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 +1,787 @@
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+ # Grant Proposal Requirements
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+
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+ Comprehensive requirements and formatting guidelines for major federal and private foundation grant programs.
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+
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+ **Last Updated**: 2024
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+
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+ ---
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+
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+ ## NSF (National Science Foundation)
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+
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+ ### Overview
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+
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+ **Agency**: National Science Foundation
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+ **Typical Award**: $100K-$500K per year, 3-5 years
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+ **Success Rate**: 20-25% (varies by program)
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+ **Review Criteria**: Intellectual Merit + Broader Impacts (equally weighted)
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+
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+ ---
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+
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+ ### NSF Standard Grant Proposal
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+
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+ **Page Limits (NSF PAPPG - Proposal & Award Policies & Procedures Guide)**:
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+
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+ | Component | Page Limit | Font | Spacing |
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+ |-----------|-----------|------|---------|
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+ | **Project Summary** | 1 page | Any readable, 10pt+ | Any |
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+ | **Project Description** | 15 pages | Times Roman 11pt or similar | Single |
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+ | **References Cited** | No limit | Times Roman 11pt | Single |
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+ | **Biographical Sketch** | 3 pages per person | Times Roman 11pt | Single |
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+ | **Budget Justification** | 3-5 pages | Any readable | Any |
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+ | **Current & Pending Support** | No limit | Times Roman 11pt | Single |
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+ | **Facilities, Equipment** | 2 pages | Any readable | Any |
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+ | **Data Management Plan** | 2 pages | Any readable | Any |
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+
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+ **Margins**: 1 inch (2.54 cm) on all sides (strictly enforced)
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+
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+ ---
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+
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+ ### NSF Project Summary (1 page)
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+
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+ **Required Sections** (clearly labeled):
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+
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+ 1. **Overview** (1-2 paragraphs)
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+ - Concise description of research activity
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+ - Objectives and methods
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+
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+ 2. **Intellectual Merit** (1 paragraph)
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+ - How project advances knowledge
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+ - Innovation and transformative potential
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+ - Qualifications of research team
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+
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+ 3. **Broader Impacts** (1 paragraph)
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+ - Benefits to society
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+ - Broadening participation
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+ - Dissemination and outreach
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+
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+ **Format**: Can be full-page text or sectioned
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+ **Audience**: Non-specialists (broad scientific community)
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+
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+ **Template**: `assets/grants/nsf_project_summary.tex`
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+
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+ ---
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+
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+ ### NSF Project Description (15 pages)
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+
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+ **Typical Structure**:
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+
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+ 1. **Introduction/Background** (2-3 pages)
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+ - Current state of knowledge
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+ - Research gap
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+ - Preliminary work/feasibility
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+ - Team qualifications
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+
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+ 2. **Research Plan** (8-10 pages)
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+ - Objectives and hypotheses
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+ - Methods and approach
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+ - Timeline and milestones
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+ - Expected outcomes
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+
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+ 3. **Broader Impacts** (1-2 pages)
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+ - Educational activities
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+ - Broadening participation (underrepresented groups)
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+ - Dissemination (publications, conferences, public outreach)
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+ - Societal benefits
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+
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+ 4. **Results from Prior NSF Support** (1 page, if applicable)
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+ - Required if PI has had NSF support in past 5 years
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+ - Intellectual merit and broader impacts of prior work
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+ - Publications from prior NSF grants
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+
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+ **Key Requirements**:
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+ - Intellectual Merit and Broader Impacts integrated throughout
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+ - Figures and tables allowed (count toward page limit)
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+ - Citations to references (use References Cited section)
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+
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+ **Template**: `assets/grants/nsf_proposal_template.tex`
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+
98
+ ---
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+
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+ ### NSF Biographical Sketch (3 pages)
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+
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+ **Required Sections**:
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+ 1. **Professional Preparation**: Institutions, degrees, fields
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+ 2. **Appointments**: Current and previous positions
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+ 3. **Products**: Up to 5 most relevant, up to 5 other significant products
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+ - Can include publications, datasets, software, patents
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+ 4. **Synergistic Activities**: Up to 5 examples of impact beyond research
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+
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+ **Format**:
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+ - NSF template must be used (SciENcv or NSF-approved format)
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+ - No longer uses "Publications" but "Products"
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+
113
+ ---
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+
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+ ### NSF Broader Impacts
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+
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+ **NSF-Recognized Categories** (demonstrate ≥1):
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+ 1. **Advance discovery while promoting teaching/learning**
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+ 2. **Broaden participation** of underrepresented groups
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+ 3. **Disseminate broadly** to enhance scientific/technological understanding
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+ 4. **Benefits to society** (economic, health, environment, national security)
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+ 5. **Develop scientific workforce** and infrastructure
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+
124
+ **Best Practices**:
125
+ - Be specific with measurable outcomes
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+ - Explain how activities will be assessed
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+ - Integrate with research (don't treat as "add-on")
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+ - Budget for broader impacts activities
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+
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+ **Examples**:
131
+ - K-12 outreach programs
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+ - Curriculum development
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+ - Training underrepresented students
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+ - Public science communication
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+ - Open-source software development
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+
137
+ ---
138
+
139
+ ### NSF Budget
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+
141
+ **Typical Categories**:
142
+ - **Senior Personnel**: PI, co-PIs (% effort, salary)
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+ - **Other Personnel**: Postdocs, graduate students, undergrads
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+ - **Fringe Benefits**: Institutional rates
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+ - **Equipment**: Items >$5,000
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+ - **Travel**: Domestic and foreign
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+ - **Participant Support**: Workshops, conferences (separate category)
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+ - **Other Direct Costs**: Materials, publication, subawards
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+ - **Indirect Costs**: Institutional F&A rate
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+
151
+ **Budget Justification**: Explain need for each item
152
+
153
+ ---
154
+
155
+ ### NSF Data Management Plan (2 pages)
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+
157
+ **Required Content**:
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+ - Types of data produced
159
+ - Standards for data format and metadata
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+ - Policies for access and sharing
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+ - Policies for re-use and redistribution
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+ - Plans for archiving and preservation
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+
164
+ **Acceptable Approaches**:
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+ - Deposit in domain-specific repository
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+ - Institutional repository
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+ - Data available upon request (with restrictions justification)
168
+
169
+ ---
170
+
171
+ ### NSF Review Process
172
+
173
+ **Review Criteria** (equally weighted):
174
+
175
+ 1. **Intellectual Merit**:
176
+ - What is the potential to advance knowledge?
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+ - How well-conceived and organized?
178
+ - Qualifications of PI and team?
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+ - Availability of resources?
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+
181
+ 2. **Broader Impacts**:
182
+ - What are the potential benefits to society?
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+ - How well-suited to achieve broader impacts?
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+
185
+ **Panel Review**: Proposals reviewed by panel of experts
186
+ **Timeline**: Typically 6 months from deadline to award decision
187
+
188
+ ---
189
+
190
+ ### NSF LaTeX Templates
191
+
192
+ - **Full Proposal**: `assets/grants/nsf_proposal_template.tex`
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+ - **Project Summary**: `assets/grants/nsf_project_summary.tex`
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+ - **Biographical Sketch**: Use NSF SciENcv or template
195
+
196
+ **Resources**:
197
+ - NSF PAPPG: https://www.nsf.gov/publications/pub_summ.jsp?ods_key=pappg
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+ - NSF Fastlane: https://www.fastlane.nsf.gov/
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+
200
+ ---
201
+
202
+ ## NIH (National Institutes of Health)
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+
204
+ ### Overview
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+
206
+ **Agency**: National Institutes of Health
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+ **Funding Mechanisms**:
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+ - **R01**: Research Project Grant (most common)
209
+ - **R21**: Exploratory/Developmental Research Grant
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+ - **K Awards**: Career Development Awards
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+ **Success Rate**: 10-20% (varies by institute and mechanism)
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+
213
+ ---
214
+
215
+ ### NIH R01 Research Grant
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+
217
+ **Page Limits** (Research Strategy):
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+
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+ | Component | Page Limit | Font | Spacing |
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+ |-----------|-----------|------|---------|
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+ | **Specific Aims** | 1 page | Arial 11pt minimum | Any |
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+ | **Research Strategy** | 12 pages | Arial 11pt minimum | 0.5 inch margins minimum |
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+ | - Significance | Part of 12 | | |
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+ | - Innovation | Part of 12 | | |
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+ | - Approach | Part of 12 | | |
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+ | **Bibliography** | No limit | Arial 11pt | |
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+ | **Biographical Sketch** | 5 pages per person | Arial 11pt | |
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+
229
+ **Margins**: 0.5 inch minimum (all sides)
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+ **Paper Size**: Letter (8.5 × 11 inches)
231
+
232
+ ---
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+
234
+ ### NIH Specific Aims Page (1 page)
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+
236
+ **THE MOST CRITICAL COMPONENT**
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+
238
+ **Structure** (recommended):
239
+
240
+ 1. **Opening paragraph** (2-3 sentences)
241
+ - Hook: Significance of problem
242
+ - Gap: What's not known
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+
244
+ 2. **Long-term goal** (1 sentence)
245
+ - Overarching research vision
246
+
247
+ 3. **Objective** (1-2 sentences)
248
+ - What this proposal will accomplish
249
+ - Central hypothesis
250
+
251
+ 4. **Rationale** (2-3 sentences)
252
+ - Why you expect success
253
+ - Preliminary data supporting hypothesis
254
+
255
+ 5. **Specific Aims** (3 aims typical)
256
+ - **Aim 1**: [Title]. [1-2 sentence description. Working hypothesis. Expected outcome.]
257
+ - **Aim 2**: [Title]. [1-2 sentence description. Working hypothesis. Expected outcome.]
258
+ - **Aim 3**: [Title]. [1-2 sentence description. Working hypothesis. Expected outcome.]
259
+
260
+ 6. **Payoff paragraph** (2-3 sentences)
261
+ - Impact and significance
262
+ - Innovation
263
+ - Future directions
264
+
265
+ **Best Practices**:
266
+ - Crystal clear, compelling narrative
267
+ - State hypothesis explicitly
268
+ - Explain expected outcomes
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+ - Show innovation and impact
270
+
271
+ **Template**: `assets/grants/nih_specific_aims.tex`
272
+
273
+ ---
274
+
275
+ ### NIH Research Strategy (12 pages)
276
+
277
+ **Required Sections**:
278
+
279
+ #### 1. Significance (typically 2-3 pages)
280
+ - **Importance**: Critical barrier to progress
281
+ - **Knowledge gap**: What's not known
282
+ - **Impact**: How project advances field
283
+ - **Rigor**: Scientific premise/prior work
284
+ - **References**: Cite key literature
285
+
286
+ #### 2. Innovation (typically 1-2 pages)
287
+ - **Novelty**: New concepts, approaches, methods
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+ - **Challenge paradigms**: Shift thinking
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+ - **Refined/new methodologies**: Technical innovation
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+ - **Novel applications**: Existing tools in new ways
291
+
292
+ #### 3. Approach (typically 7-9 pages)
293
+ **For Each Aim**:
294
+ - **Rationale**: Why this aim
295
+ - **Experimental design**: Detailed methods
296
+ - **Expected outcomes**: What results mean
297
+ - **Potential problems & alternatives**: Mitigation strategies
298
+ - **Rigor and reproducibility**: Controls, replication, statistics
299
+ - **Timeline**: When each aim completed
300
+
301
+ **Additional Approach Content**:
302
+ - Preliminary data (critical for R01)
303
+ - Power analyses for sample sizes
304
+ - Statistical analysis plans
305
+ - Rigor of prior research cited
306
+
307
+ ---
308
+
309
+ ### NIH Biographical Sketch (5 pages)
310
+
311
+ **Sections** (NIH format):
312
+ 1. **Personal Statement** (4 sentences explaining why you're suited)
313
+ 2. **Positions, Honors, and Scientific Appointments**
314
+ 3. **Contributions to Science** (Up to 5 contributions, up to 4 pubs each)
315
+ 4. **Research Support** (current and completed grants, overlap checked)
316
+
317
+ **Format**: Must use NIH template (fillable PDF or format page)
318
+
319
+ ---
320
+
321
+ ### NIH Review Criteria
322
+
323
+ **Scored Criteria** (1-9 scale, 1=best):
324
+ 1. **Significance**: Importance, impact
325
+ 2. **Investigator(s)**: Qualifications, track record
326
+ 3. **Innovation**: Novel concepts, methods
327
+ 4. **Approach**: Feasibility, rigor, design
328
+ 5. **Environment**: Institutional support, resources
329
+
330
+ **Additional Considerations** (not scored but noted):
331
+ - Vertebrate animals
332
+ - Biohazards
333
+ - Human subjects protections
334
+ - Inclusion of women, minorities, children
335
+ - Budget appropriateness
336
+
337
+ **Overall Impact Score**: 1-9 (synthesizes all criteria)
338
+
339
+ ---
340
+
341
+ ### NIH R21 (Exploratory Grant)
342
+
343
+ **Key Differences from R01**:
344
+ - **Research Strategy**: 6 pages (vs. 12 for R01)
345
+ - **Duration**: 2 years maximum
346
+ - **Budget**: $275K total costs over 2 years
347
+ - **Preliminary data**: Not required (exploratory nature)
348
+ - **Purpose**: High-risk, high-reward projects; new directions
349
+
350
+ **When to Choose R21 vs. R01**:
351
+ - R21: Early-stage, limited preliminary data, high-risk
352
+ - R01: Established line of research, strong preliminary data
353
+
354
+ ---
355
+
356
+ ### NIH K Awards (Career Development)
357
+
358
+ **Mechanisms**:
359
+ - **K01**: Mentored Research Scientist Development Award
360
+ - **K08**: Mentored Clinical Scientist Research Career Development Award
361
+ - **K23**: Mentored Patient-Oriented Research Career Development Award
362
+ - **K99/R00**: Pathway to Independence Award (postdoc to faculty)
363
+
364
+ **Key Components**:
365
+ - **Career Development Plan**: Training goals, timeline
366
+ - **Research Plan**: 6-12 pages (mechanism-dependent)
367
+ - **Mentor(s)**: Letters of support, mentoring plan
368
+ - **Institutional Commitment**: Environment, resources
369
+ - **Protected Time**: 75% research effort typical
370
+
371
+ ---
372
+
373
+ ### NIH Budget
374
+
375
+ **Modular vs. Detailed**:
376
+ - **Modular**: ≤$250K direct costs per year (25K increments)
377
+ - **Detailed**: >$250K direct costs per year
378
+
379
+ **Modular Budget**: Only need budget justification for personnel, consortium, equipment >$25K
380
+
381
+ **Budget Period**: Year-by-year (usually 5 years for R01)
382
+
383
+ ---
384
+
385
+ ### NIH LaTeX Templates
386
+
387
+ - **R01 Full Proposal**: `assets/grants/nih_r01_template.tex`
388
+ - **Specific Aims**: `assets/grants/nih_specific_aims.tex`
389
+ - **Biographical Sketch**: Use NIH fillable PDF or format page
390
+
391
+ **Resources**:
392
+ - NIH Application Guide: https://grants.nih.gov/grants/how-to-apply-application-guide.html
393
+ - SF424 Forms: https://grants.nih.gov/grants/how-to-apply-application-guide/forms-e/general-forms-e.pdf
394
+
395
+ ---
396
+
397
+ ## DOE (Department of Energy)
398
+
399
+ ### Overview
400
+
401
+ **Agency**: U.S. Department of Energy
402
+ **Offices**:
403
+ - **Office of Science**: Basic research (BES, BER, ASCR, NP, HEP, FES)
404
+ - **ARPA-E**: High-risk, high-reward energy technologies
405
+ - **EERE**: Energy efficiency and renewable energy
406
+
407
+ **Typical Award**: $200K-$1M per year, 3 years
408
+ **Success Rate**: 10-30% (varies by program)
409
+
410
+ ---
411
+
412
+ ### DOE Office of Science Proposal
413
+
414
+ **Page Limits** (typical, varies by FOA):
415
+
416
+ | Component | Page Limit | Format |
417
+ |-----------|-----------|--------|
418
+ | **Project Narrative** | 10-20 pages | Times 11pt, 1" margins |
419
+ | **References** | No limit | |
420
+ | **Budget Justification** | 3-5 pages | |
421
+ | **Biographical Sketches** | 2-3 pages each | |
422
+ | **Current & Pending** | No limit | |
423
+ | **Facilities & Resources** | No limit | |
424
+ | **Data Management Plan** | 2 pages | |
425
+
426
+ ---
427
+
428
+ ### DOE Project Narrative Structure
429
+
430
+ **Typical Sections**:
431
+
432
+ 1. **Background and Significance** (2-3 pages)
433
+ - Energy relevance
434
+ - Current state of knowledge
435
+ - Research need
436
+
437
+ 2. **Preliminary Work** (1-2 pages)
438
+ - Team's qualifications
439
+ - Relevant prior results
440
+
441
+ 3. **Research Plan** (10-15 pages)
442
+ - **Objectives**: Clear goals
443
+ - **Technical approach**: Detailed methods
444
+ - **Milestones and deliverables**: Specific, measurable
445
+ - **Timeline**: Gantt chart common
446
+ - **Team and management**: Roles, collaboration
447
+
448
+ 4. **Broader Impacts** (1-2 pages)
449
+ - Workforce development
450
+ - Technology transfer potential
451
+ - Publications and dissemination
452
+
453
+ ---
454
+
455
+ ### DOE-Specific Requirements
456
+
457
+ **Energy Relevance**: Must clearly tie to DOE mission
458
+ - Basic science: Fundamental understanding for energy applications
459
+ - Applied: Energy efficiency, renewable energy, grid, storage
460
+
461
+ **Technology Readiness Levels (TRLs)**: Often required to specify
462
+ - **TRL 1-3**: Basic research, proof of concept
463
+ - **TRL 4-6**: Component/subsystem validation
464
+ - **TRL 7-9**: System demonstration, deployment
465
+
466
+ **National Laboratory Collaboration**: Encouraged
467
+ - Include lab scientists as co-PIs or collaborators
468
+ - Letter of collaboration from lab
469
+
470
+ **Cost Sharing**: Sometimes required (check FOA)
471
+ - Can be in-kind (equipment, time)
472
+ - Must be documented
473
+
474
+ ---
475
+
476
+ ### DOE Budget Considerations
477
+
478
+ **Allowable Costs**:
479
+ - Personnel (salaries, benefits)
480
+ - Equipment
481
+ - Travel (especially to DOE national labs)
482
+ - Materials and supplies
483
+ - Subcontracts
484
+ - Indirect costs (negotiated F&A rate)
485
+
486
+ **Unallowable**:
487
+ - Construction
488
+ - Entertainment
489
+ - Some indirect costs (depends on institution type)
490
+
491
+ ---
492
+
493
+ ### DOE LaTeX Template
494
+
495
+ **Template**: `assets/grants/doe_proposal_template.tex`
496
+
497
+ **Resources**:
498
+ - DOE Office of Science Funding: https://science.osti.gov/grants
499
+ - EERE Funding: https://www.energy.gov/eere/funding/eere-funding-opportunities
500
+
501
+ ---
502
+
503
+ ## DARPA (Defense Advanced Research Projects Agency)
504
+
505
+ ### Overview
506
+
507
+ **Agency**: Defense Advanced Research Projects Agency (DoD)
508
+ **Mission**: High-risk, high-reward research for national security
509
+ **Typical Award**: $500K-$5M per year, 2-4 years
510
+ **Success Rate**: 5-15% (highly competitive)
511
+
512
+ ---
513
+
514
+ ### DARPA BAA (Broad Agency Announcement) Response
515
+
516
+ **Page Limits** (typical, varies by BAA):
517
+
518
+ | Component | Page Limit | Format |
519
+ |-----------|-----------|--------|
520
+ | **Technical and Management Proposal** | 20-25 pages | Times 12pt, 1" margins |
521
+ | **Cost Proposal** | Separate volume | |
522
+
523
+ ---
524
+
525
+ ### DARPA Technical Proposal Structure
526
+
527
+ **Key Sections**:
528
+
529
+ 1. **Executive Summary** (1 page)
530
+ - Vision and impact
531
+ - Technical approach overview
532
+ - Team qualifications
533
+
534
+ 2. **Heilmeier Catechism** (1-2 pages)
535
+ DARPA requires answering these questions:
536
+ - **What are you trying to do?** Articulate objectives without jargon
537
+ - **How is it done today? Limitations?** Current practice and shortcomings
538
+ - **What is new in your approach?** Innovation
539
+ - **Who cares?** Impact if successful
540
+ - **If successful, what difference will it make?** Transformation
541
+ - **What are the risks?** Technical risks and mitigation
542
+ - **How much will it cost?** Budget overview
543
+ - **How long will it take?** Timeline
544
+ - **What are the mid-term and final exams?** Milestones for success
545
+
546
+ 3. **Technical Approach** (10-15 pages)
547
+ - Detailed technical plan
548
+ - Task breakdown
549
+ - Risk mitigation
550
+ - Innovation justification
551
+
552
+ 4. **Management Plan** (2-3 pages)
553
+ - Team organization
554
+ - Key personnel roles
555
+ - Collaboration approach
556
+ - Milestone schedule (Gantt chart)
557
+
558
+ 5. **Capabilities and Experience** (2-3 pages)
559
+ - Team qualifications
560
+ - Relevant facilities and equipment
561
+ - Similar past programs
562
+
563
+ 6. **Transition Plan** (1-2 pages)
564
+ - Path to DoD transition
565
+ - End users identified
566
+ - Technology transfer approach
567
+
568
+ ---
569
+
570
+ ### DARPA-Specific Considerations
571
+
572
+ **Engagement with Program Manager (PM)**:
573
+ - **Strongly encouraged** to contact PM before submission
574
+ - Discuss idea alignment with program goals
575
+ - PM can provide feedback on approach
576
+
577
+ **Transformative Impact**:
578
+ - Must demonstrate potential for "game-changing" impact
579
+ - Not incremental improvements
580
+
581
+ **Technical Risk**:
582
+ - High-risk approaches acceptable (even encouraged)
583
+ - Must show mitigation strategies
584
+
585
+ **National Security Relevance**:
586
+ - Clear connection to defense applications
587
+ - Dual-use (civilian + military) often valuable
588
+
589
+ **Metrics for Success**:
590
+ - Quantifiable milestones
591
+ - "Go/no-go" decision points
592
+
593
+ ---
594
+
595
+ ### DARPA Budget
596
+
597
+ **Full Cost Accounting**: Detailed justification required
598
+ - **Labor**: Hourly rates, hours per task
599
+ - **Materials**: Itemized
600
+ - **Equipment**: Justification for purchases
601
+ - **Travel**: Specific trips with purpose
602
+ - **Subcontracts**: Detailed subcontract budgets
603
+ - **Indirect Costs**: Negotiated rates
604
+
605
+ **Cost Realism**: Budget must be realistic for proposed work
606
+
607
+ ---
608
+
609
+ ### DARPA LaTeX Template
610
+
611
+ **Template**: `assets/grants/darpa_baa_response.tex`
612
+
613
+ **Resources**:
614
+ - DARPA Opportunities: https://www.darpa.mil/work-with-us/opportunities
615
+ - BAA Listings: SAM.gov (formerly FedBizOpps)
616
+
617
+ ---
618
+
619
+ ## Private Foundations
620
+
621
+ ### Gates Foundation
622
+
623
+ **Focus Areas**: Global health, poverty alleviation, education
624
+ **Typical Award**: Varies widely ($100K to $10M+)
625
+
626
+ **Proposal Requirements**:
627
+ - **Letter of Inquiry** (2-3 pages): Initial screening
628
+ - **Full Proposal** (if invited): 10-15 pages
629
+ - **Theory of Change**: How intervention leads to impact
630
+ - **Monitoring & Evaluation**: Metrics, data collection
631
+
632
+ **Key Emphases**:
633
+ - Scalability and sustainability
634
+ - Impact in low-resource settings
635
+ - Partnerships with local organizations
636
+ - Data-driven decision making
637
+
638
+ ---
639
+
640
+ ### Wellcome Trust
641
+
642
+ **Focus**: Biomedical research, global health
643
+ **Geographic**: UK and international
644
+ **Typical Award**: £100K to £5M
645
+
646
+ **Proposal Format** (varies by scheme):
647
+ - **Investigator Awards**: Track record and research vision
648
+ - **Project Grants**: Specific research project
649
+ - **Career Development**: Early/mid-career researchers
650
+
651
+ **Requirements**:
652
+ - Research plan
653
+ - Track record
654
+ - Value for money justification
655
+ - Patient and public involvement
656
+
657
+ ---
658
+
659
+ ### Howard Hughes Medical Institute (HHMI)
660
+
661
+ **Type**: Investigator appointments (not grants)
662
+ **Award**: ~$9M over 7 years (renewable)
663
+ **Focus**: Biomedical research, early-career scientists
664
+
665
+ **Selection**:
666
+ - Nomination by institution
667
+ - Track record of innovation
668
+ - Research vision for next 5-7 years
669
+ - Scientific leadership potential
670
+
671
+ ---
672
+
673
+ ### Chan Zuckerberg Initiative (CZI)
674
+
675
+ **Focus**: Science, education, justice & opportunity
676
+ **Award Types**:
677
+ - **Imaging**: Advanced imaging technologies
678
+ - **Neurodegeneration Challenge**: AD, ALS, PD, FTD
679
+ - **Single-Cell Biology**: Tools and resources
680
+
681
+ **Emphasis**:
682
+ - Open science (data sharing, open-source)
683
+ - Collaboration across institutions
684
+ - Technology development
685
+ - Diversity and inclusion
686
+
687
+ ---
688
+
689
+ ## Quick Reference Table
690
+
691
+ | Agency | Typical Award | Duration | Key Criteria | Template |
692
+ |--------|--------------|----------|--------------|----------|
693
+ | **NSF** | $100K-500K/yr | 3-5 yrs | Intellectual Merit + Broader Impacts | `nsf_proposal_template.tex` |
694
+ | **NIH R01** | $250K-500K/yr | 5 yrs | Significance, Innovation, Approach | `nih_r01_template.tex` |
695
+ | **NIH R21** | $275K total | 2 yrs | Exploratory, high-risk | `nih_r21_template.tex` |
696
+ | **DOE** | $200K-1M/yr | 3 yrs | Energy relevance, TRLs | `doe_proposal_template.tex` |
697
+ | **DARPA** | $500K-5M/yr | 2-4 yrs | Transformative, Heilmeier | `darpa_baa_response.tex` |
698
+
699
+ ---
700
+
701
+ ## General Best Practices
702
+
703
+ ### Writing Effective Proposals
704
+
705
+ 1. **Start early**: 2-3 months minimum
706
+ 2. **Read the call carefully**: Follow requirements exactly
707
+ 3. **Know your reviewers**: Write for expert audience
708
+ 4. **Tell a story**: Compelling narrative with clear logic
709
+ 5. **Be specific**: Concrete objectives, methods, outcomes
710
+ 6. **Show feasibility**: Preliminary data, expertise
711
+ 7. **Address weaknesses**: Acknowledge and mitigate risks
712
+
713
+ ### Common Mistakes to Avoid
714
+
715
+ 1. **Vague objectives**: "Understand X" → "Determine whether X causes Y"
716
+ 2. **Lack of innovation**: Incremental vs. transformative
717
+ 3. **Poor broader impacts** (NSF): Generic, unintegrated
718
+ 4. **Weak specific aims** (NIH): Most critical page!
719
+ 5. **Missing preliminary data**: Show feasibility
720
+ 6. **Unrealistic timeline**: Be honest about what's achievable
721
+ 7. **Formatting violations**: Auto-rejection possible
722
+ 8. **Typos and errors**: Suggests lack of care
723
+
724
+ ### Timeline for Proposal Development
725
+
726
+ **3 months before deadline**:
727
+ - Identify opportunity
728
+ - Assemble team
729
+ - Outline aims/objectives
730
+
731
+ **2 months before**:
732
+ - Draft aims/objectives
733
+ - Preliminary budget
734
+ - Contact program officer (if allowed)
735
+
736
+ **1 month before**:
737
+ - Full first draft
738
+ - Internal review
739
+ - Revise based on feedback
740
+
741
+ **2 weeks before**:
742
+ - Final revisions
743
+ - Proofread carefully
744
+ - Assemble all documents
745
+
746
+ **1 week before**:
747
+ - Institutional review/approval
748
+ - Budget finalization
749
+ - Submission system upload
750
+
751
+ **2 days before**:
752
+ - Final check
753
+ - Submit (don't wait until deadline!)
754
+
755
+ ---
756
+
757
+ ## Resources
758
+
759
+ ### Grant Writing Guides
760
+ - NSF PAPPG: https://www.nsf.gov/publications/pub_summ.jsp?ods_key=pappg
761
+ - NIH Application Guide: https://grants.nih.gov/grants/how-to-apply-application-guide.html
762
+ - GrantForward (database): https://www.grantforward.com/
763
+ - Pivot (database): https://pivot.proquest.com/
764
+
765
+ ### Institutional Resources
766
+ - Office of Sponsored Research (OSR)
767
+ - Grant writing workshops
768
+ - Internal mock reviews
769
+ - Budget/compliance offices
770
+
771
+ ---
772
+
773
+ ## Summary
774
+
775
+ **Key Takeaways**:
776
+
777
+ 1. **Know the agency**: Different missions, different emphases
778
+ 2. **Follow the rules**: Page limits, fonts, margins strictly enforced
779
+ 3. **Tell a compelling story**: Clear problem, innovative solution, feasible plan
780
+ 4. **Demonstrate impact**: Intellectual merit (NSF/NIH) or mission relevance (DOE/DARPA)
781
+ 5. **Show feasibility**: Preliminary data, team expertise, resources
782
+ 6. **Budget realistically**: Justify all costs
783
+ 7. **Proofread carefully**: Typos undermine credibility
784
+ 8. **Submit early**: Technical glitches happen
785
+
786
+ **Remember**: Grant writing is a skill developed over time. Seek feedback, revise, and persist!
787
+