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
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  203. scientific_writer/.claude/skills/markitdown/QUICK_REFERENCE.md +309 -0
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  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
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  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
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  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
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  251. scientific_writer/.claude/skills/scientific-schematics/assets/circuit_template.tex +159 -0
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  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
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  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
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+ ---
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+ name: research-grants
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+ description: "Write competitive research proposals for NSF, NIH, DOE, and DARPA. Agency-specific formatting, review criteria, budget preparation, broader impacts, significance statements, innovation narratives, and compliance with submission requirements."
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+ ---
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+
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+ # Research Grant Writing
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+
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+ ## Overview
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+
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+ Research grant writing is the process of developing competitive funding proposals for federal agencies and foundations. Master agency-specific requirements, review criteria, narrative structure, budget preparation, and compliance for NSF (National Science Foundation), NIH (National Institutes of Health), DOE (Department of Energy), and DARPA (Defense Advanced Research Projects Agency) submissions.
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+
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+ **Critical Principle: Grants are persuasive documents that must simultaneously demonstrate scientific rigor, innovation, feasibility, and broader impact.** Each agency has distinct priorities, review criteria, formatting requirements, and strategic goals that must be addressed.
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+
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+ ## When to Use This Skill
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+
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+ This skill should be used when:
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+ - Writing research proposals for NSF, NIH, DOE, or DARPA programs
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+ - Preparing project descriptions, specific aims, or technical narratives
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+ - Developing broader impacts or significance statements
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+ - Creating research timelines and milestone plans
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+ - Preparing budget justifications and personnel allocation plans
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+ - Responding to program solicitations or funding announcements
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+ - Addressing reviewer comments in resubmissions
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+ - Planning multi-institutional collaborative proposals
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+ - Writing preliminary data or feasibility sections
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+ - Preparing biosketches, CVs, or facilities descriptions
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+
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+ ## Agency-Specific Overview
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+
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+ ### NSF (National Science Foundation)
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+ **Mission**: Promote the progress of science and advance national health, prosperity, and welfare
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+
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+ **Key Features**:
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+ - Intellectual Merit + Broader Impacts (equally weighted)
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+ - 15-page project description limit (most programs)
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+ - Emphasis on education, diversity, and societal benefit
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+ - Collaborative research encouraged
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+ - Open data and open science emphasis
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+ - Merit review process with panel + ad hoc reviewers
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+
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+ ### NIH (National Institutes of Health)
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+ **Mission**: Enhance health, lengthen life, and reduce illness and disability
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+
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+ **Key Features**:
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+ - Specific Aims (1 page) + Research Strategy (12 pages for R01)
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+ - Significance, Innovation, Approach as core review criteria
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+ - Preliminary data typically required for R01s
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+ - Emphasis on rigor, reproducibility, and clinical relevance
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+ - Modular budgets ($250K increments) for most R01s
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+ - Multiple resubmission opportunities
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+
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+ ### DOE (Department of Energy)
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+ **Mission**: Ensure America's security and prosperity through energy, environmental, and nuclear challenges
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+
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+ **Key Features**:
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+ - Focus on energy, climate, computational science, basic energy sciences
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+ - Often requires cost sharing or industry partnerships
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+ - Emphasis on national laboratory collaboration
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+ - Strong computational and experimental integration
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+ - Energy innovation and commercialization pathways
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+ - Varies by office (ARPA-E, Office of Science, EERE, etc.)
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+
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+ ### DARPA (Defense Advanced Research Projects Agency)
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+ **Mission**: Make pivotal investments in breakthrough technologies for national security
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+
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+ **Key Features**:
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+ - High-risk, high-reward transformative research
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+ - Focus on "DARPA-hard" problems (what if true, who cares)
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+ - Emphasis on prototypes, demonstrations, and transition paths
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+ - Often requires multiple phases (feasibility, development, demonstration)
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+ - Strong project management and milestone tracking
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+ - Teaming and collaboration often required
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+ - Varies dramatically by program manager and BAA (Broad Agency Announcement)
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+
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+ ## Core Components of Research Proposals
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+
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+ ### 1. Executive Summary / Project Summary / Abstract
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+
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+ Every proposal needs a concise overview that communicates the essential elements of the research to both technical reviewers and program officers.
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+
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+ **Purpose**: Provide a standalone summary that captures the research vision, significance, and approach
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+
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+ **Length**:
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+ - NSF: 1 page (Project Summary with separate Overview, Intellectual Merit, Broader Impacts)
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+ - NIH: 30 lines (Project Summary/Abstract)
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+ - DOE: Varies (typically 1 page)
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+ - DARPA: Varies (often 1-2 pages)
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+
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+ **Essential Elements**:
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+ - Clear statement of the problem or research question
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+ - Why this problem matters (significance, urgency, impact)
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+ - Novel approach or innovation
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+ - Expected outcomes and deliverables
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+ - Qualifications of the team
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+ - Broader impacts or translational pathway
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+
97
+ **Writing Strategy**:
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+ - Open with a compelling hook that establishes importance
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+ - Use accessible language (avoid jargon in opening sentences)
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+ - State specific, measurable objectives
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+ - Convey enthusiasm and confidence
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+ - Ensure every sentence adds value (no filler)
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+ - End with transformative vision or impact statement
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+
105
+ **Common Mistakes to Avoid**:
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+ - Being too technical or detailed (save for project description)
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+ - Failing to articulate "why now" or "why this team"
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+ - Vague objectives or outcomes
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+ - Neglecting broader impacts or significance
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+ - Generic statements that could apply to any proposal
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+
112
+ ### 2. Project Description / Research Strategy
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+
114
+ The core technical narrative that presents the research plan in detail.
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+
116
+ **Structure Varies by Agency:**
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+
118
+ **NSF Project Description** (typically 15 pages):
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+ - Introduction and background
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+ - Research objectives and questions
121
+ - Preliminary results (if applicable)
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+ - Research plan and methodology
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+ - Timeline and milestones
124
+ - Broader impacts (integrated throughout or separate section)
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+ - Prior NSF support (if applicable)
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+
127
+ **NIH Research Strategy** (12 pages for R01):
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+ - Significance (why the problem matters)
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+ - Innovation (what's novel and transformative)
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+ - Approach (detailed research plan)
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+ - Preliminary data
132
+ - Research design and methods
133
+ - Expected outcomes
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+ - Potential problems and alternative approaches
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+
136
+ **DOE Project Narrative** (varies):
137
+ - Background and significance
138
+ - Technical approach and innovation
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+ - Qualifications and experience
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+ - Facilities and resources
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+ - Project management and timeline
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+
143
+ **DARPA Technical Volume** (varies):
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+ - Technical challenge and innovation
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+ - Approach and methodology
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+ - Schedule and milestones
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+ - Deliverables and metrics
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+ - Team qualifications
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+ - Risk assessment and mitigation
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+
151
+ For detailed agency-specific guidance, refer to:
152
+ - `references/nsf_guidelines.md`
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+ - `references/nih_guidelines.md`
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+ - `references/doe_guidelines.md`
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+ - `references/darpa_guidelines.md`
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+
157
+ ### 3. Specific Aims (NIH) or Objectives (NSF/DOE/DARPA)
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+
159
+ Clear, testable goals that structure the research plan.
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+
161
+ **NIH Specific Aims Page** (1 page):
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+ - Opening paragraph: Gap in knowledge and significance
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+ - Long-term goal and immediate objectives
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+ - Central hypothesis or research question
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+ - 2-4 specific aims with sub-aims
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+ - Expected outcomes and impact
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+ - Payoff paragraph: Why this matters
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+
169
+ **Structure for Each Aim:**
170
+ - Aim statement (1-2 sentences, starts with action verb)
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+ - Rationale (why this aim, preliminary data support)
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+ - Working hypothesis (testable prediction)
173
+ - Approach summary (brief methods overview)
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+ - Expected outcomes and interpretation
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+
176
+ **Writing Strategy**:
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+ - Make aims independent but complementary
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+ - Ensure each aim is achievable within timeline and budget
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+ - Provide enough detail to judge feasibility
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+ - Include contingency plans or alternative approaches
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+ - Use parallel structure across aims
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+ - Clearly state what will be learned from each aim
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+
184
+ For detailed guidance, refer to `references/specific_aims_guide.md`.
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+
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+ ### 4. Broader Impacts (NSF) / Significance (NIH)
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+
188
+ Articulate the societal, educational, or translational value of the research.
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+
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+ **NSF Broader Impacts** (critical component, equal weight with Intellectual Merit):
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+
192
+ NSF explicitly evaluates broader impacts. Address at least one of these areas:
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+ 1. **Advancing discovery and understanding while promoting teaching, training, and learning**
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+ - Integration of research and education
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+ - Training of students and postdocs
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+ - Curriculum development
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+ - Educational materials and resources
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+
199
+ 2. **Broadening participation of underrepresented groups**
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+ - Recruitment and retention strategies
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+ - Partnerships with minority-serving institutions
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+ - Outreach to underrepresented communities
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+ - Mentoring programs
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+
205
+ 3. **Enhancing infrastructure for research and education**
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+ - Shared facilities or instrumentation
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+ - Cyberinfrastructure and data resources
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+ - Community-wide tools or databases
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+ - Open-source software or methods
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+
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+ 4. **Broad dissemination to enhance scientific and technological understanding**
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+ - Public outreach and science communication
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+ - K-12 educational programs
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+ - Museum exhibits or media engagement
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+ - Policy briefs or stakeholder engagement
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+
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+ 5. **Benefits to society**
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+ - Economic impact or commercialization
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+ - Health, environment, or national security benefits
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+ - Informed decision-making
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+ - Workforce development
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+
223
+ **Writing Strategy for NSF Broader Impacts**:
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+ - Be specific with concrete activities, not vague statements
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+ - Provide timeline and milestones for broader impacts activities
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+ - Explain how impacts will be measured and assessed
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+ - Connect to institutional resources and existing programs
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+ - Show commitment through preliminary efforts or partnerships
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+ - Integrate with research plan (not tacked on)
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+
231
+ **NIH Significance**:
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+ - Addresses important problem or critical barrier to progress
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+ - Improves scientific knowledge, technical capability, or clinical practice
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+ - Potential to lead to better outcomes, interventions, or understanding
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+ - Rigor of prior research in the field
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+ - Alignment with NIH mission and institute priorities
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+
238
+ For detailed guidance, refer to `references/broader_impacts.md`.
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+
240
+ ### 5. Innovation and Transformative Potential
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+
242
+ Articulate what is novel, creative, and paradigm-shifting about the research.
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+
244
+ **Innovation Elements to Highlight**:
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+ - **Conceptual Innovation**: New frameworks, models, or theories
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+ - **Methodological Innovation**: Novel techniques, approaches, or technologies
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+ - **Integrative Innovation**: Combining disciplines or approaches in new ways
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+ - **Translational Innovation**: New pathways from discovery to application
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+ - **Scale Innovation**: Unprecedented scope or resolution
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+
251
+ **Writing Strategy**:
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+ - Clearly state what is innovative (don't assume it's obvious)
253
+ - Explain why current approaches are insufficient
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+ - Describe how your innovation overcomes limitations
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+ - Provide evidence that innovation is feasible (preliminary data, proof-of-concept)
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+ - Distinguish incremental from transformative advances
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+ - Balance innovation with feasibility (not too risky)
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+
259
+ **Common Mistakes**:
260
+ - Claiming novelty without demonstrating knowledge of prior work
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+ - Confusing "new to me" with "new to the field"
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+ - Over-promising without supporting evidence
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+ - Being too incremental (minor variation on existing work)
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+ - Being too speculative (no path to success)
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+
266
+ ### 6. Research Approach and Methods
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+
268
+ Detailed description of how the research will be conducted.
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+
270
+ **Essential Components**:
271
+ - Overall research design and framework
272
+ - Detailed methods for each aim/objective
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+ - Sample sizes, statistical power, and analysis plans
274
+ - Timeline and sequence of activities
275
+ - Data collection, management, and analysis
276
+ - Quality control and validation approaches
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+ - Potential problems and alternative strategies
278
+ - Rigor and reproducibility measures
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+
280
+ **Writing Strategy**:
281
+ - Provide enough detail for reproducibility and feasibility assessment
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+ - Use subheadings and figures to improve organization
283
+ - Justify choice of methods and approaches
284
+ - Address potential limitations proactively
285
+ - Include preliminary data demonstrating feasibility
286
+ - Show that you've thought through the research process
287
+ - Balance detail with readability (use supplementary materials for extensive details)
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+
289
+ **For Experimental Research**:
290
+ - Describe experimental design (controls, replicates, blinding)
291
+ - Specify materials, reagents, and equipment
292
+ - Detail data collection protocols
293
+ - Explain statistical analysis plans
294
+ - Address rigor and reproducibility
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+
296
+ **For Computational Research**:
297
+ - Describe algorithms, models, and software
298
+ - Specify datasets and validation approaches
299
+ - Explain computational resources required
300
+ - Address code availability and documentation
301
+ - Describe benchmarking and performance metrics
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+
303
+ **For Clinical or Translational Research**:
304
+ - Describe study population and recruitment
305
+ - Detail intervention or treatment protocols
306
+ - Explain outcome measures and assessments
307
+ - Address regulatory approvals (IRB, IND, IDE)
308
+ - Describe clinical trial design and monitoring
309
+
310
+ For detailed methodology guidance by discipline, refer to `references/research_methods.md`.
311
+
312
+ ### 7. Preliminary Data and Feasibility
313
+
314
+ Demonstrate that the research is achievable and the team is capable.
315
+
316
+ **Purpose**:
317
+ - Prove that the proposed approach can work
318
+ - Show that the team has necessary expertise
319
+ - Demonstrate access to required resources
320
+ - Reduce perceived risk for reviewers
321
+ - Provide foundation for proposed work
322
+
323
+ **What to Include**:
324
+ - Pilot studies or proof-of-concept results
325
+ - Method development or optimization
326
+ - Access to unique resources (samples, data, collaborators)
327
+ - Relevant publications from your team
328
+ - Preliminary models or simulations
329
+ - Feasibility assessments or power calculations
330
+
331
+ **NIH Requirements**:
332
+ - R01 applications typically require substantial preliminary data
333
+ - R21 applications may have less stringent requirements
334
+ - New investigators may have less preliminary data
335
+ - Preliminary data should directly support proposed aims
336
+
337
+ **NSF Approach**:
338
+ - Preliminary data less commonly required than NIH
339
+ - May be important for high-risk or novel approaches
340
+ - Can strengthen proposal for competitive programs
341
+
342
+ **Writing Strategy**:
343
+ - Present most compelling data that supports your approach
344
+ - Clearly connect preliminary data to proposed aims
345
+ - Acknowledge limitations and how proposed work will address them
346
+ - Use figures and data visualizations effectively
347
+ - Avoid over-interpreting or overstating preliminary findings
348
+ - Show trajectory of your research program
349
+
350
+ ### 8. Timeline, Milestones, and Management Plan
351
+
352
+ Demonstrate that the project is well-planned and achievable within the proposed timeframe.
353
+
354
+ **Essential Elements**:
355
+ - Phased timeline with clear milestones
356
+ - Logical sequence and dependencies
357
+ - Realistic timeframes for each activity
358
+ - Decision points and go/no-go criteria
359
+ - Risk mitigation strategies
360
+ - Resource allocation across time
361
+ - Coordination plan for multi-institutional teams
362
+
363
+ **Presentation Formats**:
364
+ - Gantt charts showing overlapping activities
365
+ - Year-by-year breakdown of activities
366
+ - Quarterly milestones and deliverables
367
+ - Table of aims/tasks with timeline and personnel
368
+
369
+ **Writing Strategy**:
370
+ - Be realistic about what can be accomplished
371
+ - Build in time for unexpected delays or setbacks
372
+ - Show that timeline aligns with budget and personnel
373
+ - Demonstrate understanding of regulatory timelines (IRB, IACUC)
374
+ - Include time for dissemination and broader impacts
375
+ - Address how progress will be monitored and assessed
376
+
377
+ **DARPA Emphasis**:
378
+ - Particularly important for DARPA proposals
379
+ - Clear technical milestones with measurable metrics
380
+ - Quarterly deliverables and reporting
381
+ - Phase-based structure with exit criteria
382
+ - Demonstration and transition planning
383
+
384
+ For detailed guidance, refer to `references/timeline_planning.md`.
385
+
386
+ ### 9. Team Qualifications and Collaboration
387
+
388
+ Demonstrate that the team has the expertise, experience, and resources to succeed.
389
+
390
+ **Essential Elements**:
391
+ - PI qualifications and relevant expertise
392
+ - Co-I and collaborator roles and contributions
393
+ - Track record in the research area
394
+ - Complementary expertise across team
395
+ - Institutional support and resources
396
+ - Prior collaboration history (if applicable)
397
+ - Mentoring and training plan (for students/postdocs)
398
+
399
+ **Writing Strategy**:
400
+ - Highlight most relevant publications and accomplishments
401
+ - Clearly define roles and responsibilities
402
+ - Show that team composition is necessary (not just convenient)
403
+ - Demonstrate successful prior collaborations
404
+ - Address how team will be managed and coordinated
405
+ - Explain institutional commitment and support
406
+
407
+ **Biosketches / CVs**:
408
+ - Follow agency-specific formats (NSF, NIH, DOE, DARPA differ)
409
+ - Highlight most relevant publications and accomplishments
410
+ - Include synergistic activities and collaborations
411
+ - Show trajectory and productivity
412
+ - Address any career gaps or interruptions
413
+
414
+ **Letters of Collaboration**:
415
+ - Specific commitments and contributions
416
+ - Demonstrates genuine partnership
417
+ - Includes resource sharing or access agreements
418
+ - Signed and on letterhead
419
+
420
+ For detailed guidance, refer to `references/team_building.md`.
421
+
422
+ ### 10. Budget and Budget Justification
423
+
424
+ Develop realistic budgets that align with the proposed work and agency guidelines.
425
+
426
+ **Budget Categories** (typical):
427
+ - **Personnel**: Salary and fringe for PI, co-Is, postdocs, students, staff
428
+ - **Equipment**: Items >$5,000 (varies by agency)
429
+ - **Travel**: Conferences, collaborations, fieldwork
430
+ - **Materials and Supplies**: Consumables, reagents, software
431
+ - **Other Direct Costs**: Publication costs, participant incentives, consulting
432
+ - **Indirect Costs (F&A)**: Institutional overhead (rates vary)
433
+ - **Subawards**: Costs for collaborating institutions
434
+
435
+ **Agency-Specific Considerations**:
436
+
437
+ **NSF**:
438
+ - Full budget justification required
439
+ - Cost sharing generally not required (but may strengthen proposal)
440
+ - Up to 2 months summer salary for faculty
441
+ - Graduate student support encouraged
442
+
443
+ **NIH**:
444
+ - Modular budgets for ≤$250K direct costs per year (R01)
445
+ - Detailed budgets for >$250K or complex awards
446
+ - Salary cap applies (~$221,900 for 2024)
447
+ - Limited to 1 month (8.33% FTE) for most PIs
448
+
449
+ **DOE**:
450
+ - Often requires cost sharing (especially ARPA-E)
451
+ - Detailed budget with quarterly breakdown
452
+ - Requires institutional commitment letters
453
+ - National laboratory collaboration budgets separate
454
+
455
+ **DARPA**:
456
+ - Detailed budgets by phase and task
457
+ - Requires supporting cost data for large procurements
458
+ - Often requires cost-plus or firm-fixed-price structures
459
+ - Travel budget for program meetings
460
+
461
+ **Budget Justification Writing**:
462
+ - Justify each line item in terms of the research plan
463
+ - Explain effort percentages for personnel
464
+ - Describe specific equipment and why necessary
465
+ - Justify travel (conferences, collaborations)
466
+ - Explain consultant roles and rates
467
+ - Show how budget aligns with timeline
468
+
469
+ For detailed budget guidance, refer to `references/budget_preparation.md`.
470
+
471
+ ## Review Criteria by Agency
472
+
473
+ Understanding how proposals are evaluated is critical for writing competitive applications.
474
+
475
+ ### NSF Review Criteria
476
+
477
+ **Intellectual Merit** (primary):
478
+ - What is the potential for the proposed activity to advance knowledge?
479
+ - How well-conceived and organized is the proposed activity?
480
+ - Is there sufficient access to resources?
481
+ - How well-qualified is the individual, team, or institution to conduct proposed activities?
482
+
483
+ **Broader Impacts** (equally important):
484
+ - What is the potential for the proposed activity to benefit society?
485
+ - To what extent does the proposal address broader impacts in meaningful ways?
486
+
487
+ **Additional Considerations**:
488
+ - Integration of research and education
489
+ - Diversity and inclusion
490
+ - Results from prior NSF support (if applicable)
491
+
492
+ ### NIH Review Criteria
493
+
494
+ **Scored Criteria** (1-9 scale, 1 = exceptional, 9 = poor):
495
+
496
+ 1. **Significance**
497
+ - Addresses important problem or critical barrier
498
+ - Improves scientific knowledge, technical capability, or clinical practice
499
+ - Aligns with NIH mission
500
+
501
+ 2. **Investigator(s)**
502
+ - Well-suited to the project
503
+ - Track record of accomplishments
504
+ - Adequate training and expertise
505
+
506
+ 3. **Innovation**
507
+ - Novel concepts, approaches, methodologies, or interventions
508
+ - Challenges existing paradigms
509
+ - Addresses important problem in creative ways
510
+
511
+ 4. **Approach**
512
+ - Well-reasoned and appropriate
513
+ - Rigorous and reproducible
514
+ - Adequately accounts for potential problems
515
+ - Feasible within timeline
516
+
517
+ 5. **Environment**
518
+ - Institutional support and resources
519
+ - Scientific environment contributes to probability of success
520
+
521
+ **Additional Review Considerations** (not scored but discussed):
522
+ - Protections for human subjects
523
+ - Inclusion of women, minorities, and children
524
+ - Vertebrate animal welfare
525
+ - Biohazards
526
+ - Resubmission response (if applicable)
527
+ - Budget and timeline appropriateness
528
+
529
+ ### DOE Review Criteria
530
+
531
+ Varies by program office, but generally includes:
532
+ - Scientific and/or technical merit
533
+ - Appropriateness of proposed method or approach
534
+ - Competency of personnel and adequacy of facilities
535
+ - Reasonableness and appropriateness of budget
536
+ - Relevance to DOE mission and program goals
537
+
538
+ ### DARPA Review Criteria
539
+
540
+ **DARPA-specific considerations**:
541
+ - Overall scientific and technical merit
542
+ - Potential contribution to DARPA mission
543
+ - Relevance to stated program goals
544
+ - Plans and capability to accomplish technology transition
545
+ - Qualifications and experience of proposed team
546
+ - Realism of proposed costs and availability of funds
547
+
548
+ **Key Questions DARPA Asks**:
549
+ - **What if you succeed?** (Impact if the research works)
550
+ - **What if you're right?** (Implications of your hypothesis)
551
+ - **Who cares?** (Why it matters for national security)
552
+
553
+ For detailed review criteria by agency, refer to `references/review_criteria.md`.
554
+
555
+ ## Writing Principles for Competitive Proposals
556
+
557
+ ### Clarity and Accessibility
558
+
559
+ **Write for Multiple Audiences**:
560
+ - Technical reviewers in your field (will scrutinize methods)
561
+ - Reviewers in related but not identical fields (need context)
562
+ - Program officers (look for alignment with agency goals)
563
+ - Panel members reading 15+ proposals (need clear organization)
564
+
565
+ **Strategies**:
566
+ - Use clear section headings and subheadings
567
+ - Start sections with overview paragraphs
568
+ - Define technical terms and abbreviations
569
+ - Use figures, diagrams, and tables to clarify complex ideas
570
+ - Avoid jargon when possible; explain when necessary
571
+ - Use topic sentences to guide readers
572
+
573
+ ### Persuasive Argumentation
574
+
575
+ **Build a Compelling Narrative**:
576
+ - Establish the problem and its importance
577
+ - Show gaps in current knowledge or approaches
578
+ - Present your solution as innovative and feasible
579
+ - Demonstrate that you're the right team
580
+ - Show that success will have significant impact
581
+
582
+ **Structure of Persuasion**:
583
+ 1. **Hook**: Capture attention with significance
584
+ 2. **Problem**: Establish what's not known or not working
585
+ 3. **Solution**: Present your innovative approach
586
+ 4. **Evidence**: Support with preliminary data
587
+ 5. **Impact**: Show transformative potential
588
+ 6. **Team**: Demonstrate capability to deliver
589
+
590
+ **Language Choices**:
591
+ - Use active voice for clarity and confidence
592
+ - Choose strong verbs (investigate, elucidate, discover vs. look at, study)
593
+ - Be confident but not arrogant (avoid "obviously," "clearly")
594
+ - Acknowledge uncertainty appropriately
595
+ - Use precise language (avoid vague terms like "several," "various")
596
+
597
+ ### Visual Communication
598
+
599
+ **Effective Use of Figures**:
600
+ - Conceptual diagrams showing research framework
601
+ - Preliminary data demonstrating feasibility
602
+ - Timelines and Gantt charts
603
+ - Workflow diagrams showing methodology
604
+ - Expected results or predictions
605
+
606
+ **Design Principles**:
607
+ - Make figures self-explanatory with complete captions
608
+ - Use consistent color schemes and fonts
609
+ - Ensure readability (large enough fonts, clear labels)
610
+ - Integrate figures with text (refer to specific figures)
611
+ - Follow agency-specific formatting requirements
612
+
613
+ ### Addressing Risk and Feasibility
614
+
615
+ **Balance Innovation and Risk**:
616
+ - Acknowledge potential challenges
617
+ - Provide alternative approaches
618
+ - Show preliminary data reducing risk
619
+ - Demonstrate expertise to handle challenges
620
+ - Include contingency plans
621
+
622
+ **Common Concerns**:
623
+ - Too ambitious for timeline/budget
624
+ - Technically infeasible
625
+ - Team lacks necessary expertise
626
+ - Preliminary data insufficient
627
+ - Methods not adequately described
628
+ - Lack of innovation or significance
629
+
630
+ ### Integration and Coherence
631
+
632
+ **Ensure All Parts Align**:
633
+ - Budget supports activities in project description
634
+ - Timeline matches aims and milestones
635
+ - Team composition matches required expertise
636
+ - Broader impacts connect to research plan
637
+ - Letters of support confirm stated collaborations
638
+
639
+ **Avoid Contradictions**:
640
+ - Preliminary data vs. stated gaps
641
+ - Claimed expertise vs. publication record
642
+ - Stated aims vs. actual methods
643
+ - Budget vs. stated activities
644
+
645
+ ## Common Proposal Types
646
+
647
+ ### NSF Proposal Types
648
+
649
+ - **Standard Research Proposals**: Most common, up to $500K and 5 years
650
+ - **CAREER Awards**: Early career faculty, integrated research/education, $400-500K over 5 years
651
+ - **Collaborative Research**: Multiple institutions, separately submitted, shared research plan
652
+ - **RAPID**: Urgent research opportunities, up to $200K, no preliminary data required
653
+ - **EAGER**: High-risk, high-reward exploratory research, up to $300K
654
+ - **EArly-concept Grants for Exploratory Research (EAGER)**: Early-stage exploratory work
655
+
656
+ ### NIH Award Mechanisms
657
+
658
+ - **R01**: Research Project Grant, $250K+ per year, 3-5 years, most common
659
+ - **R21**: Exploratory/Developmental Research, up to $275K over 2 years, no preliminary data
660
+ - **R03**: Small Grant Program, up to $100K over 2 years
661
+ - **R15**: Academic Research Enhancement Awards (AREA), for primarily undergraduate institutions
662
+ - **R35**: MIRA (Maximizing Investigators' Research Award), program-specific
663
+ - **P01**: Program Project Grant, multi-project integrated research
664
+ - **U01**: Research Project Cooperative Agreement, NIH involvement in conduct
665
+
666
+ **Fellowship Mechanisms**:
667
+ - **F30**: Predoctoral MD/PhD Fellowship
668
+ - **F31**: Predoctoral Fellowship
669
+ - **F32**: Postdoctoral Fellowship
670
+ - **K99/R00**: Pathway to Independence Award
671
+ - **K08**: Mentored Clinical Scientist Research Career Development Award
672
+
673
+ ### DOE Programs
674
+
675
+ - **Office of Science**: Basic research in physical sciences, biological sciences, computing
676
+ - **ARPA-E**: Transformative energy technologies, requires cost sharing
677
+ - **EERE**: Applied research in renewable energy and energy efficiency
678
+ - **National Laboratories**: Collaborative research with DOE labs
679
+
680
+ ### DARPA Programs
681
+
682
+ - **Varies by Office**: BTO, DSO, I2O, MTO, STO, TTO
683
+ - **Program-Specific BAAs**: Broad Agency Announcements for specific thrusts
684
+ - **Young Faculty Award (YFA)**: Early career researchers, up to $500K
685
+ - **Director's Fellowship**: High-risk, paradigm-shifting research
686
+
687
+ For detailed program guidance, refer to `references/funding_mechanisms.md`.
688
+
689
+ ## Resubmission Strategies
690
+
691
+ ### NIH Resubmission (A1)
692
+
693
+ **Introduction to Resubmission** (1 page):
694
+ - Summarize major criticisms from previous review
695
+ - Describe specific changes made in response
696
+ - Use bullet points for clarity
697
+ - Be respectful of reviewers' comments
698
+ - Highlight substantial improvements
699
+
700
+ **Strategies**:
701
+ - Address every major criticism
702
+ - Make changes visible (but don't use track changes in final)
703
+ - Strengthen weak areas (preliminary data, methods, significance)
704
+ - Consider changing aims if fundamentally flawed
705
+ - Get external feedback before resubmitting
706
+ - Use full 37-month window if needed for new data
707
+
708
+ **When Not to Resubmit**:
709
+ - Fundamental conceptual flaws
710
+ - Lack of innovation or significance
711
+ - Missing key expertise or resources
712
+ - Extensive revisions needed (consider new submission)
713
+
714
+ ### NSF Resubmission
715
+
716
+ **NSF allows resubmission after revision**:
717
+ - Address reviewer concerns in revised proposal
718
+ - No formal "introduction to resubmission" section
719
+ - May be reviewed by same or different panel
720
+ - Consider program officer feedback
721
+ - May need to wait for next submission cycle
722
+
723
+ For detailed resubmission guidance, refer to `references/resubmission_strategies.md`.
724
+
725
+ ## Common Mistakes to Avoid
726
+
727
+ ### Conceptual Mistakes
728
+
729
+ 1. **Failing to Address Review Criteria**: Not explicitly discussing significance, innovation, approach, etc.
730
+ 2. **Mismatch with Agency Mission**: Proposing research that doesn't align with agency goals
731
+ 3. **Unclear Significance**: Failing to articulate why the research matters
732
+ 4. **Insufficient Innovation**: Incremental work presented as transformative
733
+ 5. **Vague Objectives**: Goals that are not specific or measurable
734
+
735
+ ### Writing Mistakes
736
+
737
+ 1. **Poor Organization**: Lack of clear structure and flow
738
+ 2. **Excessive Jargon**: Inaccessible to broader review panel
739
+ 3. **Verbosity**: Unnecessarily complex or wordy writing
740
+ 4. **Missing Context**: Assuming reviewers know your field deeply
741
+ 5. **Inconsistent Terminology**: Using different terms for same concept
742
+
743
+ ### Technical Mistakes
744
+
745
+ 1. **Inadequate Methods**: Insufficient detail to judge feasibility
746
+ 2. **Overly Ambitious**: Too much proposed for timeline/budget
747
+ 3. **No Preliminary Data**: For mechanisms requiring demonstrated feasibility
748
+ 4. **Poor Timeline**: Unrealistic or poorly justified schedule
749
+ 5. **Misaligned Budget**: Budget doesn't support proposed activities
750
+
751
+ ### Formatting Mistakes
752
+
753
+ 1. **Exceeding Page Limits**: Automatic rejection
754
+ 2. **Wrong Font or Margins**: Non-compliant formatting
755
+ 3. **Missing Required Sections**: Incomplete application
756
+ 4. **Poor Figure Quality**: Illegible or unprofessional figures
757
+ 5. **Inconsistent Citations**: Formatting errors in references
758
+
759
+ ### Strategic Mistakes
760
+
761
+ 1. **Wrong Program or Mechanism**: Proposing to inappropriate opportunity
762
+ 2. **Weak Team**: Insufficient expertise or missing key collaborators
763
+ 3. **No Broader Impacts**: For NSF, failing to adequately address
764
+ 4. **Ignoring Program Priorities**: Not aligning with current emphasis areas
765
+ 5. **Late Submission**: Technical issues or rushed preparation
766
+
767
+ ## Workflow for Grant Development
768
+
769
+ ### Phase 1: Planning and Preparation (2-6 months before deadline)
770
+
771
+ **Activities**:
772
+ - Identify appropriate funding opportunities
773
+ - Review program announcements and requirements
774
+ - Consult with program officers (if appropriate)
775
+ - Assemble team and confirm collaborations
776
+ - Develop preliminary data (if needed)
777
+ - Outline research plan and specific aims
778
+ - Review successful proposals (if available)
779
+
780
+ **Outputs**:
781
+ - Selected funding opportunity
782
+ - Assembled team with defined roles
783
+ - Preliminary outline of specific aims
784
+ - Gap analysis of needed preliminary data
785
+
786
+ ### Phase 2: Drafting (2-3 months before deadline)
787
+
788
+ **Activities**:
789
+ - Write specific aims or objectives (start here!)
790
+ - Develop project description/research strategy
791
+ - Create figures and data visualizations
792
+ - Draft timeline and milestones
793
+ - Prepare preliminary budget
794
+ - Write broader impacts or significance sections
795
+ - Request letters of support/collaboration
796
+
797
+ **Outputs**:
798
+ - Complete first draft of narrative sections
799
+ - Preliminary budget with justification
800
+ - Timeline and management plan
801
+ - Requested letters from collaborators
802
+
803
+ ### Phase 3: Internal Review (1-2 months before deadline)
804
+
805
+ **Activities**:
806
+ - Circulate draft to co-investigators
807
+ - Seek feedback from colleagues and mentors
808
+ - Request institutional review (if required)
809
+ - Mock review session (if possible)
810
+ - Revise based on feedback
811
+ - Refine budget and budget justification
812
+
813
+ **Outputs**:
814
+ - Revised draft incorporating feedback
815
+ - Refined budget aligned with revised plan
816
+ - Identified weaknesses and mitigation strategies
817
+
818
+ ### Phase 4: Finalization (2-4 weeks before deadline)
819
+
820
+ **Activities**:
821
+ - Final revisions to narrative
822
+ - Prepare all required forms and documents
823
+ - Finalize budget and budget justification
824
+ - Compile biosketches, CVs, and current & pending
825
+ - Collect letters of support
826
+ - Prepare data management plan (if required)
827
+ - Write project summary/abstract
828
+ - Proofread all materials
829
+
830
+ **Outputs**:
831
+ - Complete, polished proposal
832
+ - All required supplementary documents
833
+ - Formatted according to agency requirements
834
+
835
+ ### Phase 5: Submission (1 week before deadline)
836
+
837
+ **Activities**:
838
+ - Institutional review and approval
839
+ - Upload to submission portal
840
+ - Verify all documents and formatting
841
+ - Submit 24-48 hours before deadline
842
+ - Confirm successful submission
843
+ - Receive confirmation and proposal number
844
+
845
+ **Outputs**:
846
+ - Submitted proposal
847
+ - Submission confirmation
848
+ - Archived copy of all materials
849
+
850
+ **Critical Tip**: Never wait until the deadline. Portals crash, files corrupt, and emergencies happen. Aim for 48 hours early.
851
+
852
+ ## Integration with Other Skills
853
+
854
+ This skill works effectively with:
855
+ - **Scientific Writing**: For clear, compelling prose
856
+ - **Literature Review**: For comprehensive background sections
857
+ - **Peer Review**: For self-assessment before submission
858
+ - **Research Lookup**: For finding relevant citations and prior work
859
+ - **Data Visualization**: For creating effective figures
860
+
861
+ ## Resources
862
+
863
+ This skill includes comprehensive reference files covering specific aspects of grant writing:
864
+
865
+ - `references/nsf_guidelines.md`: NSF-specific requirements, formatting, and strategies
866
+ - `references/nih_guidelines.md`: NIH mechanisms, review criteria, and submission requirements
867
+ - `references/doe_guidelines.md`: DOE programs, emphasis areas, and application procedures
868
+ - `references/darpa_guidelines.md`: DARPA BAAs, program offices, and proposal strategies
869
+ - `references/broader_impacts.md`: Strategies for compelling broader impacts statements
870
+ - `references/specific_aims_guide.md`: Writing effective specific aims pages
871
+ - `references/budget_preparation.md`: Budget development and justification
872
+ - `references/review_criteria.md`: Detailed review criteria by agency
873
+ - `references/timeline_planning.md`: Creating realistic timelines and milestones
874
+ - `references/team_building.md`: Assembling and presenting effective teams
875
+ - `references/resubmission_strategies.md`: Responding to reviews and revising proposals
876
+
877
+ Load these references as needed when working on specific aspects of grant writing.
878
+
879
+ ## Templates and Assets
880
+
881
+ - `assets/nsf_project_summary_template.md`: NSF project summary structure
882
+ - `assets/nih_specific_aims_template.md`: NIH specific aims page template
883
+ - `assets/timeline_gantt_template.md`: Timeline and Gantt chart examples
884
+ - `assets/budget_justification_template.md`: Budget justification structure
885
+ - `assets/biosketch_templates/`: Agency-specific biosketch formats
886
+
887
+ ## Scripts and Tools
888
+
889
+ - `scripts/compliance_checker.py`: Verify formatting requirements
890
+ - `scripts/budget_calculator.py`: Calculate budgets with inflation and fringe
891
+ - `scripts/deadline_tracker.py`: Track submission deadlines and milestones
892
+
893
+ ---
894
+
895
+ **Final Note**: Grant writing is both an art and a science. Success requires not only excellent research ideas but also clear communication, strategic positioning, and meticulous attention to detail. Start early, seek feedback, and remember that even the best researchers face rejection—persistence and revision are key to funding success.
896
+