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
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+ # NSF (National Science Foundation) Grant Writing Guidelines
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+
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+ ## Agency Overview
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+
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+ **Mission**: To promote the progress of science; to advance the national health, prosperity, and welfare; to secure the national defense
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+
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+ **Annual Budget**: ~$9-10 billion
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+
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+ **Website**: https://www.nsf.gov
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+
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+ **Key Characteristics**:
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+ - Supports all fields of fundamental science and engineering (except medical sciences)
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+ - Emphasis on education and workforce development
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+ - Strong commitment to diversity, equity, and inclusion
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+ - Promotes open science and data sharing
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+ - Collaborative research across institutions encouraged
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+
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+ ## NSF Directorates
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+
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+ 1. **BIO** - Biological Sciences
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+ 2. **CISE** - Computer and Information Science and Engineering
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+ 3. **EHR** - Education and Human Resources
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+ 4. **ENG** - Engineering
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+ 5. **GEO** - Geosciences
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+ 6. **MPS** - Mathematical and Physical Sciences
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+ 7. **SBE** - Social, Behavioral, and Economic Sciences
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+ 8. **TIP** - Technology, Innovation, and Partnerships (formerly EDA)
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+ 9. **OPP** - Office of Polar Programs
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+ 10. **OISE** - Office of International Science and Engineering
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+
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+ ## Core Review Criteria
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+
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+ NSF uses two equally weighted criteria for all proposals:
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+
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+ ### Intellectual Merit
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+
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+ **Definition**: The potential to advance knowledge
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+
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+ **Evaluation Questions**:
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+ - How important is the proposed activity to advancing knowledge and understanding within its own field or across different fields?
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+ - How well-qualified is the proposer (individual or team) to conduct the project?
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+ - To what extent does the proposed activity suggest and explore creative, original, or potentially transformative concepts?
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+ - How well-conceived and organized is the proposed activity?
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+ - Is there sufficient access to resources?
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+
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+ **Writing Strategy**:
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+ - Lead with the research question and its importance
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+ - Demonstrate deep knowledge of the field
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+ - Articulate the knowledge gap clearly
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+ - Present innovative approach to address the gap
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+ - Show preliminary results or proof-of-concept
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+ - Demonstrate team qualifications
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+ - Present feasible, well-organized plan
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+
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+ ### Broader Impacts
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+
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+ **Definition**: The potential to benefit society and contribute to the achievement of specific, desired societal outcomes
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+
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+ **Evaluation Questions**:
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+ - What is the potential for the proposed activity to:
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+ - Benefit society or advance desired societal outcomes?
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+ - Broaden participation of underrepresented groups?
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+ - Enhance infrastructure for research and education?
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+ - Enhance scientific and technological understanding?
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+ - Foster partnerships between academia, industry, and others?
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+
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+ **Critical Point**: Broader Impacts are NOT an afterthought. They carry equal weight with Intellectual Merit and must be substantive, specific, and measurable.
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+
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+ **Five Pillars of Broader Impacts** (address at least one substantively):
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+
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+ 1. **Advance discovery and understanding while promoting teaching, training, and learning**
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+ - Integrate research into courses
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+ - Develop new curriculum materials
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+ - Train undergraduate, graduate, and postdoctoral researchers
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+ - Provide research experiences for students
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+ - Create educational resources (videos, software, databases)
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+ - Offer workshops or training programs
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+
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+ *Example*: "We will develop a 10-module online course on computational genomics, incorporating data from this project, to be offered to 500+ students annually across 15 partner institutions. Course materials will be open-access and include Jupyter notebooks for hands-on analysis."
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+
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+ 2. **Broaden participation of underrepresented groups (in STEM)**
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+ - Partner with minority-serving institutions (HBCUs, HSIs, TCUs)
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+ - Recruit students from underrepresented groups
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+ - Provide mentoring and support programs
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+ - Address systemic barriers to participation
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+ - Create inclusive research environments
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+ - Engage underrepresented communities in research
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+
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+ *Example*: "We will establish a summer research program for 8 undergraduates annually from 4 partner HBCUs, providing stipends, housing, and year-round mentoring. Program will include professional development workshops and pathways to graduate school."
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+
91
+ 3. **Enhance infrastructure for research and education**
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+ - Develop shared instrumentation or facilities
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+ - Create cyberinfrastructure, software, or databases
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+ - Build collaborative networks
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+ - Establish living stock centers or repositories
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+ - Develop standards or protocols
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+ - Create open-source tools
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+
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+ *Example*: "We will develop and maintain an open-source software platform for analyzing spatial transcriptomics data, with comprehensive documentation, tutorials, and user support forum. Software will be deposited on GitHub and indexed in bio.tools."
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+
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+ 4. **Disseminate to enhance scientific and technological understanding**
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+ - Public outreach and science communication
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+ - Engagement with K-12 students and teachers
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+ - Museum exhibits or science festivals
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+ - Media engagement (podcasts, videos, articles)
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+ - Policy briefs for decision-makers
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+ - Community science projects
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+
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+ *Example*: "We will partner with the City Science Museum to create a hands-on exhibit on AI and climate modeling, reaching 50,000+ annual visitors. Exhibit will include interactive simulations and bilingual materials. We will also host quarterly 'Science Saturdays' for local K-12 students."
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+
111
+ 5. **Benefit society**
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+ - Economic development and competitiveness
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+ - Health and quality of life improvements
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+ - Environmental sustainability
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+ - National security
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+ - Societal well-being
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+ - Workforce development
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+
119
+ *Example*: "Our drought prediction models will be integrated into USDA's decision support system, benefiting 15,000+ farmers in the Southwest. We will work with extension agents to provide training and accessible interfaces for non-technical users."
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+
121
+ **Common Broader Impacts Mistakes**:
122
+ - ❌ Vague statements: "We will train graduate students" (everyone does this)
123
+ - ❌ No plan: Aspirational goals without concrete activities
124
+ - ❌ No metrics: No way to assess success
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+ - ❌ Tacked on: Not integrated with research plan
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+ - ❌ Unrealistic: Grand claims without resources or expertise
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+ - ✅ Specific and measurable: Clear activities, timelines, and assessment
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+
129
+ ## Proposal Sections and Page Limits
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+
131
+ ### Project Summary (1 page)
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+
133
+ **Required Structure** (NSF mandates three labeled sections):
134
+
135
+ **Overview** (first paragraph):
136
+ - Research question and approach in accessible language
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+ - Suitable for public dissemination
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+
139
+ **Intellectual Merit**:
140
+ - Potential to advance knowledge
141
+ - Innovative aspects
142
+ - Qualifications of team
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+
144
+ **Broader Impacts**:
145
+ - Societal benefits and specific activities
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+ - How success will be measured
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+
148
+ **Formatting**: Must use section headings exactly as shown above
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+
150
+ ### Project Description (15 pages for most programs)
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+
152
+ **No required structure, but typical organization**:
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+
154
+ 1. **Introduction / Background** (1-2 pages)
155
+ - Research question and significance
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+ - Current state of knowledge
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+ - Knowledge gaps
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+ - Preliminary results (if applicable)
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+
160
+ 2. **Research Objectives** (0.5-1 page)
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+ - Specific, measurable goals
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+ - Hypotheses or research questions
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+
164
+ 3. **Research Plan / Methodology** (8-10 pages)
165
+ - Detailed approach for each objective
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+ - Methods and techniques
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+ - Timeline and milestones
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+ - Expected outcomes
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+ - Potential challenges and alternatives
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+
171
+ 4. **Broader Impacts** (1-2 pages)
172
+ - Can be integrated throughout OR separate section
173
+ - Specific activities and timelines
174
+ - Assessment and evaluation plan
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+
176
+ 5. **Results from Prior NSF Support** (if applicable, up to 5 pages)
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+ - Required if PI or co-PI has had NSF award in past 5 years
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+ - Intellectual merit of prior work
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+ - Broader impacts of prior work
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+ - Publications and products
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+
182
+ **Formatting Requirements**:
183
+ - Font: 11-point or larger (Times Roman, Arial, Palatino, Computer Modern)
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+ - Margins: 1 inch all sides
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+ - Line spacing: No more than 6 lines per inch
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+ - Page size: 8.5 x 11 inches
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+ - No smaller fonts in figures (must be legible)
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+
189
+ ### References Cited (no page limit)
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+
191
+ - Each reference must include:
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+ - Names of all authors
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+ - Article and journal title
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+ - Volume, page numbers, year
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+ - DOI if available
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+ - Use consistent format (doesn't have to match specific style)
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+ - Sufficient information for reviewers to locate references
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+
199
+ ### Biographical Sketch (3 pages max per person)
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+
201
+ **Required NSF Format** (as of 2023 PAPPG):
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+
203
+ **Section A: Professional Preparation**
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+ - Undergraduate, graduate, postdoctoral institutions
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+ - Majors and degrees with years
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+
207
+ **Section B: Appointments and Positions**
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+ - Last 5 positions, current first
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+
210
+ **Section C: Products** (up to 5 most relevant to proposal)
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+ - Publications, datasets, software, patents, etc.
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+ - Can include products in preparation
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+
214
+ **Section D: Synergistic Activities** (up to 5)
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+ - Service, teaching, mentoring, outreach
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+ - Demonstrates broader engagement beyond research
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+
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+ ### Current and Pending Support (no page limit)
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+
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+ - All current and pending support for PI and co-PIs
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+ - Include project/proposal title, source, award amount, dates
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+ - Describe overlap with proposed project (if any)
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+ - Must be updated until award/decline
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+
225
+ ### Facilities, Equipment, and Other Resources (no page limit)
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+
227
+ - Describe available facilities (labs, computational, libraries)
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+ - Major equipment accessible to project
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+ - Other resources (personnel, core facilities, partnerships)
230
+ - Demonstrate institutional commitment
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+
232
+ ### Data Management and Sharing Plan (2 pages max)
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+
234
+ **Required for all proposals** (as of 2023 PAPPG)
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+
236
+ **Must address**:
237
+ 1. **Types of data**: What data will be generated?
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+ 2. **Standards**: Formats, metadata, standards for data and metadata
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+ 3. **Access**: How and when will data be shared?
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+ 4. **Reuse**: Who can access and under what conditions?
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+ 5. **Repository**: Where will data be archived long-term?
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+ 6. **Protection**: Privacy, confidentiality, intellectual property considerations
243
+
244
+ **NSF Expectations**:
245
+ - Data should be made publicly available in a timely manner
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+ - Use discipline-specific repositories when available
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+ - Justify any restrictions on data sharing
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+ - Plan for data preservation beyond project period
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+
250
+ ### Postdoctoral Researcher Mentoring Plan (1 page max)
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+
252
+ **Required if funding postdocs**
253
+
254
+ **Must address**:
255
+ - Career development objectives
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+ - Mentoring activities (research, teaching, professional skills)
257
+ - Metrics for success
258
+ - Mentoring plan should be specific, not generic
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+
260
+ ## Special NSF Proposal Types
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+
262
+ ### CAREER (Faculty Early Career Development Program)
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+
264
+ **Eligibility**: Tenure-track (or equivalent) faculty who have not yet received tenure, within 6 years of PhD (or equivalent)
265
+
266
+ **Requirements**:
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+ - Integration of research and education
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+ - Demonstrate potential for leadership
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+ - Department chair letter required
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+ - 5-year project plan
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+ - Typical budget: $400,000-$500,000
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+
273
+ **Key Elements**:
274
+ - Ambitious research plan
275
+ - Innovative educational component
276
+ - Strong integration (not just parallel tracks)
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+ - Path to independence and leadership
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+ - Institutional commitment
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+
280
+ **Review Criteria**: Same two criteria (Intellectual Merit, Broader Impacts) but with emphasis on:
281
+ - Integration of research and education
282
+ - Innovative educational component
283
+ - Potential for leadership in field
284
+
285
+ **Common CAREER Mistakes**:
286
+ - Education component feels tacked on
287
+ - Overly ambitious research plan
288
+ - Weak integration between research and education
289
+ - Generic mentoring or teaching plans
290
+ - Insufficient preliminary data
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+
292
+ ### Collaborative Research
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+
294
+ **Structure**: Multiple proposals submitted separately from different institutions, reviewed as a single project
295
+
296
+ **Requirements**:
297
+ - Lead institution designated
298
+ - All proposals must have identical titles (except institution name)
299
+ - Project descriptions should be substantially similar
300
+ - Clear division of labor
301
+ - Coordination plan
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+
303
+ **Budget**: Each institution submits own budget for their portion
304
+
305
+ **Review**: Reviewed together as single integrated project
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+
307
+ **Benefits**: Brings together complementary expertise and resources
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+
309
+ ### RAPID (Rapid Response Research)
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+
311
+ **Purpose**: Support time-sensitive research opportunities
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+
313
+ **Examples**:
314
+ - Natural disasters
315
+ - Disease outbreaks
316
+ - Unique astronomical events
317
+ - Rare opportunities for data collection
318
+
319
+ **Requirements**:
320
+ - Urgent need justification
321
+ - Up to $200,000
322
+ - Up to 1 year duration
323
+ - Simplified review process (program officer discretion)
324
+ - No preliminary data required
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+
326
+ **Submission**: Contact program officer first, then submit proposal
327
+
328
+ ### EAGER (Early-concept Grants for Exploratory Research)
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+
330
+ **Purpose**: Support exploratory work on untested, but potentially transformative, ideas
331
+
332
+ **Requirements**:
333
+ - High-risk, high-reward research
334
+ - Radically different approaches
335
+ - Up to $300,000
336
+ - Up to 2 years
337
+ - Program officer approval required before submission
338
+ - No panel review (program officer decision)
339
+
340
+ **Key**: Must be truly exploratory and high-risk, not incremental
341
+
342
+ ## Budget Considerations
343
+
344
+ ### Allowable Costs
345
+
346
+ **Personnel**:
347
+ - Senior personnel: Up to 2 months (summer salary) for 9-month faculty
348
+ - Postdoctoral scholars: Full salary and benefits
349
+ - Graduate students: Stipend (tuition typically covered under fringe/indirect)
350
+ - Undergraduate students: Hourly or stipend
351
+ - Technical and administrative staff
352
+
353
+ **Fringe Benefits**: Follow institutional rates
354
+
355
+ **Equipment**: Items ≥$5,000 per unit
356
+ - Must be justified
357
+ - Shared equipment requires letters from collaborators
358
+
359
+ **Travel**:
360
+ - Domestic and international scientific meetings
361
+ - Collaboration and fieldwork
362
+ - Justification required
363
+
364
+ **Participant Support Costs**: For workshops, training, conferences
365
+ - Stipends, travel, subsistence for participants
366
+ - Not subject to indirect costs
367
+
368
+ **Other Direct Costs**:
369
+ - Publication costs
370
+ - Consulting services
371
+ - Computer services
372
+ - Materials and supplies
373
+ - Subawards to collaborating institutions
374
+
375
+ **Indirect Costs (F&A)**: Institutional negotiated rate applies to modified total direct costs (MTDC)
376
+ - MTDC excludes: equipment, participant support, subawards >$25K
377
+
378
+ ### Cost Sharing
379
+
380
+ **NSF Policy**: Cost sharing is not required and should not be voluntary
381
+
382
+ **Exceptions**: Some programs require cost sharing (check program solicitation)
383
+
384
+ **When Included**: Must be documented, verifiable, auditable, and necessary for project
385
+
386
+ ## Submission and Review Process
387
+
388
+ ### Submission Deadlines
389
+
390
+ **Varies by program**:
391
+ - Some programs have specific deadlines (e.g., twice per year)
392
+ - Some programs accept proposals anytime (check with program officer)
393
+ - CAREER: July deadline (directorate-specific)
394
+
395
+ **Submission Windows**: NSF deadlines are typically 5 PM submitter's local time
396
+
397
+ ### Submission Portal
398
+
399
+ **Research.gov** or **Grants.gov**: NSF accepts both
400
+
401
+ **Process**:
402
+ 1. Institutional authorization required
403
+ 2. Upload all required documents
404
+ 3. Verify PDF compilation
405
+ 4. Submit (aim for 48 hours early)
406
+ 5. Receive confirmation and proposal number
407
+
408
+ ### Review Process
409
+
410
+ **Timeline**: Typically 6 months from submission to decision
411
+
412
+ **Steps**:
413
+ 1. **Administrative Review**: NSF checks compliance (1-2 weeks)
414
+ 2. **Program Officer Assignment**: Assigned to appropriate program (1-2 weeks)
415
+ 3. **Reviewer Selection**: Panel and/or ad hoc reviewers identified (2-4 weeks)
416
+ 4. **Review**: Reviewers assess proposals (4-8 weeks)
417
+ 5. **Panel Discussion**: Panel meets (virtual or in-person) to discuss proposals (1 week)
418
+ 6. **Program Officer Recommendation**: Based on reviews and panel discussion (2-4 weeks)
419
+ 7. **Division/Directorate Approval**: Final decision (2-4 weeks)
420
+
421
+ **Review Formats**:
422
+ - **Panel Review**: 10-20 proposals discussed at panel meeting
423
+ - **Ad hoc Review**: External reviewers submit written reviews
424
+ - **Hybrid**: Combination of panel and ad hoc reviews
425
+
426
+ **Number of Reviewers**: Typically 3-5 reviewers per proposal
427
+
428
+ ### Review Outcomes
429
+
430
+ **Possible Decisions**:
431
+ - **Funded**: Congratulations! Award forthcoming
432
+ - **Declined**: Not recommended for funding
433
+ - **Returned Without Review**: Non-compliant with requirements
434
+
435
+ **Feedback**: Panel summary and individual reviews provided regardless of outcome
436
+
437
+ **Success Rates**: Vary by program, typically 15-30%
438
+
439
+ ## Communicating with Program Officers
440
+
441
+ ### When to Contact
442
+
443
+ **Appropriate**:
444
+ - Before submission: Discuss fit with program, feasibility of idea
445
+ - After reviews: Discuss feedback, resubmission strategy
446
+ - During project: Report significant changes, request no-cost extensions
447
+
448
+ **How to Contact**:
449
+ - Email program officer (contact info in program solicitation)
450
+ - Request 15-30 minute phone call
451
+ - Prepare concise summary of research idea (1 page)
452
+
453
+ ### What to Ask
454
+
455
+ **Good Questions**:
456
+ - Is my research appropriate for this program?
457
+ - Are there upcoming solicitations or special initiatives?
458
+ - What are key areas of emphasis for the program?
459
+ - Is the scope and budget appropriate?
460
+ - After reviews: What are key issues to address in resubmission?
461
+
462
+ **Avoid**:
463
+ - Asking for guarantee of funding
464
+ - Arguing with review outcome
465
+ - Inappropriate requests for information about reviewers
466
+
467
+ ## Resubmission Strategy
468
+
469
+ ### NSF Resubmission Policies
470
+
471
+ **No Formal Resubmission Category**: NSF treats resubmissions as new proposals
472
+
473
+ **Can Resubmit**:
474
+ - To same program (after addressing reviews)
475
+ - To different program (if better fit)
476
+ - After substantial revision
477
+
478
+ **No Introduction Section**: Unlike NIH, NSF doesn't have formal resubmission response
479
+
480
+ **Strategy**:
481
+ - Carefully review panel summary and individual reviews
482
+ - Address all major criticisms
483
+ - Strengthen weak areas (prelim data, broader impacts, methods)
484
+ - Consider discussing with program officer
485
+ - May want to wait for next funding cycle to gather more data
486
+
487
+ **Tracking**: Proposals reviewed previously may be assigned same reviewers (sometimes)
488
+
489
+ ## Recent NSF Policy Updates
490
+
491
+ ### 2023-2024 Changes
492
+
493
+ 1. **Data Management and Sharing Plan**: Now required for all proposals (2 pages max)
494
+ 2. **Biographical Sketch Format**: Updated to include "Products" instead of "Publications"
495
+ 3. **Open Science**: Increased emphasis on open-access publications and data
496
+ 4. **Plan for Dissemination**: Some programs require explicit dissemination plans
497
+ 5. **Mentoring Plans**: Enhanced requirements for postdoc mentoring plans
498
+
499
+ ### NSF Priorities (2024-2025)
500
+
501
+ - **Climate and Clean Energy**: Climate change mitigation and adaptation
502
+ - **Quantum Information Science**: Quantum computing, sensing, networking
503
+ - **AI and Machine Learning**: Trustworthy AI, AI for science
504
+ - **Biotechnology**: Synthetic biology, bioengineering
505
+ - **Microelectronics**: Semiconductor research and workforce
506
+ - **STEM Education**: Broadening participation, innovative pedagogy
507
+ - **Convergence Accelerators**: Use-inspired research with pathway to impact
508
+
509
+ ## NSF Big Ideas and Special Initiatives
510
+
511
+ ### NSF "Big Ideas"
512
+
513
+ 1. **Harnessing the Data Revolution (HDR)**
514
+ 2. **The Future of Work at the Human-Technology Frontier**
515
+ 3. **Navigating the New Arctic**
516
+ 4. **Windows on the Universe**
517
+ 5. **The Quantum Leap**
518
+ 6. **Understanding the Rules of Life**
519
+ 7. **Mid-scale Research Infrastructure**
520
+
521
+ ### Major NSF Initiatives
522
+
523
+ - **National AI Research Institutes**: $20M over 5 years per institute
524
+ - **Science and Technology Centers (STCs)**: Large-scale collaborative centers
525
+ - **Engineering Research Centers (ERCs)**: Engineering innovation ecosystems
526
+ - **Materials Research Science and Engineering Centers (MRSECs)**: Materials research
527
+ - **NSF Graduate Research Fellowship Program (GRFP)**: Student fellowships
528
+
529
+ ## Tips for Competitive NSF Proposals
530
+
531
+ ### Do's
532
+
533
+ ✅ **Start with specific aims/objectives** - Crystal clear research goals
534
+ ✅ **Make broader impacts substantive** - Specific activities, not platitudes
535
+ ✅ **Use figures effectively** - Conceptual diagrams, preliminary data, timelines
536
+ ✅ **Be realistic about scope** - Achievable within 3-5 years
537
+ ✅ **Address both review criteria explicitly** - Don't make reviewers search
538
+ ✅ **Get external feedback** - Mock review before submission
539
+ ✅ **Follow formatting requirements exactly** - Auto-rejection for non-compliance
540
+ ✅ **Explain jargon and acronyms** - Panel members may not be in your subfield
541
+ ✅ **Integrate research and education** - Show natural connections
542
+ ✅ **Demonstrate team qualifications** - Track record in proposed area
543
+
544
+ ### Don'ts
545
+
546
+ ❌ **Don't exceed page limits** - Automatic return without review
547
+ ❌ **Don't use smaller fonts in figures** - Must be legible
548
+ ❌ **Don't make broader impacts generic** - "Train students" is not enough
549
+ ❌ **Don't ignore prior NSF support** - Must report if you've had NSF funding
550
+ ❌ **Don't be overly ambitious** - Reviewers will see through unrealistic plans
551
+ ❌ **Don't skip data management plan** - Required for all proposals
552
+ ❌ **Don't forget biosketches for all personnel** - Common mistake
553
+ ❌ **Don't submit at deadline** - Technical issues happen
554
+ ❌ **Don't ignore program solicitation** - Requirements vary by program
555
+ ❌ **Don't assume reviewers know your work** - Provide context
556
+
557
+ ## Resources and Links
558
+
559
+ - **NSF Homepage**: https://www.nsf.gov
560
+ - **Award Search**: https://www.nsf.gov/awardsearch/
561
+ - **Proposal & Award Policies & Procedures Guide (PAPPG)**: https://www.nsf.gov/publications/pub_summ.jsp?ods_key=pappg
562
+ - **FastLane**: https://www.fastlane.nsf.gov/
563
+ - **Research.gov**: https://www.research.gov/
564
+ - **Broader Impacts Resources**: https://www.nsf.gov/od/oia/special/broaderimpacts/
565
+ - **NSF Funding Statistics**: https://www.nsf.gov/statistics/
566
+
567
+ ---
568
+
569
+ **Key Takeaway**: NSF values both scientific excellence (Intellectual Merit) and societal benefit (Broader Impacts) equally. Successful proposals demonstrate innovative, feasible research that advances knowledge while contributing to education, diversity, infrastructure, or societal well-being in specific, measurable ways.
570
+