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

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  1. scientific_writer/.claude/settings.local.json +30 -0
  2. scientific_writer/.claude/skills/citation-management/SKILL.md +1046 -0
  3. scientific_writer/.claude/skills/citation-management/assets/bibtex_template.bib +264 -0
  4. scientific_writer/.claude/skills/citation-management/assets/citation_checklist.md +386 -0
  5. scientific_writer/.claude/skills/citation-management/references/bibtex_formatting.md +908 -0
  6. scientific_writer/.claude/skills/citation-management/references/citation_validation.md +794 -0
  7. scientific_writer/.claude/skills/citation-management/references/google_scholar_search.md +725 -0
  8. scientific_writer/.claude/skills/citation-management/references/metadata_extraction.md +870 -0
  9. scientific_writer/.claude/skills/citation-management/references/pubmed_search.md +839 -0
  10. scientific_writer/.claude/skills/citation-management/scripts/doi_to_bibtex.py +204 -0
  11. scientific_writer/.claude/skills/citation-management/scripts/extract_metadata.py +569 -0
  12. scientific_writer/.claude/skills/citation-management/scripts/format_bibtex.py +349 -0
  13. scientific_writer/.claude/skills/citation-management/scripts/search_google_scholar.py +282 -0
  14. scientific_writer/.claude/skills/citation-management/scripts/search_pubmed.py +398 -0
  15. scientific_writer/.claude/skills/citation-management/scripts/validate_citations.py +497 -0
  16. scientific_writer/.claude/skills/clinical-reports/IMPLEMENTATION_SUMMARY.md +641 -0
  17. scientific_writer/.claude/skills/clinical-reports/README.md +236 -0
  18. scientific_writer/.claude/skills/clinical-reports/SKILL.md +1088 -0
  19. scientific_writer/.claude/skills/clinical-reports/assets/case_report_template.md +352 -0
  20. scientific_writer/.claude/skills/clinical-reports/assets/clinical_trial_csr_template.md +353 -0
  21. scientific_writer/.claude/skills/clinical-reports/assets/clinical_trial_sae_template.md +359 -0
  22. scientific_writer/.claude/skills/clinical-reports/assets/consult_note_template.md +305 -0
  23. scientific_writer/.claude/skills/clinical-reports/assets/discharge_summary_template.md +453 -0
  24. scientific_writer/.claude/skills/clinical-reports/assets/hipaa_compliance_checklist.md +395 -0
  25. scientific_writer/.claude/skills/clinical-reports/assets/history_physical_template.md +305 -0
  26. scientific_writer/.claude/skills/clinical-reports/assets/lab_report_template.md +309 -0
  27. scientific_writer/.claude/skills/clinical-reports/assets/pathology_report_template.md +249 -0
  28. scientific_writer/.claude/skills/clinical-reports/assets/quality_checklist.md +338 -0
  29. scientific_writer/.claude/skills/clinical-reports/assets/radiology_report_template.md +318 -0
  30. scientific_writer/.claude/skills/clinical-reports/assets/soap_note_template.md +253 -0
  31. scientific_writer/.claude/skills/clinical-reports/references/case_report_guidelines.md +570 -0
  32. scientific_writer/.claude/skills/clinical-reports/references/clinical_trial_reporting.md +693 -0
  33. scientific_writer/.claude/skills/clinical-reports/references/data_presentation.md +530 -0
  34. scientific_writer/.claude/skills/clinical-reports/references/diagnostic_reports_standards.md +629 -0
  35. scientific_writer/.claude/skills/clinical-reports/references/medical_terminology.md +588 -0
  36. scientific_writer/.claude/skills/clinical-reports/references/patient_documentation.md +744 -0
  37. scientific_writer/.claude/skills/clinical-reports/references/peer_review_standards.md +585 -0
  38. scientific_writer/.claude/skills/clinical-reports/references/regulatory_compliance.md +577 -0
  39. scientific_writer/.claude/skills/clinical-reports/scripts/check_deidentification.py +346 -0
  40. scientific_writer/.claude/skills/clinical-reports/scripts/compliance_checker.py +78 -0
  41. scientific_writer/.claude/skills/clinical-reports/scripts/extract_clinical_data.py +102 -0
  42. scientific_writer/.claude/skills/clinical-reports/scripts/format_adverse_events.py +103 -0
  43. scientific_writer/.claude/skills/clinical-reports/scripts/generate_report_template.py +163 -0
  44. scientific_writer/.claude/skills/clinical-reports/scripts/terminology_validator.py +133 -0
  45. scientific_writer/.claude/skills/clinical-reports/scripts/validate_case_report.py +334 -0
  46. scientific_writer/.claude/skills/clinical-reports/scripts/validate_trial_report.py +89 -0
  47. scientific_writer/.claude/skills/document-skills/docx/LICENSE.txt +30 -0
  48. scientific_writer/.claude/skills/document-skills/docx/SKILL.md +197 -0
  49. scientific_writer/.claude/skills/document-skills/docx/docx-js.md +350 -0
  50. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
  51. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
  52. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
  53. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
  54. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
  55. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
  56. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
  57. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
  58. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
  59. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
  60. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
  61. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
  62. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
  63. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
  64. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
  65. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
  66. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
  67. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
  68. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
  69. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
  70. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
  71. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
  72. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
  73. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
  74. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
  75. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
  76. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
  77. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
  78. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
  79. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
  80. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
  81. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/mce/mc.xsd +75 -0
  82. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2010.xsd +560 -0
  83. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2012.xsd +67 -0
  84. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2018.xsd +14 -0
  85. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-cex-2018.xsd +20 -0
  86. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-cid-2016.xsd +13 -0
  87. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
  88. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-symex-2015.xsd +8 -0
  89. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/pack.py +159 -0
  90. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/unpack.py +29 -0
  91. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validate.py +69 -0
  92. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/__init__.py +15 -0
  93. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/base.py +951 -0
  94. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/docx.py +274 -0
  95. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/pptx.py +315 -0
  96. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/redlining.py +279 -0
  97. scientific_writer/.claude/skills/document-skills/docx/ooxml.md +610 -0
  98. scientific_writer/.claude/skills/document-skills/docx/scripts/__init__.py +1 -0
  99. scientific_writer/.claude/skills/document-skills/docx/scripts/document.py +1276 -0
  100. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/comments.xml +3 -0
  101. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/commentsExtended.xml +3 -0
  102. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/commentsExtensible.xml +3 -0
  103. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/commentsIds.xml +3 -0
  104. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/people.xml +3 -0
  105. scientific_writer/.claude/skills/document-skills/docx/scripts/utilities.py +374 -0
  106. scientific_writer/.claude/skills/document-skills/pdf/LICENSE.txt +30 -0
  107. scientific_writer/.claude/skills/document-skills/pdf/SKILL.md +294 -0
  108. scientific_writer/.claude/skills/document-skills/pdf/forms.md +205 -0
  109. scientific_writer/.claude/skills/document-skills/pdf/reference.md +612 -0
  110. scientific_writer/.claude/skills/document-skills/pdf/scripts/check_bounding_boxes.py +70 -0
  111. scientific_writer/.claude/skills/document-skills/pdf/scripts/check_bounding_boxes_test.py +226 -0
  112. scientific_writer/.claude/skills/document-skills/pdf/scripts/check_fillable_fields.py +12 -0
  113. scientific_writer/.claude/skills/document-skills/pdf/scripts/convert_pdf_to_images.py +35 -0
  114. scientific_writer/.claude/skills/document-skills/pdf/scripts/create_validation_image.py +41 -0
  115. scientific_writer/.claude/skills/document-skills/pdf/scripts/extract_form_field_info.py +152 -0
  116. scientific_writer/.claude/skills/document-skills/pdf/scripts/fill_fillable_fields.py +114 -0
  117. scientific_writer/.claude/skills/document-skills/pdf/scripts/fill_pdf_form_with_annotations.py +108 -0
  118. scientific_writer/.claude/skills/document-skills/pptx/LICENSE.txt +30 -0
  119. scientific_writer/.claude/skills/document-skills/pptx/SKILL.md +484 -0
  120. scientific_writer/.claude/skills/document-skills/pptx/html2pptx.md +625 -0
  121. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
  122. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
  123. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
  124. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
  125. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
  126. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
  127. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
  128. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
  129. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
  130. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
  131. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
  132. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
  133. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
  134. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
  135. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
  136. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
  137. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
  138. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
  139. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
  140. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
  141. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
  142. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
  143. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
  144. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
  145. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
  146. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
  147. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
  148. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
  149. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
  150. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
  151. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
  152. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/mce/mc.xsd +75 -0
  153. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2010.xsd +560 -0
  154. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2012.xsd +67 -0
  155. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2018.xsd +14 -0
  156. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-cex-2018.xsd +20 -0
  157. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-cid-2016.xsd +13 -0
  158. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
  159. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-symex-2015.xsd +8 -0
  160. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/pack.py +159 -0
  161. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/unpack.py +29 -0
  162. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validate.py +69 -0
  163. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/__init__.py +15 -0
  164. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/base.py +951 -0
  165. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/docx.py +274 -0
  166. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/pptx.py +315 -0
  167. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/redlining.py +279 -0
  168. scientific_writer/.claude/skills/document-skills/pptx/ooxml.md +427 -0
  169. scientific_writer/.claude/skills/document-skills/pptx/scripts/html2pptx.js +979 -0
  170. scientific_writer/.claude/skills/document-skills/pptx/scripts/inventory.py +1020 -0
  171. scientific_writer/.claude/skills/document-skills/pptx/scripts/rearrange.py +231 -0
  172. scientific_writer/.claude/skills/document-skills/pptx/scripts/replace.py +385 -0
  173. scientific_writer/.claude/skills/document-skills/pptx/scripts/thumbnail.py +450 -0
  174. scientific_writer/.claude/skills/document-skills/xlsx/LICENSE.txt +30 -0
  175. scientific_writer/.claude/skills/document-skills/xlsx/SKILL.md +289 -0
  176. scientific_writer/.claude/skills/document-skills/xlsx/recalc.py +178 -0
  177. scientific_writer/.claude/skills/hypothesis-generation/SKILL.md +155 -0
  178. scientific_writer/.claude/skills/hypothesis-generation/assets/hypothesis_output_template.md +302 -0
  179. scientific_writer/.claude/skills/hypothesis-generation/references/experimental_design_patterns.md +327 -0
  180. scientific_writer/.claude/skills/hypothesis-generation/references/hypothesis_quality_criteria.md +196 -0
  181. scientific_writer/.claude/skills/hypothesis-generation/references/literature_search_strategies.md +505 -0
  182. scientific_writer/.claude/skills/latex-posters/README.md +417 -0
  183. scientific_writer/.claude/skills/latex-posters/SKILL.md +919 -0
  184. scientific_writer/.claude/skills/latex-posters/assets/baposter_template.tex +257 -0
  185. scientific_writer/.claude/skills/latex-posters/assets/beamerposter_template.tex +244 -0
  186. scientific_writer/.claude/skills/latex-posters/assets/poster_quality_checklist.md +358 -0
  187. scientific_writer/.claude/skills/latex-posters/assets/tikzposter_template.tex +251 -0
  188. scientific_writer/.claude/skills/latex-posters/references/latex_poster_packages.md +745 -0
  189. scientific_writer/.claude/skills/latex-posters/references/poster_content_guide.md +748 -0
  190. scientific_writer/.claude/skills/latex-posters/references/poster_design_principles.md +806 -0
  191. scientific_writer/.claude/skills/latex-posters/references/poster_layout_design.md +900 -0
  192. scientific_writer/.claude/skills/latex-posters/scripts/review_poster.sh +214 -0
  193. scientific_writer/.claude/skills/literature-review/SKILL.md +546 -0
  194. scientific_writer/.claude/skills/literature-review/assets/review_template.md +412 -0
  195. scientific_writer/.claude/skills/literature-review/references/citation_styles.md +166 -0
  196. scientific_writer/.claude/skills/literature-review/references/database_strategies.md +381 -0
  197. scientific_writer/.claude/skills/literature-review/scripts/generate_pdf.py +176 -0
  198. scientific_writer/.claude/skills/literature-review/scripts/search_databases.py +303 -0
  199. scientific_writer/.claude/skills/literature-review/scripts/verify_citations.py +222 -0
  200. scientific_writer/.claude/skills/markitdown/INSTALLATION_GUIDE.md +318 -0
  201. scientific_writer/.claude/skills/markitdown/LICENSE.txt +22 -0
  202. scientific_writer/.claude/skills/markitdown/OPENROUTER_INTEGRATION.md +359 -0
  203. scientific_writer/.claude/skills/markitdown/QUICK_REFERENCE.md +309 -0
  204. scientific_writer/.claude/skills/markitdown/README.md +184 -0
  205. scientific_writer/.claude/skills/markitdown/SKILL.md +450 -0
  206. scientific_writer/.claude/skills/markitdown/SKILL_SUMMARY.md +307 -0
  207. scientific_writer/.claude/skills/markitdown/assets/example_usage.md +463 -0
  208. scientific_writer/.claude/skills/markitdown/references/api_reference.md +399 -0
  209. scientific_writer/.claude/skills/markitdown/references/file_formats.md +542 -0
  210. scientific_writer/.claude/skills/markitdown/scripts/batch_convert.py +228 -0
  211. scientific_writer/.claude/skills/markitdown/scripts/convert_literature.py +283 -0
  212. scientific_writer/.claude/skills/markitdown/scripts/convert_with_ai.py +243 -0
  213. scientific_writer/.claude/skills/paper-2-web/SKILL.md +455 -0
  214. scientific_writer/.claude/skills/paper-2-web/references/installation.md +141 -0
  215. scientific_writer/.claude/skills/paper-2-web/references/paper2poster.md +346 -0
  216. scientific_writer/.claude/skills/paper-2-web/references/paper2video.md +305 -0
  217. scientific_writer/.claude/skills/paper-2-web/references/paper2web.md +187 -0
  218. scientific_writer/.claude/skills/paper-2-web/references/usage_examples.md +436 -0
  219. scientific_writer/.claude/skills/peer-review/SKILL.md +375 -0
  220. scientific_writer/.claude/skills/peer-review/references/common_issues.md +552 -0
  221. scientific_writer/.claude/skills/peer-review/references/reporting_standards.md +290 -0
  222. scientific_writer/.claude/skills/research-grants/README.md +285 -0
  223. scientific_writer/.claude/skills/research-grants/SKILL.md +896 -0
  224. scientific_writer/.claude/skills/research-grants/assets/budget_justification_template.md +453 -0
  225. scientific_writer/.claude/skills/research-grants/assets/nih_specific_aims_template.md +166 -0
  226. scientific_writer/.claude/skills/research-grants/assets/nsf_project_summary_template.md +92 -0
  227. scientific_writer/.claude/skills/research-grants/references/broader_impacts.md +392 -0
  228. scientific_writer/.claude/skills/research-grants/references/darpa_guidelines.md +636 -0
  229. scientific_writer/.claude/skills/research-grants/references/doe_guidelines.md +586 -0
  230. scientific_writer/.claude/skills/research-grants/references/nih_guidelines.md +851 -0
  231. scientific_writer/.claude/skills/research-grants/references/nsf_guidelines.md +570 -0
  232. scientific_writer/.claude/skills/research-grants/references/specific_aims_guide.md +458 -0
  233. scientific_writer/.claude/skills/research-lookup/README.md +116 -0
  234. scientific_writer/.claude/skills/research-lookup/SKILL.md +443 -0
  235. scientific_writer/.claude/skills/research-lookup/examples.py +174 -0
  236. scientific_writer/.claude/skills/research-lookup/lookup.py +93 -0
  237. scientific_writer/.claude/skills/research-lookup/research_lookup.py +335 -0
  238. scientific_writer/.claude/skills/research-lookup/scripts/research_lookup.py +261 -0
  239. scientific_writer/.claude/skills/scholar-evaluation/SKILL.md +254 -0
  240. scientific_writer/.claude/skills/scholar-evaluation/references/evaluation_framework.md +663 -0
  241. scientific_writer/.claude/skills/scholar-evaluation/scripts/calculate_scores.py +378 -0
  242. scientific_writer/.claude/skills/scientific-critical-thinking/SKILL.md +530 -0
  243. scientific_writer/.claude/skills/scientific-critical-thinking/references/common_biases.md +364 -0
  244. scientific_writer/.claude/skills/scientific-critical-thinking/references/evidence_hierarchy.md +484 -0
  245. scientific_writer/.claude/skills/scientific-critical-thinking/references/experimental_design.md +496 -0
  246. scientific_writer/.claude/skills/scientific-critical-thinking/references/logical_fallacies.md +478 -0
  247. scientific_writer/.claude/skills/scientific-critical-thinking/references/scientific_method.md +169 -0
  248. scientific_writer/.claude/skills/scientific-critical-thinking/references/statistical_pitfalls.md +506 -0
  249. scientific_writer/.claude/skills/scientific-schematics/SKILL.md +2035 -0
  250. scientific_writer/.claude/skills/scientific-schematics/assets/block_diagram_template.tex +199 -0
  251. scientific_writer/.claude/skills/scientific-schematics/assets/circuit_template.tex +159 -0
  252. scientific_writer/.claude/skills/scientific-schematics/assets/flowchart_template.tex +161 -0
  253. scientific_writer/.claude/skills/scientific-schematics/assets/pathway_template.tex +162 -0
  254. scientific_writer/.claude/skills/scientific-schematics/assets/tikz_styles.tex +422 -0
  255. scientific_writer/.claude/skills/scientific-schematics/references/best_practices.md +562 -0
  256. scientific_writer/.claude/skills/scientific-schematics/references/diagram_types.md +637 -0
  257. scientific_writer/.claude/skills/scientific-schematics/references/python_libraries.md +791 -0
  258. scientific_writer/.claude/skills/scientific-schematics/references/tikz_guide.md +734 -0
  259. scientific_writer/.claude/skills/scientific-schematics/scripts/circuit_generator.py +307 -0
  260. scientific_writer/.claude/skills/scientific-schematics/scripts/compile_tikz.py +292 -0
  261. scientific_writer/.claude/skills/scientific-schematics/scripts/generate_flowchart.py +281 -0
  262. scientific_writer/.claude/skills/scientific-schematics/scripts/pathway_diagram.py +406 -0
  263. scientific_writer/.claude/skills/scientific-writing/SKILL.md +443 -0
  264. scientific_writer/.claude/skills/scientific-writing/references/citation_styles.md +720 -0
  265. scientific_writer/.claude/skills/scientific-writing/references/figures_tables.md +806 -0
  266. scientific_writer/.claude/skills/scientific-writing/references/imrad_structure.md +658 -0
  267. scientific_writer/.claude/skills/scientific-writing/references/reporting_guidelines.md +748 -0
  268. scientific_writer/.claude/skills/scientific-writing/references/writing_principles.md +824 -0
  269. scientific_writer/.claude/skills/treatment-plans/README.md +483 -0
  270. scientific_writer/.claude/skills/treatment-plans/SKILL.md +817 -0
  271. scientific_writer/.claude/skills/treatment-plans/assets/chronic_disease_management_plan.tex +636 -0
  272. scientific_writer/.claude/skills/treatment-plans/assets/general_medical_treatment_plan.tex +616 -0
  273. scientific_writer/.claude/skills/treatment-plans/assets/mental_health_treatment_plan.tex +745 -0
  274. scientific_writer/.claude/skills/treatment-plans/assets/pain_management_plan.tex +770 -0
  275. scientific_writer/.claude/skills/treatment-plans/assets/perioperative_care_plan.tex +724 -0
  276. scientific_writer/.claude/skills/treatment-plans/assets/quality_checklist.md +471 -0
  277. scientific_writer/.claude/skills/treatment-plans/assets/rehabilitation_treatment_plan.tex +727 -0
  278. scientific_writer/.claude/skills/treatment-plans/references/goal_setting_frameworks.md +411 -0
  279. scientific_writer/.claude/skills/treatment-plans/references/intervention_guidelines.md +507 -0
  280. scientific_writer/.claude/skills/treatment-plans/references/regulatory_compliance.md +476 -0
  281. scientific_writer/.claude/skills/treatment-plans/references/specialty_specific_guidelines.md +607 -0
  282. scientific_writer/.claude/skills/treatment-plans/references/treatment_plan_standards.md +456 -0
  283. scientific_writer/.claude/skills/treatment-plans/scripts/check_completeness.py +318 -0
  284. scientific_writer/.claude/skills/treatment-plans/scripts/generate_template.py +244 -0
  285. scientific_writer/.claude/skills/treatment-plans/scripts/timeline_generator.py +369 -0
  286. scientific_writer/.claude/skills/treatment-plans/scripts/validate_treatment_plan.py +367 -0
  287. scientific_writer/.claude/skills/venue-templates/SKILL.md +590 -0
  288. scientific_writer/.claude/skills/venue-templates/assets/grants/nih_specific_aims.tex +235 -0
  289. scientific_writer/.claude/skills/venue-templates/assets/grants/nsf_proposal_template.tex +375 -0
  290. scientific_writer/.claude/skills/venue-templates/assets/journals/nature_article.tex +171 -0
  291. scientific_writer/.claude/skills/venue-templates/assets/journals/neurips_article.tex +283 -0
  292. scientific_writer/.claude/skills/venue-templates/assets/journals/plos_one.tex +317 -0
  293. scientific_writer/.claude/skills/venue-templates/assets/posters/beamerposter_academic.tex +311 -0
  294. scientific_writer/.claude/skills/venue-templates/references/conferences_formatting.md +564 -0
  295. scientific_writer/.claude/skills/venue-templates/references/grants_requirements.md +787 -0
  296. scientific_writer/.claude/skills/venue-templates/references/journals_formatting.md +486 -0
  297. scientific_writer/.claude/skills/venue-templates/references/posters_guidelines.md +628 -0
  298. scientific_writer/.claude/skills/venue-templates/scripts/customize_template.py +206 -0
  299. scientific_writer/.claude/skills/venue-templates/scripts/query_template.py +260 -0
  300. scientific_writer/.claude/skills/venue-templates/scripts/validate_format.py +255 -0
  301. scientific_writer/CLAUDE.md +748 -0
  302. scientific_writer/__init__.py +2 -2
  303. scientific_writer/api.py +14 -7
  304. scientific_writer/cli.py +12 -7
  305. scientific_writer/core.py +27 -5
  306. {scientific_writer-2.1.1.dist-info → scientific_writer-2.2.2.dist-info}/METADATA +5 -1
  307. scientific_writer-2.2.2.dist-info/RECORD +312 -0
  308. scientific_writer-2.1.1.dist-info/RECORD +0 -11
  309. {scientific_writer-2.1.1.dist-info → scientific_writer-2.2.2.dist-info}/WHEEL +0 -0
  310. {scientific_writer-2.1.1.dist-info → scientific_writer-2.2.2.dist-info}/entry_points.txt +0 -0
  311. {scientific_writer-2.1.1.dist-info → scientific_writer-2.2.2.dist-info}/licenses/LICENSE +0 -0
@@ -0,0 +1,564 @@
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+ # Conference Formatting Requirements
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+
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+ Comprehensive formatting requirements and submission guidelines for major academic conferences across disciplines.
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+
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+ **Last Updated**: 2024
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+
7
+ ---
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+
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+ ## Machine Learning & Artificial Intelligence
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+
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+ ### NeurIPS (Neural Information Processing Systems)
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+
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+ **Conference Type**: Top-tier machine learning conference
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+ **Frequency**: Annual (December)
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+
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+ **Formatting Requirements**:
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+ - **Page Limit**:
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+ - Main paper: 8 pages (excluding references)
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+ - References: Unlimited
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+ - Appendix/Supplementary: Unlimited (optional, reviewed at discretion)
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+ - **Format**: Two-column
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+ - **Font**: Times or Times New Roman, 10pt for body text
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+ - **Line spacing**: Single-spaced
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+ - **Margins**: 1 inch (2.54 cm) all sides
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+ - **Column separation**: 0.25 inch (0.635 cm)
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+ - **Paper size**: US Letter (8.5 × 11 inches)
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+ - **Anonymization**: **Required** for initial submission (double-blind review)
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+ - Remove author names, affiliations
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+ - Anonymize self-citations ("Author et al." → "Anonymous et al.")
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+ - Remove acknowledgments revealing identity
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+ - **Citations**: Numbered in square brackets [1], [2-4]
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+ - **References**: Any consistent style (commonly uses numbered references)
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+ - **Figures**:
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+ - High resolution (300+ dpi)
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+ - Colorblind-friendly palettes recommended
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+ - Can span both columns if needed
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+ - **Tables**: Clear, readable at publication size
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+ - **Equations**: Numbered if referenced
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+ - **LaTeX Class**: `neurips_2024.sty` (updated annually)
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+ - **Supplementary Materials**:
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+ - Code strongly encouraged (GitHub, anonymous repo for review)
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+ - Additional experiments, proofs
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+ - Not counted toward page limit
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+
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+ **LaTeX Template**: `assets/journals/neurips_article.tex`
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+
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+ **Submission Notes**:
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+ - Use official style file (changes yearly)
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+ - Paper ID on first page (auto-generated during submission)
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+ - Include "broader impact" statement (varies by year)
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+ - Reproducibility checklist required
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+
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+ **Website**: https://neurips.cc/
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+
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+ ---
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+
57
+ ### ICML (International Conference on Machine Learning)
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+
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+ **Conference Type**: Top-tier machine learning conference
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+ **Frequency**: Annual (July)
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+
62
+ **Formatting Requirements**:
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+ - **Page Limit**:
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+ - Main paper: 8 pages (excluding references and appendix)
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+ - References: Unlimited
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+ - Appendix: Unlimited (optional)
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+ - **Format**: Two-column
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+ - **Font**: Times, 10pt
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+ - **Line spacing**: Single-spaced
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+ - **Margins**: 1 inch all sides
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+ - **Paper size**: US Letter
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+ - **Anonymization**: **Required** (double-blind)
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+ - **Citations**: Numbered or author-year (consistent style)
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+ - **Figures**: High resolution, colorblind-safe recommended
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+ - **LaTeX Class**: `icml2024.sty` (updated yearly)
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+ - **Supplementary**: Strongly encouraged (code, data, appendix)
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+
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+ **LaTeX Template**: `assets/journals/icml_article.tex`
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+
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+ **Submission Notes**:
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+ - Must use official ICML style file
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+ - Checklist for reproducibility
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+ - Ethics statement if applicable
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+
85
+ **Website**: https://icml.cc/
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+
87
+ ---
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+
89
+ ### ICLR (International Conference on Learning Representations)
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+
91
+ **Conference Type**: Top-tier deep learning conference
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+ **Frequency**: Annual (April/May)
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+
94
+ **Formatting Requirements**:
95
+ - **Page Limit**:
96
+ - Main paper: 8 pages (excluding references, appendix, ethics statement)
97
+ - References: Unlimited
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+ - Appendix: Unlimited
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+ - **Format**: Two-column
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+ - **Font**: Times, 10pt
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+ - **Anonymization**: **Required** (double-blind)
102
+ - **Citations**: Numbered [1] or author-year
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+ - **LaTeX Class**: `iclr2024_conference.sty`
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+ - **Supplementary**: Code and data encouraged (anonymous GitHub)
105
+ - **Open Review**: Reviews and responses are public post-decision
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+
107
+ **LaTeX Template**: `assets/journals/iclr_article.tex`
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+
109
+ **Unique Features**:
110
+ - OpenReview platform (transparent review process)
111
+ - Author-reviewer discussion during review
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+ - Camera-ready can exceed 8 pages
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+
114
+ **Website**: https://iclr.cc/
115
+
116
+ ---
117
+
118
+ ### CVPR (Computer Vision and Pattern Recognition)
119
+
120
+ **Conference Type**: Top-tier computer vision conference
121
+ **Frequency**: Annual (June)
122
+
123
+ **Formatting Requirements**:
124
+ - **Page Limit**:
125
+ - Main paper: 8 pages (including figures and tables, excluding references)
126
+ - References: Unlimited (separate section)
127
+ - **Format**: Two-column
128
+ - **Font**: Times Roman, 10pt
129
+ - **Anonymization**: **Required** (double-blind)
130
+ - Blur faces in images if needed
131
+ - Anonymize datasets if they reveal identity
132
+ - **Paper size**: US Letter
133
+ - **Citations**: Numbered [1]
134
+ - **Figures**: High resolution, can be color
135
+ - **LaTeX Template**: CVPR official template (changes yearly)
136
+ - **Supplementary Material**:
137
+ - Video demonstrations encouraged
138
+ - Additional results, code
139
+ - 100 MB limit for all supplementary files
140
+
141
+ **LaTeX Template**: `assets/journals/cvpr_article.tex`
142
+
143
+ **Website**: https://cvpr.thecvf.com/
144
+
145
+ ---
146
+
147
+ ### AAAI (Association for the Advancement of Artificial Intelligence)
148
+
149
+ **Conference Type**: Major AI conference
150
+ **Frequency**: Annual (February)
151
+
152
+ **Formatting Requirements**:
153
+ - **Page Limit**:
154
+ - Technical papers: 7 pages (excluding references)
155
+ - References: Unlimited
156
+ - **Format**: Two-column
157
+ - **Font**: Times Roman, 10pt
158
+ - **Anonymization**: **Required** (double-blind)
159
+ - **Paper size**: US Letter
160
+ - **Citations**: Various styles accepted (be consistent)
161
+ - **LaTeX Template**: AAAI official style
162
+ - **Supplementary**: Optional appendix
163
+
164
+ **LaTeX Template**: `assets/journals/aaai_article.tex`
165
+
166
+ **Website**: https://aaai.org/conference/aaai/
167
+
168
+ ---
169
+
170
+ ### IJCAI (International Joint Conference on Artificial Intelligence)
171
+
172
+ **Conference Type**: Major AI conference
173
+ **Frequency**: Annual
174
+
175
+ **Formatting Requirements**:
176
+ - **Page Limit**: 7 pages (excluding references)
177
+ - **Format**: Two-column
178
+ - **Font**: Times, 10pt
179
+ - **Anonymization**: **Required**
180
+ - **LaTeX Template**: IJCAI official style
181
+
182
+ ---
183
+
184
+ ## Computer Science
185
+
186
+ ### ACM CHI (Human-Computer Interaction)
187
+
188
+ **Conference Type**: Premier HCI conference
189
+ **Frequency**: Annual (April/May)
190
+
191
+ **Formatting Requirements**:
192
+ - **Page Limit**:
193
+ - Papers: 10 pages (excluding references)
194
+ - Late-Breaking Work: 4 pages
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+ - **Format**: Single-column ACM format
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+ - **Font**: Depends on ACM template
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+ - **Anonymization**: **Required** for Papers track
198
+ - **LaTeX Class**: `acmart` with CHI proceedings format
199
+ - **Citations**: ACM style (numbered or author-year)
200
+ - **Figures**: High quality, accessibility considered
201
+ - **Accessibility**: Alt text for figures encouraged
202
+
203
+ **LaTeX Template**: `assets/journals/chi_article.tex`
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+
205
+ **Website**: https://chi.acm.org/
206
+
207
+ ---
208
+
209
+ ### SIGKDD (Knowledge Discovery and Data Mining)
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+
211
+ **Conference Type**: Top data mining conference
212
+ **Frequency**: Annual (August)
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+
214
+ **Formatting Requirements**:
215
+ - **Page Limit**:
216
+ - Research Track: 9 pages (excluding references)
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+ - Applied Data Science: 9 pages
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+ - **Format**: Two-column
219
+ - **LaTeX Class**: `acmart` (sigconf format)
220
+ - **Font**: ACM template default
221
+ - **Anonymization**: **Required** (double-blind)
222
+ - **Citations**: ACM numbered style
223
+ - **Supplementary**: Code and data encouraged
224
+
225
+ **LaTeX Template**: `assets/journals/kdd_article.tex`
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+
227
+ **Website**: https://kdd.org/
228
+
229
+ ---
230
+
231
+ ### EMNLP (Empirical Methods in Natural Language Processing)
232
+
233
+ **Conference Type**: Top NLP conference
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+ **Frequency**: Annual (November/December)
235
+
236
+ **Formatting Requirements**:
237
+ - **Page Limit**:
238
+ - Long papers: 8 pages (+ unlimited references and appendix)
239
+ - Short papers: 4 pages (+ unlimited references)
240
+ - **Format**: Two-column
241
+ - **Font**: Times New Roman, 11pt
242
+ - **Anonymization**: **Required** (double-blind)
243
+ - Do not include author names or affiliations
244
+ - Self-citations should be anonymized
245
+ - **Paper size**: US Letter or A4
246
+ - **Citations**: Named style similar to ACL
247
+ - **LaTeX Template**: ACL/EMNLP official style
248
+ - **Supplementary**: Appendix unlimited, code encouraged
249
+
250
+ **LaTeX Template**: `assets/journals/emnlp_article.tex`
251
+
252
+ **Website**: https://www.emnlp.org/
253
+
254
+ ---
255
+
256
+ ### ACL (Association for Computational Linguistics)
257
+
258
+ **Conference Type**: Premier NLP conference
259
+ **Frequency**: Annual (July)
260
+
261
+ **Formatting Requirements**:
262
+ - **Page Limit**: 8 pages (long), 4 pages (short), excluding references
263
+ - **Format**: Two-column
264
+ - **Font**: Times, 11pt
265
+ - **Anonymization**: **Required**
266
+ - **LaTeX Template**: ACL official style (acl.sty)
267
+
268
+ **LaTeX Template**: `assets/journals/acl_article.tex`
269
+
270
+ ---
271
+
272
+ ### USENIX Security Symposium
273
+
274
+ **Conference Type**: Top security conference
275
+ **Frequency**: Annual (August)
276
+
277
+ **Formatting Requirements**:
278
+ - **Page Limit**:
279
+ - Papers: No strict limit (typically 15-20 pages including everything)
280
+ - Well-written, concise papers preferred
281
+ - **Format**: Two-column
282
+ - **Font**: Times, 10pt
283
+ - **Anonymization**: **Required** (double-blind)
284
+ - **LaTeX Template**: USENIX official template
285
+ - **Citations**: Numbered
286
+ - **Paper size**: US Letter
287
+
288
+ **LaTeX Template**: `assets/journals/usenix_article.tex`
289
+
290
+ **Website**: https://www.usenix.org/conference/usenixsecurity
291
+
292
+ ---
293
+
294
+ ### SIGIR (Information Retrieval)
295
+
296
+ **Conference Type**: Top information retrieval conference
297
+ **Frequency**: Annual (July)
298
+
299
+ **Formatting Requirements**:
300
+ - **Page Limit**:
301
+ - Full papers: 10 pages (excluding references)
302
+ - Short papers: 4 pages (excluding references)
303
+ - **Format**: Single-column ACM format
304
+ - **LaTeX Class**: `acmart` (sigconf)
305
+ - **Anonymization**: **Required**
306
+ - **Citations**: ACM style
307
+
308
+ **LaTeX Template**: `assets/journals/sigir_article.tex`
309
+
310
+ ---
311
+
312
+ ## Biology & Bioinformatics
313
+
314
+ ### ISMB (Intelligent Systems for Molecular Biology)
315
+
316
+ **Conference Type**: Premier computational biology conference
317
+ **Frequency**: Annual (July)
318
+
319
+ **Formatting Requirements**:
320
+ - **Publication**: Proceedings published in *Bioinformatics* journal
321
+ - **Page Limit**:
322
+ - Typically 7-8 pages including figures and references
323
+ - **Format**: Two-column
324
+ - **Font**: Times, 10pt
325
+ - **Citations**: Numbered (Oxford style similar to Bioinformatics journal)
326
+ - **LaTeX Template**: Oxford Bioinformatics template
327
+ - **Anonymization**: **Not required** (single-blind)
328
+ - **Figures**: High resolution, color acceptable
329
+ - **Supplementary**: Encouraged for additional data/methods
330
+
331
+ **LaTeX Template**: `assets/journals/ismb_article.tex`
332
+
333
+ **Website**: https://www.iscb.org/ismb
334
+
335
+ ---
336
+
337
+ ### RECOMB (Research in Computational Molecular Biology)
338
+
339
+ **Conference Type**: Top computational biology conference
340
+ **Frequency**: Annual (April/May)
341
+
342
+ **Formatting Requirements**:
343
+ - **Publication**: Proceedings published as Springer LNCS (Lecture Notes in Computer Science)
344
+ - **Page Limit**:
345
+ - Extended abstracts: 12-15 pages (including references)
346
+ - **Format**: Single-column
347
+ - **Font**: Based on Springer LNCS template
348
+ - **LaTeX Class**: `llncs` (Springer)
349
+ - **Citations**: Numbered or author-year
350
+ - **Anonymization**: **Required** (double-blind)
351
+ - **Supplementary**: Appendix can be submitted
352
+
353
+ **LaTeX Template**: `assets/journals/recomb_article.tex`
354
+
355
+ **Website**: https://www.recomb.org/
356
+
357
+ ---
358
+
359
+ ### PSB (Pacific Symposium on Biocomputing)
360
+
361
+ **Conference Type**: Biomedical informatics conference
362
+ **Frequency**: Annual (January)
363
+
364
+ **Formatting Requirements**:
365
+ - **Page Limit**: 12 pages including figures and references
366
+ - **Format**: Single-column
367
+ - **Font**: Times, 11pt
368
+ - **Margins**: 1 inch all sides
369
+ - **Citations**: Numbered
370
+ - **Anonymization**: **Not required**
371
+ - **Figures**: Embedded in text
372
+ - **LaTeX Template**: PSB official template
373
+
374
+ **LaTeX Template**: `assets/journals/psb_article.tex`
375
+
376
+ **Website**: https://psb.stanford.edu/
377
+
378
+ ---
379
+
380
+ ## Engineering
381
+
382
+ ### IEEE International Conference on Robotics and Automation (ICRA)
383
+
384
+ **Formatting Requirements**:
385
+ - **Page Limit**: 8 pages (including figures and references)
386
+ - **Format**: Two-column
387
+ - **Font**: Times, 10pt
388
+ - **LaTeX Class**: IEEEtran
389
+ - **Citations**: IEEE style [1]
390
+ - **Anonymization**: **Required** for initial submission
391
+ - **Video**: Optional video submissions encouraged
392
+
393
+ **LaTeX Template**: `assets/journals/icra_article.tex`
394
+
395
+ ---
396
+
397
+ ### IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS)
398
+
399
+ **Formatting**: Same as ICRA (IEEE robotics template)
400
+
401
+ ---
402
+
403
+ ### International Conference on Computer-Aided Design (ICCAD)
404
+
405
+ **Formatting Requirements**:
406
+ - **Page Limit**: 8 pages
407
+ - **Format**: Two-column
408
+ - **LaTeX Class**: IEEE template
409
+ - **Citations**: IEEE style
410
+
411
+ ---
412
+
413
+ ### Design Automation Conference (DAC)
414
+
415
+ **Formatting Requirements**:
416
+ - **Page Limit**: 6 pages
417
+ - **Format**: Two-column
418
+ - **Font**: Times, 10pt
419
+ - **LaTeX Class**: ACM or IEEE template (check yearly guidelines)
420
+
421
+ ---
422
+
423
+ ## Multidisciplinary
424
+
425
+ ### AAAS Annual Meeting
426
+
427
+ **Conference Type**: Broad scientific conference
428
+ **Formatting**: Varies by symposium (typically extended abstracts)
429
+
430
+ ---
431
+
432
+ ## Quick Reference Table
433
+
434
+ | Conference | Pages | Format | Blind | Citations | Template |
435
+ |------------|-------|--------|-------|-----------|----------|
436
+ | **NeurIPS** | 8 + refs | Two-col | Double | [1] | `neurips_article.tex` |
437
+ | **ICML** | 8 + refs | Two-col | Double | [1] | `icml_article.tex` |
438
+ | **ICLR** | 8 + refs | Two-col | Double | [1] | `iclr_article.tex` |
439
+ | **CVPR** | 8 + refs | Two-col | Double | [1] | `cvpr_article.tex` |
440
+ | **AAAI** | 7 + refs | Two-col | Double | Various | `aaai_article.tex` |
441
+ | **CHI** | 10 + refs | Single-col | Double | ACM | `chi_article.tex` |
442
+ | **SIGKDD** | 9 + refs | Two-col | Double | ACM [1] | `kdd_article.tex` |
443
+ | **EMNLP** | 8 + refs | Two-col | Double | Named | `emnlp_article.tex` |
444
+ | **ISMB** | 7-8 pages | Two-col | Single | [1] | `ismb_article.tex` |
445
+ | **RECOMB** | 12-15 pages | Single-col | Double | Springer | `recomb_article.tex` |
446
+
447
+ ---
448
+
449
+ ## General Conference Submission Guidelines
450
+
451
+ ### Anonymization Best Practices (Double-Blind Review)
452
+
453
+ **Remove**:
454
+ - Author names, affiliations, emails from title page
455
+ - Acknowledgments section
456
+ - Funding information that reveals identity
457
+ - Any "our previous work" citations that make identity obvious
458
+
459
+ **Anonymize**:
460
+ - Self-citations: "Smith et al. [5]" → "Anonymous et al. [5]" or "Prior work [5]"
461
+ - Institution-specific details: "our university" → "a large research university"
462
+ - Dataset names if they reveal identity
463
+
464
+ **Keep Anonymous**:
465
+ - Code repositories (use anonymous GitHub for review)
466
+ - Supplementary materials
467
+ - Any URLs or links
468
+
469
+ ### Supplementary Materials
470
+
471
+ **Common Inclusions**:
472
+ - Source code (GitHub repository, zip file)
473
+ - Additional experimental results
474
+ - Proofs and derivations
475
+ - Extended related work
476
+ - Dataset descriptions
477
+ - Video demonstrations
478
+ - Interactive demos
479
+
480
+ **Best Practices**:
481
+ - Keep supplementary well-organized
482
+ - Reference supplementary clearly from main paper
483
+ - Ensure supplementary is anonymized for blind review
484
+ - Check file size limits (typically 50-100 MB)
485
+
486
+ ### Camera-Ready Preparation
487
+
488
+ After acceptance:
489
+ 1. **De-anonymize**: Add author names, affiliations
490
+ 2. **Add acknowledgments**: Funding, contributions
491
+ 3. **Copyright**: Add conference copyright notice
492
+ 4. **Formatting**: Follow camera-ready specific guidelines
493
+ 5. **Page limit**: May allow 1-2 extra pages (check guidelines)
494
+ 6. **PDF/A compliance**: Some conferences require PDF/A format
495
+
496
+ ### Accessibility Considerations
497
+
498
+ **For All Conferences**:
499
+ - Use colorblind-safe color palettes
500
+ - Ensure sufficient contrast
501
+ - Provide alt text for figures (where supported)
502
+ - Use clear, readable fonts
503
+ - Avoid solely color-based distinctions
504
+
505
+ ---
506
+
507
+ ## Common Mistakes to Avoid
508
+
509
+ 1. **Wrong style file**: Using outdated conference style file
510
+ 2. **Page limit violation**: Figures/tables pushing over limit
511
+ 3. **Font size manipulation**: Changing fonts to fit more content
512
+ 4. **Margin adjustments**: Modifying margins to gain space
513
+ 5. **De-anonymization**: Accidentally revealing identity in blind review
514
+ 6. **Missing references**: Not citing relevant prior work
515
+ 7. **Low-quality figures**: Pixelated or illegible figures
516
+ 8. **Inconsistent formatting**: Different sections using different styles
517
+
518
+ ---
519
+
520
+ ## Getting Official Templates
521
+
522
+ **Where to Find Official Templates**:
523
+ 1. **Conference website**: "Call for Papers" or "Author Instructions"
524
+ 2. **GitHub**: Many conferences host templates on GitHub
525
+ 3. **Overleaf**: Many official templates available on Overleaf
526
+ 4. **CTAN**: LaTeX class files often on CTAN repository
527
+
528
+ **Template Naming**:
529
+ - Conferences often update templates yearly
530
+ - Use the correct year's template (e.g., `neurips_2024.sty`)
531
+ - Check for "camera-ready" vs. "submission" versions
532
+
533
+ ---
534
+
535
+ ## Notes
536
+
537
+ 1. **Annual updates**: Conference requirements change; always check current year's CFP
538
+ 2. **Deadline types**:
539
+ - Abstract deadline (often 1 week before paper deadline)
540
+ - Paper deadline (firm, no extensions typically)
541
+ - Supplementary deadline (may be a few days after paper)
542
+ 3. **Timezone**: Pay attention to deadline timezone (often AOE - Anywhere on Earth)
543
+ 4. **Rebuttal**: Many conferences have author response/rebuttal periods
544
+ 5. **Dual submission**: Check conference policy on concurrent submissions
545
+ 6. **Poster/Oral**: Acceptance often comes with presentation format
546
+
547
+ ## Conference Tiers (Informal)
548
+
549
+ **Machine Learning**:
550
+ - **Tier 1**: NeurIPS, ICML, ICLR
551
+ - **Tier 2**: AAAI, IJCAI, UAI
552
+
553
+ **Computer Vision**:
554
+ - **Tier 1**: CVPR, ICCV, ECCV
555
+
556
+ **Natural Language Processing**:
557
+ - **Tier 1**: ACL, EMNLP, NAACL
558
+
559
+ **Bioinformatics**:
560
+ - **Tier 1**: RECOMB, ISMB
561
+ - **Tier 2**: PSB, WABI
562
+
563
+ (Tiers are informal and field-dependent; not official rankings)
564
+