **Characteristics**:
74
+ - Balanced, professional appearance
75
+ - Optimal for A0 posters
76
+ - Versatile content distribution
77
+ - Natural visual rhythm
78
+ - Industry standard
79
+
80
+ **Content Organization**:
81
+ ```
82
+ +--------------------------------+
83
+ | Title/Header |
84
+ +--------------------------------+
85
+ | Column 1 | Column 2 | Column 3|
86
+ | | | |
87
+ | Intro | Results | Results |
88
+ | | (Fig 1) | (Fig 2) |
89
+ | Methods | | |
90
+ | | Results | Discuss |
91
+ | Methods | (Fig 3) | |
92
+ | (cont.) | | Concl. |
93
+ +--------------------------------+
94
+ | Acknowledgments/Refs |
95
+ +--------------------------------+
96
+ ```
97
+
98
+ **LaTeX Implementation (tikzposter)**:
99
+ ```latex
100
+ \begin{columns}
101
+ \column{0.33}
102
+ \block{Introduction}{...}
103
+ \block{Methods}{...}
104
+
105
+ \column{0.33}
106
+ \block{Results Part 1}{...}
107
+ \block{Results Part 2}{...}
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+
109
+ \column{0.33}
110
+ \block{Results Part 3}{...}
111
+ \block{Discussion}{...}
112
+ \block{Conclusions}{...}
113
+ \end{columns}
114
+ ```
115
+
116
+ **Best For**:
117
+ - Standard A0 conference posters
118
+ - Multiple results/figures (4-6)
119
+ - Balanced content distribution
120
+ - Professional academic presentations
121
+
122
+ **Strengths**:
123
+ - Visual balance and symmetry
124
+ - Adequate space for text and figures
125
+ - Clear section delineation
126
+ - Easy to scan left-to-right
127
+
128
+ #### 3. Four-Column Layout
129
+
130
+ **Characteristics**:
131
+ - Information-dense
132
+ - Modern, structured appearance
133
+ - Best for large posters (>A0)
134
+ - Requires careful design
135
+ - More complex to balance
136
+
137
+ **Content Organization**:
138
+ ```
139
+ +----------------------------------------+
140
+ | Title/Header |
141
+ +----------------------------------------+
142
+ | Col 1 | Col 2 | Col 3 | Col 4 |
143
+ | | | | |
144
+ | Intro | Method | Results | Results |
145
+ | | (Flow) | (Fig 1) | (Fig 3) |
146
+ | Motiv. | | | |
147
+ | | Method | Results | Discuss. |
148
+ | Hypoth.| (Stats)| (Fig 2) | |
149
+ | | | | Concl. |
150
+ +----------------------------------------+
151
+ | References/Contact |
152
+ +----------------------------------------+
153
+ ```
154
+
155
+ **LaTeX Implementation (baposter)**:
156
+ ```latex
157
+ \begin{poster}{columns=4, colspacing=1em, ...}
158
+
159
+ \headerbox{Intro}{name=intro, column=0, row=0}{...}
160
+ \headerbox{Methods}{name=methods, column=1, row=0}{...}
161
+ \headerbox{Results 1}{name=res1, column=2, row=0}{...}
162
+ \headerbox{Results 2}{name=res2, column=3, row=0}{...}
163
+
164
+ % Continue with below=... for stacking
165
+
166
+ \end{poster}
167
+ ```
168
+
169
+ **Best For**:
170
+ - Large format posters (48×72")
171
+ - Data-heavy presentations
172
+ - Comparison studies (multiple conditions)
173
+ - Engineering/technical posters
174
+
175
+ **Challenges**:
176
+ - Can appear crowded
177
+ - Requires more white space management
178
+ - Harder to achieve visual balance
179
+ - Risk of overwhelming viewers
180
+
181
+ #### 4. Asymmetric Layouts
182
+
183
+ **Characteristics**:
184
+ - Dynamic, modern appearance
185
+ - Flexible content arrangement
186
+ - Emphasizes hierarchy
187
+ - Requires design expertise
188
+ - Best for creative fields
189
+
190
+ **Example Pattern**:
191
+ ```
192
+ +--------------------------------+
193
+ | Title/Header |
194
+ +--------------------------------+
195
+ | Wide Column | Narrow Column |
196
+ | (66%) | (33%) |
197
+ | | |
198
+ | Intro + | Key |
199
+ | Methods | Figure |
200
+ | (narrative) | (emphasized) |
201
+ | | |
202
+ +--------------------------------+
203
+ | Results (spanning full width) |
204
+ +--------------------------------+
205
+ | Discussion | Conclusions |
206
+ | (50%) | (50%) |
207
+ +--------------------------------+
208
+ ```
209
+
210
+ **LaTeX Implementation (tikzposter)**:
211
+ ```latex
212
+ \begin{columns}
213
+ \column{0.65}
214
+ \block{Introduction and Methods}{
215
+ % Combined narrative section
216
+ }
217
+
218
+ \column{0.35}
219
+ \block{}{
220
+ % Key figure with minimal text
221
+ \includegraphics[width=\linewidth]{key-figure.pdf}
222
+ }
223
+ \end{columns}
224
+
225
+ \block[width=1.0\linewidth]{Results}{
226
+ % Full-width results section
227
+ }
228
+ ```
229
+
230
+ **Best For**:
231
+ - Design-oriented conferences
232
+ - Single key finding with supporting content
233
+ - Modern, non-traditional fields
234
+ - Experienced poster designers
235
+
236
+ ### Grid Alignment Principles
237
+
238
+ **Baseline Grid**:
239
+ - Establish invisible horizontal lines
240
+ - Align all text blocks to grid
241
+ - Typical spacing: 5mm or 10mm increments
242
+ - Creates visual rhythm and professionalism
243
+
244
+ **Column Grid**:
245
+ - Divide width into equal units (12, 16, or 24 units common)
246
+ - Elements span multiple units
247
+ - Allows flexible but structured layouts
248
+
249
+ **Example 12-Column Grid**:
250
+ ```
251
+ | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 |10 |11 |12 |
252
+ |-------|-------|-------|-------|-------|-------|
253
+ | Block spanning 6 units| Block spanning 6 units|
254
+ | Block spanning 12 units |
255
+ | 4 units | 8 units (emphasized) |
256
+ ```
257
+
258
+ **LaTeX Grid Helper**:
259
+ ```latex
260
+ % Debug grid overlay (remove for final version)
261
+ \usepackage{tikz}
262
+ \AddToShipoutPictureBG{
263
+ \begin{tikzpicture}[remember picture, overlay]
264
+ \draw[help lines, step=5cm, very thin, gray!30]
265
+ (current page.south west) grid (current page.north east);
266
+ \end{tikzpicture}
267
+ }
268
+ ```
269
+
270
+ ## Visual Flow and Reading Patterns
271
+
272
+ ### Z-Pattern (Landscape Posters)
273
+
274
+ Viewers' eyes naturally follow a Z-shape on landscape layouts:
275
+
276
+ ```
277
+ START → → → → → → → → → → → → → → TOP RIGHT
278
+ ↓ ↓
279
+ ↓ ↓
280
+ MIDDLE LEFT → → → → → → → → → MIDDLE RIGHT
281
+ ↓ ↓
282
+ ↓ ↓
283
+ BOTTOM LEFT → → → → → → → → → → → → END
284
+ ```
285
+
286
+ **Design Strategy**:
287
+ 1. **Top-left**: Title and introduction (entry point)
288
+ 2. **Top-right**: Institution logo, QR code
289
+ 3. **Center**: Key result or main figure
290
+ 4. **Bottom-right**: Conclusions and contact (exit point)
291
+
292
+ **Content Placement**:
293
+ - Critical information at corners and center
294
+ - Support information along diagonal paths
295
+ - Use arrows or visual cues to reinforce flow
296
+
297
+ ### F-Pattern (Portrait Posters)
298
+
299
+ Portrait posters follow F-shaped eye movement:
300
+
301
+ ```
302
+ TITLE → → → → → → → → → → → →
303
+
304
+ INTRO → → → →
305
+
306
+ METHODS
307
+
308
+ RESULTS → → →
309
+
310
+ RESULTS (cont.)
311
+
312
+ DISCUSSION
313
+
314
+ CONCLUSIONS → → → → → → → → →
315
+ ```
316
+
317
+ **Design Strategy**:
318
+ 1. Place engaging content at top-left
319
+ 2. Use section headers to create horizontal scan points
320
+ 3. Most important figures in upper-middle area
321
+ 4. Conclusions visible without scrolling (if digital) or from distance
322
+
323
+ ### Gutenberg Diagram
324
+
325
+ Classic newspaper layout principle:
326
+
327
+ ```
328
+ +------------------+------------------+
329
+ | PRIMARY AREA | STRONG FALLOW |
330
+ | (most attention) | (moderate attn) |
331
+ | ↓ | ↓ |
332
+ +------------------+------------------+
333
+ | WEAK FALLOW | TERMINAL AREA |
334
+ | (least attention)| (final resting) |
335
+ | | ↑ |
336
+ +------------------+------------------+
337
+ ```
338
+
339
+ **Optimization**:
340
+ - **Primary Area** (top-left): Introduction, problem statement
341
+ - **Strong Fallow** (top-right): Supporting figure, logo
342
+ - **Weak Fallow** (bottom-left): Methods details, references
343
+ - **Terminal Area** (bottom-right): Conclusions, take-home message
344
+
345
+ ### Directional Cues
346
+
347
+ Guide viewers explicitly through content:
348
+
349
+ **Numerical Ordering**:
350
+ ```latex
351
+ \block{❶ Introduction}{...}
352
+ \block{❷ Methods}{...}
353
+ \block{❸ Results}{...}
354
+ \block{❹ Conclusions}{...}
355
+ ```
356
+
357
+ **Arrows and Lines**:
358
+ ```latex
359
+ \begin{tikzpicture}
360
+ \node[block] (intro) {Introduction};
361
+ \node[block, right=of intro] (methods) {Methods};
362
+ \node[block, right=of methods] (results) {Results};
363
+ \draw[->, thick, blue] (intro) -- (methods);
364
+ \draw[->, thick, blue] (methods) -- (results);
365
+ \end{tikzpicture}
366
+ ```
367
+
368
+ **Color Progression**:
369
+ - Light to dark shades indicating progression
370
+ - Cool to warm colors showing importance increase
371
+ - Consistent color for related sections
372
+
373
+ ## Spatial Organization Strategies
374
+
375
+ ### Header/Title Area
376
+
377
+ **Typical Size**: 10-15% of total poster height
378
+
379
+ **Essential Elements**:
380
+ - **Title**: Concise, descriptive (10-15 words max)
381
+ - **Authors**: Full names, presenting author emphasized
382
+ - **Affiliations**: Institutions, departments
383
+ - **Logos**: University, funding agencies (2-4 max)
384
+ - **Conference info** (optional): Name, date, location
385
+
386
+ **Layout Options**:
387
+
388
+ **Centered**:
389
+ ```
390
+ +----------------------------------------+
391
+ | [Logo] POSTER TITLE HERE [Logo]|
392
+ | Authors and Affiliations |
393
+ | email@university.edu |
394
+ +----------------------------------------+
395
+ ```
396
+
397
+ **Left-aligned**:
398
+ ```
399
+ +----------------------------------------+
400
+ | POSTER TITLE HERE [Logo] |
401
+ | Authors and Affiliations [Logo] |
402
+ +----------------------------------------+
403
+ ```
404
+
405
+ **Split**:
406
+ ```
407
+ +----------------------------------------+
408
+ | [Logo] | Authors & Affil. |
409
+ | POSTER TITLE | email@edu |
410
+ | | [QR Code] |
411
+ +----------------------------------------+
412
+ ```
413
+
414
+ **LaTeX Header (beamerposter)**:
415
+ ```latex
416
+ \begin{columns}[T]
417
+ \begin{column}{.15\linewidth}
418
+ \includegraphics[width=\linewidth]{logo1.pdf}
419
+ \end{column}
420
+
421
+ \begin{column}{.7\linewidth}
422
+ \centering
423
+ {\VeryHuge\textbf{Your Research Title Here}}\\[0.5cm]
424
+ {\Large Author One\textsuperscript{1}, Author Two\textsuperscript{2}}\\[0.3cm]
425
+ {\normalsize \textsuperscript{1}University A, \textsuperscript{2}University B}
426
+ \end{column}
427
+
428
+ \begin{column}{.15\linewidth}
429
+ \includegraphics[width=\linewidth]{logo2.pdf}
430
+ \end{column}
431
+ \end{columns}
432
+ ```
433
+
434
+ ### Main Content Area
435
+
436
+ **Typical Size**: 70-80% of total poster
437
+
438
+ **Organization Principles**:
439
+
440
+ **1. Top-to-Bottom Flow**:
441
+ ```
442
+ Introduction/Background
443
+
444
+ Methods/Approach
445
+
446
+ Results (Multiple panels)
447
+
448
+ Discussion/Conclusions
449
+ ```
450
+
451
+ **2. Left-to-Right, Top-to-Bottom**:
452
+ ```
453
+ [Intro] [Results 1] [Results 3]
454
+ [Methods] [Results 2] [Discussion]
455
+ ```
456
+
457
+ **3. Centralized Main Figure**:
458
+ ```
459
+ [Intro] [Main Figure] [Discussion]
460
+ [Methods] (center) [Conclusions]
461
+ ```
462
+
463
+ **Section Sizing**:
464
+ - Introduction: 10-15% of content area
465
+ - Methods: 15-20%
466
+ - Results: 40-50% (largest section)
467
+ - Discussion/Conclusions: 15-20%
468
+
469
+ ### Footer Area
470
+
471
+ **Typical Size**: 5-10% of total poster height
472
+
473
+ **Common Elements**:
474
+ - References (abbreviated, 5-10 key citations)
475
+ - Acknowledgments (funding, collaborators)
476
+ - Contact information
477
+ - QR codes (paper, code, data)
478
+ - Social media handles (optional)
479
+ - Conference hashtags
480
+
481
+ **Layout**:
482
+ ```
483
+ +----------------------------------------+
484
+ | References: 1. Author (2023) ... | 📱 |
485
+ | Acknowledgments: Funded by ... | QR |
486
+ | Contact: name@email.edu | Code |
487
+ +----------------------------------------+
488
+ ```
489
+
490
+ **LaTeX Footer**:
491
+ ```latex
492
+ \begin{block}{}
493
+ \footnotesize
494
+ \begin{columns}[T]
495
+ \begin{column}{0.7\linewidth}
496
+ \textbf{References}
497
+ \begin{enumerate}
498
+ \item Author A et al. (2023). Journal. doi:...
499
+ \item Author B et al. (2024). Conference.
500
+ \end{enumerate}
501
+
502
+ \textbf{Acknowledgments}
503
+ This work was supported by Grant XYZ.
504
+
505
+ \textbf{Contact}: firstname.lastname@university.edu
506
+ \end{column}
507
+
508
+ \begin{column}{0.25\linewidth}
509
+ \centering
510
+ \qrcode[height=3cm]{https://doi.org/10.1234/paper}\\
511
+ \tiny Scan for full paper
512
+ \end{column}
513
+ \end{columns}
514
+ \end{block}
515
+ ```
516
+
517
+ ## White Space Management
518
+
519
+ ### Margins and Padding
520
+
521
+ **Outer Margins**:
522
+ - Minimum: 2-3cm (0.75-1 inch)
523
+ - Recommended: 3-5cm (1-2 inches)
524
+ - Prevents edge trimming issues in printing
525
+ - Provides visual breathing room
526
+
527
+ **Inner Spacing**:
528
+ - Between columns: 1-2cm
529
+ - Between blocks: 1-2cm
530
+ - Inside blocks (padding): 0.5-1.5cm
531
+ - Around figures: 0.5-1cm
532
+
533
+ **LaTeX Margin Control**:
534
+ ```latex
535
+ % beamerposter
536
+ \usepackage[size=a0, scale=1.4]{beamerposter}
537
+ \setbeamersize{text margin left=3cm, text margin right=3cm}
538
+
539
+ % tikzposter
540
+ \documentclass[..., margin=30mm, innermargin=15mm]{tikzposter}
541
+
542
+ % baposter
543
+ \begin{poster}{
544
+ colspacing=1.5em, % Horizontal spacing
545
+ ...
546
+ }
547
+ ```
548
+
549
+ ### Active White Space vs. Passive White Space
550
+
551
+ **Active White Space**: Intentionally placed for specific purpose
552
+ - Around key figures (draws attention)
553
+ - Between major sections (creates clear separation)
554
+ - Above/below titles (emphasizes hierarchy)
555
+
556
+ **Passive White Space**: Natural result of layout
557
+ - Margins and borders
558
+ - Line spacing
559
+ - Gaps between elements
560
+
561
+ **Balance**: Aim for 30-40% white space overall
562
+
563
+ ### Visual Breathing Room
564
+
565
+ **Avoid**:
566
+ - ❌ Elements touching edges
567
+ - ❌ Text blocks directly adjacent
568
+ - ❌ Figures without surrounding space
569
+ - ❌ Cramped, claustrophobic feel
570
+
571
+ **Implement**:
572
+ - ✅ Clear separation between sections
573
+ - ✅ Space around focal points
574
+ - ✅ Generous padding inside boxes
575
+ - ✅ Balanced distribution of content
576
+
577
+ ## Block and Box Design
578
+
579
+ ### Block Types and Functions
580
+
581
+ **Title Block**: Poster header
582
+ - Full width, top position
583
+ - High visual weight
584
+ - Contains identifying information
585
+
586
+ **Content Blocks**: Main sections
587
+ - Column-based or free-floating
588
+ - Hierarchical sizing (larger = more important)
589
+ - Clear headers and structure
590
+
591
+ **Callout Blocks**: Emphasized information
592
+ - Key findings or quotes
593
+ - Different color or style
594
+ - Visually distinct
595
+
596
+ **Reference Blocks**: Supporting info
597
+ - Footer position
598
+ - Smaller, less prominent
599
+ - Informational, not critical
600
+
601
+ ### Block Styling Options
602
+
603
+ **Border Styles**:
604
+ ```latex
605
+ % Rounded corners (friendly, modern)
606
+ \begin{block}{Title}
607
+ % beamerposter with rounded
608
+ \setbeamertemplate{block begin}[rounded]
609
+
610
+ % Sharp corners (formal, traditional)
611
+ \setbeamertemplate{block begin}[default]
612
+
613
+ % No border (minimal, clean)
614
+ \setbeamercolor{block title}{bg=white, fg=black}
615
+ \setbeamercolor{block body}{bg=white, fg=black}
616
+ ```
617
+
618
+ **Shadow and Depth**:
619
+ ```latex
620
+ % tikzposter shadow
621
+ \tikzset{
622
+ block/.append style={
623
+ drop shadow={shadow xshift=2mm, shadow yshift=-2mm}
624
+ }
625
+ }
626
+
627
+ % tcolorbox drop shadow
628
+ \usepackage{tcolorbox}
629
+ \begin{tcolorbox}[enhanced, drop shadow]
630
+ Content with shadow
631
+ \end{tcolorbox}
632
+ ```
633
+
634
+ **Background Shading**:
635
+ - **Solid**: Clean, professional
636
+ - **Gradient**: Modern, dynamic
637
+ - **Transparent**: Layered, sophisticated
638
+
639
+ ### Relationship and Grouping
640
+
641
+ **Visual Grouping Techniques**:
642
+
643
+ **1. Proximity**: Place related items close
644
+ ```
645
+ [Intro Text]
646
+ [Related Figure]
647
+ ↓ grouped
648
+ [Methods Text]
649
+ [Methods Diagram]
650
+ ```
651
+
652
+ **2. Color Coding**: Use color to show relationships
653
+ - All "Methods" blocks in blue
654
+ - All "Results" blocks in green
655
+ - Conclusions in orange
656
+
657
+ **3. Borders**: Enclose related elements
658
+ ```latex
659
+ \begin{tcolorbox}[title=Experimental Pipeline]
660
+ \begin{enumerate}
661
+ \item Sample preparation
662
+ \item Data collection
663
+ \item Analysis
664
+ \end{enumerate}
665
+ \end{tcolorbox}
666
+ ```
667
+
668
+ **4. Alignment**: Aligned elements appear related
669
+ ```
670
+ [Block A Left-aligned]
671
+ [Block B Left-aligned]
672
+ vs.
673
+ [Block C Centered]
674
+ ```
675
+
676
+ ## Responsive and Adaptive Layouts
677
+
678
+ ### Designing for Different Poster Sizes
679
+
680
+ **Scaling Strategy**:
681
+ - Design for target size (e.g., A0)
682
+ - Test at other common sizes (A1, 36×48")
683
+ - Use relative sizing (percentages, not absolute)
684
+
685
+ **Font Scaling**:
686
+ ```latex
687
+ % Scale fonts proportionally
688
+ \usepackage[size=a0, scale=1.4]{beamerposter} % A0 at 140%
689
+ \usepackage[size=a1, scale=1.0]{beamerposter} % A1 at 100%
690
+
691
+ % Or define sizes relatively
692
+ \newcommand{\titlesize}{\fontsize{96}{110}\selectfont}
693
+ \newcommand{\headersize}{\fontsize{60}{72}\selectfont}
694
+ ```
695
+
696
+ **Content Adaptation**:
697
+ - **A0 (full)**: All content, 5-6 figures
698
+ - **A1 (reduced)**: Condense to 3-4 main figures
699
+ - **A2 (compact)**: Key finding only, 1-2 figures
700
+
701
+ ### Portrait vs. Landscape Orientation
702
+
703
+ **Portrait (Vertical)**:
704
+ - **Pros**: Traditional, more common stands, natural reading flow
705
+ - **Cons**: Less width for figures, can feel cramped
706
+ - **Best for**: Text-heavy posters, multi-section flow, conferences
707
+
708
+ **Landscape (Horizontal)**:
709
+ - **Pros**: Wide figures, natural for timelines, modern feel
710
+ - **Cons**: Harder to read from distance, less common
711
+ - **Best for**: Timelines, wide data visualizations, non-traditional venues
712
+
713
+ **LaTeX Orientation**:
714
+ ```latex
715
+ % Portrait
716
+ \usepackage[size=a0, orientation=portrait]{beamerposter}
717
+ \documentclass[..., portrait]{tikzposter}
718
+
719
+ % Landscape
720
+ \usepackage[size=a0, orientation=landscape]{beamerposter}
721
+ \documentclass[..., landscape]{tikzposter}
722
+ ```
723
+
724
+ ## Layout Patterns by Research Type
725
+
726
+ ### Experimental Research
727
+
728
+ **Typical Flow**:
729
+ ```
730
+ [Title and Authors]
731
+ +---------------------------+
732
+ | Background | Methods |
733
+ | Problem | (Diagram) |
734
+ +---------------------------+
735
+ | Results (Figure 1) |
736
+ | Results (Figure 2) |
737
+ +---------------------------+
738
+ | Discussion | Conclusions |
739
+ | Limitations| Future Work |
740
+ +---------------------------+
741
+ [References and Contact]
742
+ ```
743
+
744
+ **Emphasis**: Visual results, clear methodology
745
+
746
+ ### Computational/Modeling
747
+
748
+ **Typical Flow**:
749
+ ```
750
+ [Title and Authors]
751
+ +---------------------------+
752
+ | Motivation | Algorithm |
753
+ | | (Flowchart) |
754
+ +---------------------------+
755
+ | Implementation Details |
756
+ +---------------------------+
757
+ | Results | Results |
758
+ | (Benchmark)| (Comparison) |
759
+ +---------------------------+
760
+ | Conclusions| Code QR |
761
+ +---------------------------+
762
+ [GitHub, Docker, Documentation]
763
+ ```
764
+
765
+ **Emphasis**: Algorithm clarity, reproducibility
766
+
767
+ ### Clinical/Medical
768
+
769
+ **Typical Flow**:
770
+ ```
771
+ [Title and Authors]
772
+ +---------------------------+
773
+ | Background | Methods |
774
+ | Clinical | - Design |
775
+ | Need | - Population |
776
+ | | - Outcomes |
777
+ +---------------------------+
778
+ | Results | |
779
+ | (Primary Outcome) | Key|
780
+ | | Fig|
781
+ +---------------------------+
782
+ | Discussion | Clinical |
783
+ | | Implications |
784
+ +---------------------------+
785
+ [Trial Registration, Ethics, Funding]
786
+ ```
787
+
788
+ **Emphasis**: Patient outcomes, clinical relevance
789
+
790
+ ### Review/Meta-Analysis
791
+
792
+ **Typical Flow**:
793
+ ```
794
+ [Title and Authors]
795
+ +---------------------------+
796
+ | Research | Search |
797
+ | Question | Strategy |
798
+ | | (PRISMA Flow) |
799
+ +---------------------------+
800
+ | Included Studies Overview |
801
+ +---------------------------+
802
+ | Findings | Findings |
803
+ | (Theme 1) | (Theme 2) |
804
+ +---------------------------+
805
+ | Synthesis | Gaps & |
806
+ | | Future Needs |
807
+ +---------------------------+
808
+ [Systematic Review Registration]
809
+ ```
810
+
811
+ **Emphasis**: Comprehensive coverage, synthesis
812
+
813
+ ## Layout Testing and Iteration
814
+
815
+ ### Design Iteration Process
816
+
817
+ **1. Sketch Phase**:
818
+ - Hand-draw rough layout
819
+ - Experiment with different arrangements
820
+ - Mark primary, secondary, tertiary content
821
+
822
+ **2. Digital Mockup**:
823
+ - Create low-fidelity version in LaTeX
824
+ - Use placeholder text/figures
825
+ - Test different grid systems
826
+
827
+ **3. Content Integration**:
828
+ - Replace placeholders with actual content
829
+ - Adjust spacing and sizing
830
+ - Refine visual hierarchy
831
+
832
+ **4. Refinement**:
833
+ - Fine-tune alignment
834
+ - Balance visual weight
835
+ - Optimize white space
836
+
837
+ **5. Testing**:
838
+ - Print at reduced scale (25%)
839
+ - View from distance
840
+ - Get colleague feedback
841
+
842
+ ### Feedback Checklist
843
+
844
+ **Visual Balance**:
845
+ - [ ] No single area feels too heavy or too light
846
+ - [ ] Color distributed evenly across poster
847
+ - [ ] Text and figures balanced
848
+ - [ ] White space well-distributed
849
+
850
+ **Hierarchy and Flow**:
851
+ - [ ] Clear entry point (title visible)
852
+ - [ ] Logical reading path
853
+ - [ ] Section relationships clear
854
+ - [ ] Conclusions easy to find
855
+
856
+ **Technical Execution**:
857
+ - [ ] Consistent alignment
858
+ - [ ] Uniform spacing
859
+ - [ ] Professional appearance
860
+ - [ ] No awkward breaks or orphans
861
+
862
+ ## Common Layout Mistakes
863
+
864
+ **1. Unbalanced Visual Weight**
865
+ - ❌ All content on left, empty right side
866
+ - ❌ Large figure dominating, tiny text elsewhere
867
+ - ✅ Distribute content evenly across poster
868
+
869
+ **2. Inconsistent Spacing**
870
+ - ❌ Random gaps between blocks
871
+ - ❌ Elements touching in some places, spaced in others
872
+ - ✅ Use consistent spacing values throughout
873
+
874
+ **3. Poor Column Width**
875
+ - ❌ Extremely narrow columns (hard to read)
876
+ - ❌ Very wide columns (eye tracking difficult)
877
+ - ✅ Optimal: 40-80 characters per line
878
+
879
+ **4. Ignoring Grid**
880
+ - ❌ Random placement of elements
881
+ - ❌ Misaligned blocks
882
+ - ✅ Align to invisible grid, consistent positioning
883
+
884
+ **5. Overcrowding**
885
+ - ❌ No white space, cramped feel
886
+ - ❌ Trying to fit too much content
887
+ - ✅ Generous margins, clear separation
888
+
889
+ ## Conclusion
890
+
891
+ Effective layout design:
892
+ - Uses appropriate grid systems (2, 3, or 4 columns)
893
+ - Follows natural eye movement patterns
894
+ - Maintains visual balance and hierarchy
895
+ - Provides adequate white space
896
+ - Groups related content clearly
897
+ - Adapts to different poster sizes and orientations
898
+
899
+ Remember: Layout should support content, not compete with it. When viewers focus on your research rather than your design, you've succeeded.
900
+