@pikaa-ai/pikaa 0.3.1 → 0.3.4

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (1870) hide show
  1. package/dist/cli.js +1169 -601
  2. package/dist/index.js +525 -204
  3. package/package.json +5 -3
  4. package/skills/adaptyv/references/api-endpoints.md +0 -690
  5. package/skills/aeon/references/anomaly_detection.md +0 -154
  6. package/skills/aeon/references/classification.md +0 -144
  7. package/skills/aeon/references/clustering.md +0 -123
  8. package/skills/aeon/references/datasets_benchmarking.md +0 -392
  9. package/skills/aeon/references/distances.md +0 -256
  10. package/skills/aeon/references/forecasting.md +0 -109
  11. package/skills/aeon/references/networks.md +0 -289
  12. package/skills/aeon/references/regression.md +0 -118
  13. package/skills/aeon/references/segmentation.md +0 -163
  14. package/skills/aeon/references/similarity_search.md +0 -187
  15. package/skills/aeon/references/transformations.md +0 -246
  16. package/skills/analytical-method-validation/assets/validation-protocol-template.md +0 -106
  17. package/skills/analytical-method-validation/assets/validation-report-template.md +0 -116
  18. package/skills/analytical-method-validation/references/compendial-and-clsi.md +0 -96
  19. package/skills/analytical-method-validation/references/framework-selection.md +0 -87
  20. package/skills/analytical-method-validation/references/ich-m10-bioanalytical.md +0 -123
  21. package/skills/analytical-method-validation/references/ich-q2r2.md +0 -229
  22. package/skills/analytical-method-validation/references/source-ledger.md +0 -125
  23. package/skills/analytical-method-validation/references/statistics.md +0 -209
  24. package/skills/analytical-method-validation/scripts/_catalog.py +0 -499
  25. package/skills/analytical-method-validation/scripts/_common.py +0 -955
  26. package/skills/analytical-method-validation/scripts/check_accuracy_precision.py +0 -328
  27. package/skills/analytical-method-validation/scripts/check_bioanalytical_run.py +0 -293
  28. package/skills/analytical-method-validation/scripts/check_detection_limits.py +0 -310
  29. package/skills/analytical-method-validation/scripts/check_response.py +0 -243
  30. package/skills/analytical-method-validation/scripts/compare_methods.py +0 -215
  31. package/skills/analytical-method-validation/scripts/plan_validation.py +0 -381
  32. package/skills/anndata/references/best_practices.md +0 -532
  33. package/skills/anndata/references/concatenation.md +0 -399
  34. package/skills/anndata/references/data_structure.md +0 -314
  35. package/skills/anndata/references/io_operations.md +0 -466
  36. package/skills/anndata/references/manipulation.md +0 -516
  37. package/skills/arbor/references/arbor-upstream.md +0 -91
  38. package/skills/arbor/references/executor-brief.md +0 -68
  39. package/skills/arbor/references/htr-methodology.md +0 -177
  40. package/skills/arbor/references/report-template.md +0 -39
  41. package/skills/arbor/scripts/tree.py +0 -564
  42. package/skills/arboreto/references/algorithms.md +0 -152
  43. package/skills/arboreto/references/basic_inference.md +0 -181
  44. package/skills/arboreto/references/distributed_computing.md +0 -242
  45. package/skills/arboreto/scripts/basic_grn_inference.py +0 -107
  46. package/skills/astropy/references/coordinates.md +0 -280
  47. package/skills/astropy/references/cosmology.md +0 -309
  48. package/skills/astropy/references/fits.md +0 -398
  49. package/skills/astropy/references/tables.md +0 -495
  50. package/skills/astropy/references/time.md +0 -412
  51. package/skills/astropy/references/units.md +0 -178
  52. package/skills/astropy/references/wcs_and_other_modules.md +0 -377
  53. package/skills/autoskill/config.yaml +0 -53
  54. package/skills/autoskill/references/https-proxy.md +0 -62
  55. package/skills/autoskill/references/screenpipe-config.yaml +0 -61
  56. package/skills/autoskill/scripts/autoskill.py +0 -35
  57. package/skills/autoskill/scripts/backends.py +0 -116
  58. package/skills/autoskill/scripts/cluster.py +0 -54
  59. package/skills/autoskill/scripts/doctor.py +0 -108
  60. package/skills/autoskill/scripts/fetch_window.py +0 -33
  61. package/skills/autoskill/scripts/match_skills.py +0 -46
  62. package/skills/autoskill/scripts/promote.py +0 -58
  63. package/skills/autoskill/scripts/redact.py +0 -40
  64. package/skills/autoskill/scripts/run.py +0 -194
  65. package/skills/autoskill/scripts/synthesize.py +0 -72
  66. package/skills/benchling-integration/references/api_endpoints.md +0 -883
  67. package/skills/benchling-integration/references/authentication.md +0 -390
  68. package/skills/benchling-integration/references/core_capabilities.md +0 -355
  69. package/skills/benchling-integration/references/eventbridge.md +0 -255
  70. package/skills/benchling-integration/references/sdk_reference.md +0 -772
  71. package/skills/bids/references/beps.yml +0 -637
  72. package/skills/bids/references/bids_schema.json +0 -21015
  73. package/skills/bids/references/bids_specification.md +0 -165
  74. package/skills/bids/references/conversion_tools.md +0 -475
  75. package/skills/bids/references/core_workflows.md +0 -552
  76. package/skills/bids/references/metadata_fields.md +0 -365
  77. package/skills/bids/scripts/update_schema.py +0 -89
  78. package/skills/biopython/references/advanced.md +0 -580
  79. package/skills/biopython/references/alignment.md +0 -377
  80. package/skills/biopython/references/blast.md +0 -463
  81. package/skills/biopython/references/databases.md +0 -492
  82. package/skills/biopython/references/phylogenetics.md +0 -566
  83. package/skills/biopython/references/sequence_io.md +0 -289
  84. package/skills/biopython/references/structure.md +0 -564
  85. package/skills/bioservices/references/identifier_mapping.md +0 -685
  86. package/skills/bioservices/references/services_reference.md +0 -638
  87. package/skills/bioservices/references/workflow_patterns.md +0 -813
  88. package/skills/bioservices/scripts/batch_id_converter.py +0 -347
  89. package/skills/bioservices/scripts/compound_cross_reference.py +0 -387
  90. package/skills/bioservices/scripts/pathway_analysis.py +0 -309
  91. package/skills/bioservices/scripts/protein_analysis_workflow.py +0 -441
  92. package/skills/bulk-rnaseq/references/counts-and-handoff.md +0 -91
  93. package/skills/bulk-rnaseq/references/design-and-qc.md +0 -68
  94. package/skills/bulk-rnaseq/references/upstream-manual.md +0 -128
  95. package/skills/bulk-rnaseq/references/upstream-nfcore.md +0 -108
  96. package/skills/bulk-rnaseq/scripts/build_counts_matrix.py +0 -203
  97. package/skills/bulk-rnaseq/scripts/validate_samplesheet.py +0 -206
  98. package/skills/cellxgene-census/references/census_schema.md +0 -218
  99. package/skills/cellxgene-census/references/common_patterns.md +0 -368
  100. package/skills/cellxgene-census/references/core_workflow_patterns.md +0 -297
  101. package/skills/cirq/references/building.md +0 -307
  102. package/skills/cirq/references/experiments.md +0 -572
  103. package/skills/cirq/references/hardware.md +0 -527
  104. package/skills/cirq/references/noise.md +0 -514
  105. package/skills/cirq/references/simulation.md +0 -353
  106. package/skills/cirq/references/transformation.md +0 -416
  107. package/skills/citation-management/assets/bibtex_template.bib +0 -264
  108. package/skills/citation-management/assets/citation_checklist.md +0 -386
  109. package/skills/citation-management/references/best_practices.md +0 -91
  110. package/skills/citation-management/references/bibtex_formatting.md +0 -908
  111. package/skills/citation-management/references/citation_validation.md +0 -835
  112. package/skills/citation-management/references/core_workflow.md +0 -569
  113. package/skills/citation-management/references/example_workflows.md +0 -126
  114. package/skills/citation-management/references/google_scholar_search.md +0 -732
  115. package/skills/citation-management/references/metadata_extraction.md +0 -870
  116. package/skills/citation-management/references/pubmed_search.md +0 -839
  117. package/skills/citation-management/references/script_reference.md +0 -250
  118. package/skills/citation-management/references/search_strategies.md +0 -110
  119. package/skills/citation-management/scripts/_common.py +0 -331
  120. package/skills/citation-management/scripts/doi_to_bibtex.py +0 -204
  121. package/skills/citation-management/scripts/extract_metadata.py +0 -690
  122. package/skills/citation-management/scripts/format_bibtex.py +0 -356
  123. package/skills/citation-management/scripts/search_google_scholar.py +0 -268
  124. package/skills/citation-management/scripts/search_openalex.py +0 -297
  125. package/skills/citation-management/scripts/search_pubmed.py +0 -419
  126. package/skills/citation-management/scripts/validate_citations.py +0 -688
  127. package/skills/clinical-decision-support/assets/aggregate_cohort_table_template.json +0 -114
  128. package/skills/clinical-decision-support/assets/aggregate_model_evaluation_template.json +0 -115
  129. package/skills/clinical-decision-support/assets/artifact_intended_use_template.json +0 -81
  130. package/skills/clinical-decision-support/assets/decision_logic_traceability_template.json +0 -108
  131. package/skills/clinical-decision-support/assets/deidentification_checklist_template.json +0 -176
  132. package/skills/clinical-decision-support/assets/evidence_profile_template.json +0 -139
  133. package/skills/clinical-decision-support/assets/survival_analysis_plan_template.json +0 -134
  134. package/skills/clinical-decision-support/references/cohort_evaluation.md +0 -142
  135. package/skills/clinical-decision-support/references/decision_logic_traceability.md +0 -146
  136. package/skills/clinical-decision-support/references/evidence_profiles.md +0 -153
  137. package/skills/clinical-decision-support/references/model_biomarker_evaluation.md +0 -152
  138. package/skills/clinical-decision-support/references/privacy_and_disclosure.md +0 -144
  139. package/skills/clinical-decision-support/references/regulatory_and_governance.md +0 -104
  140. package/skills/clinical-decision-support/references/safety_and_scope.md +0 -103
  141. package/skills/clinical-decision-support/references/security_validation.md +0 -60
  142. package/skills/clinical-decision-support/references/sources.md +0 -119
  143. package/skills/clinical-decision-support/references/study_reporting.md +0 -134
  144. package/skills/clinical-decision-support/references/survival_analysis.md +0 -156
  145. package/skills/clinical-decision-support/scripts/_common.py +0 -223
  146. package/skills/clinical-decision-support/scripts/cohort_table_generator.py +0 -288
  147. package/skills/clinical-decision-support/scripts/decision_logic_traceability.py +0 -313
  148. package/skills/clinical-decision-support/scripts/deidentification_checklist.py +0 -260
  149. package/skills/clinical-decision-support/scripts/evidence_profile_check.py +0 -259
  150. package/skills/clinical-decision-support/scripts/model_biomarker_evaluation.py +0 -345
  151. package/skills/clinical-decision-support/scripts/survival_plan_validator.py +0 -294
  152. package/skills/clinical-decision-support/scripts/validate_cds_artifact.py +0 -269
  153. package/skills/clinical-reports/assets/adverse_event_aggregate_input_template.csv +0 -1
  154. package/skills/clinical-reports/assets/case_report_template.json +0 -43
  155. package/skills/clinical-reports/assets/clinical_trial_csr_template.json +0 -51
  156. package/skills/clinical-reports/assets/clinical_trial_results_template.json +0 -66
  157. package/skills/clinical-reports/assets/clinical_trial_safety_aggregate_template.json +0 -49
  158. package/skills/clinical-reports/assets/consistency_manifest_template.json +0 -15
  159. package/skills/clinical-reports/assets/deidentification_process_checklist.json +0 -56
  160. package/skills/clinical-reports/assets/lab_report_template.json +0 -36
  161. package/skills/clinical-reports/assets/pathology_report_template.json +0 -36
  162. package/skills/clinical-reports/assets/provenance_manifest_template.json +0 -17
  163. package/skills/clinical-reports/assets/quality_review_checklist.json +0 -34
  164. package/skills/clinical-reports/assets/radiology_report_template.json +0 -34
  165. package/skills/clinical-reports/assets/research_summary_template.json +0 -36
  166. package/skills/clinical-reports/assets/terminology_manifest_template.json +0 -11
  167. package/skills/clinical-reports/assets/trial_protocol_reporting_checklist.json +0 -70
  168. package/skills/clinical-reports/references/case_report_guidelines.md +0 -72
  169. package/skills/clinical-reports/references/clinical_trial_reporting.md +0 -97
  170. package/skills/clinical-reports/references/data_presentation.md +0 -92
  171. package/skills/clinical-reports/references/diagnostic_reports_standards.md +0 -76
  172. package/skills/clinical-reports/references/medical_terminology.md +0 -84
  173. package/skills/clinical-reports/references/privacy_and_deidentification.md +0 -84
  174. package/skills/clinical-reports/references/professional_review.md +0 -78
  175. package/skills/clinical-reports/references/report_type_routing.md +0 -57
  176. package/skills/clinical-reports/references/safety_reporting.md +0 -109
  177. package/skills/clinical-reports/references/sources.md +0 -75
  178. package/skills/clinical-reports/scripts/_common.py +0 -263
  179. package/skills/clinical-reports/scripts/check_deidentification.py +0 -298
  180. package/skills/clinical-reports/scripts/consistency_checker.py +0 -390
  181. package/skills/clinical-reports/scripts/format_adverse_events.py +0 -455
  182. package/skills/clinical-reports/scripts/generate_report_template.py +0 -115
  183. package/skills/clinical-reports/scripts/provenance_validator.py +0 -263
  184. package/skills/clinical-reports/scripts/terminology_validator.py +0 -277
  185. package/skills/clinical-reports/scripts/validate_case_report.py +0 -278
  186. package/skills/clinical-reports/scripts/validate_trial_report.py +0 -534
  187. package/skills/cobrapy/references/api_quick_reference.md +0 -665
  188. package/skills/cobrapy/references/workflows.md +0 -600
  189. package/skills/consciousness-council/references/advanced-configurations.md +0 -96
  190. package/skills/dask/references/arrays.md +0 -495
  191. package/skills/dask/references/bags.md +0 -468
  192. package/skills/dask/references/best-practices.md +0 -277
  193. package/skills/dask/references/dataframes.md +0 -370
  194. package/skills/dask/references/futures.md +0 -541
  195. package/skills/dask/references/schedulers.md +0 -517
  196. package/skills/database-lookup/references/addgene.md +0 -38
  197. package/skills/database-lookup/references/alphafold.md +0 -52
  198. package/skills/database-lookup/references/alphavantage.md +0 -261
  199. package/skills/database-lookup/references/bea.md +0 -409
  200. package/skills/database-lookup/references/bindingdb.md +0 -85
  201. package/skills/database-lookup/references/biogrid.md +0 -110
  202. package/skills/database-lookup/references/bls.md +0 -235
  203. package/skills/database-lookup/references/brenda.md +0 -71
  204. package/skills/database-lookup/references/cbioportal.md +0 -206
  205. package/skills/database-lookup/references/census.md +0 -251
  206. package/skills/database-lookup/references/chebi.md +0 -103
  207. package/skills/database-lookup/references/chembl.md +0 -80
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  210. package/skills/database-lookup/references/clinvar.md +0 -91
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  212. package/skills/database-lookup/references/cosmic.md +0 -59
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  218. package/skills/database-lookup/references/drugbank.md +0 -54
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  229. package/skills/database-lookup/references/gene-ontology.md +0 -147
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  236. package/skills/database-lookup/references/human-protein-atlas.md +0 -57
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- # DOE (Department of Energy) Grant Writing Guidelines
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-
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- ## Agency Overview
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-
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- **Mission**: Ensure America's security and prosperity by addressing energy, environmental, and nuclear challenges through transformative science and technology solutions
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-
7
- **Annual Budget**: ~$50 billion (includes national laboratories, energy programs, nuclear security)
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-
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- **Website**: https://www.energy.gov
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-
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- **Key Characteristics**:
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- - Focus on energy, climate, environmental, computational, and physical sciences
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- - Operates 17 national laboratories (largest science infrastructure in US)
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- - Strong emphasis on industry partnerships and commercialization
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- - Basic science through applied research and development
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- - Cost sharing often required
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- - National security and energy security priorities
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-
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- ## Major DOE Offices and Programs
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-
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- ### Office of Science (SC)
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-
23
- **Budget**: ~$8 billion (largest supporter of physical sciences research in US)
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-
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- **Mission**: Deliver scientific discoveries and major scientific tools to transform our understanding of nature and advance energy, economic, and national security
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-
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- **Program Offices**:
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-
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- 1. **Advanced Scientific Computing Research (ASCR)**
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- - High-performance computing
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- - Applied mathematics
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- - Computational sciences
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- - Exascale computing
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-
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- 2. **Basic Energy Sciences (BES)**
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- - Materials science and engineering
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- - Chemical sciences
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- - Condensed matter and materials physics
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- - User facilities (light sources, neutron sources)
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-
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- 3. **Biological and Environmental Research (BER)**
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- - Biological systems science
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- - Climate and environmental sciences
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- - Environmental molecular sciences laboratory
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-
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- 4. **Fusion Energy Sciences (FES)**
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- - Plasma physics
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- - Fusion energy development
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- - ITER collaboration
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-
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- 5. **High Energy Physics (HEP)**
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- - Particle physics
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- - Accelerator science
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- - Quantum information science
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-
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- 6. **Nuclear Physics (NP)**
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- - Nuclear structure and dynamics
58
- - Relativistic heavy ions
59
- - Fundamental symmetries
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-
61
- **Funding Mechanisms**:
62
- - **Early Career Research Program**: $750K over 5 years for early career scientists
63
- - **Funding Opportunity Announcements (FOAs)**: Program-specific solicitations
64
- - **Laboratory Directed Research and Development (LDRD)**: For national lab staff
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-
66
- ### ARPA-E (Advanced Research Projects Agency-Energy)
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-
68
- **Mission**: Advance high-potential, high-impact energy technologies that are too early for private-sector investment
69
-
70
- **Characteristics**:
71
- - High-risk, high-reward transformative energy technologies
72
- - Requires cost sharing (typically 20% for universities, more for industry)
73
- - Emphasis on pathway to commercialization
74
- - Strong project management and milestones
75
- - Budget: ~$500M annually
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-
77
- **Program Types**:
78
- - **Focused Programs**: Specific technology areas (announced via FOAs)
79
- - **OPEN**: General solicitation across all energy technologies
80
- - **SCALEUP**: Bridging from lab to market
81
-
82
- **Typical Funding**:
83
- - $1-10M per project
84
- - 1-3 years duration
85
- - Technology transition focus
86
-
87
- ### Office of Energy Efficiency and Renewable Energy (EERE)
88
-
89
- **Mission**: Accelerate development and deployment of clean energy technologies
90
-
91
- **Program Areas**:
92
- - **Solar Energy Technologies Office (SETO)**
93
- - **Wind Energy Technologies Office (WETO)**
94
- - **Water Power Technologies Office (WPTO)**
95
- - **Geothermal Technologies Office (GTO)**
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- - **Building Technologies Office (BTO)**
97
- - **Advanced Manufacturing Office (AMO)**
98
- - **Vehicle Technologies Office (VTO)**
99
- - **Bioenergy Technologies Office (BETO)**
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- - **Hydrogen and Fuel Cell Technologies Office (HFTO)**
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-
102
- **Funding Mechanisms**:
103
- - FOAs for specific technology areas
104
- - Small Business Innovation Research (SBIR)
105
- - Technology Commercialization Fund (TCF)
106
-
107
- ### Office of Fossil Energy and Carbon Management (FECM)
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-
109
- **Focus**: Carbon capture, utilization, and storage; hydrogen; critical minerals
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-
111
- ### Office of Nuclear Energy (NE)
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-
113
- **Focus**: Advanced reactor technologies, nuclear fuel cycle, university programs
114
-
115
- ## DOE Proposal Structure
116
-
117
- DOE proposal requirements vary significantly by program office and FOA. **Always read the specific FOA carefully.**
118
-
119
- ### Common Elements
120
-
121
- #### Project Narrative (varies, typically 10-20 pages)
122
-
123
- **Typical Structure**:
124
-
125
- 1. **Executive Summary / Abstract** (1 page)
126
- - Project objectives and technical approach
127
- - Expected outcomes and impact
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- - Team qualifications
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- - Alignment with DOE mission
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-
131
- 2. **Background and Motivation** (2-3 pages)
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- - Current state of technology or knowledge
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- - Problem or opportunity
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- - Why DOE investment is needed
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- - Alignment with program goals
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-
137
- 3. **Technical Approach and Innovation** (5-10 pages)
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- - Detailed technical plan
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- - Methodology and approach
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- - Innovation and novelty
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- - Risk assessment and mitigation
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- - Go/no-go decision points
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- - Performance metrics
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145
- 4. **Impact and Energy Relevance** (1-2 pages)
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- - Expected technical outcomes
147
- - Energy impact (cost, efficiency, emissions)
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- - Pathway to deployment or commercialization
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- - Economic benefits
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- - Timeline to market (for applied programs)
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152
- 5. **Management Plan** (1-2 pages)
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- - Team organization and roles
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- - Timeline and milestones
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- - Risk management
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- - Communication and reporting
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- 6. **Qualifications and Resources** (1-2 pages)
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- - Team expertise and experience
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- - Relevant prior work
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- - Facilities and equipment
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- - National lab or industry partners
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164
- #### Budget and Budget Justification
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-
166
- **Federal Cost Share**:
167
- - Specify DOE funding requested by year
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- - Break down by category (labor, equipment, travel, etc.)
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- - Detailed justification for each item
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-
171
- **Cost Share** (often required):
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- - Specify source (cash vs. in-kind)
173
- - Document commitment (letters from sponsors)
174
- - Typical requirements:
175
- - Universities: 20% (ARPA-E)
176
- - Industry: 50% or more
177
- - National labs: Varies
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-
179
- **Budget Categories**:
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- - Labor (personnel with hours/rates)
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- - Fringe benefits
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- - Travel
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- - Equipment and capital items
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- - Materials and supplies
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- - Other direct costs
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- - Subawards/subcontracts
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- - Indirect costs (F&A)
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189
- #### Biographical Sketches
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-
191
- **Format**: Often DOE-specific or NSF-style
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- - Professional preparation
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- - Appointments
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- - Relevant publications (5-10 most relevant)
195
- - Synergistic activities
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- - Collaborators
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198
- #### Work Breakdown Structure (WBS)
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-
200
- **Often Required**: Detailed breakdown of tasks, milestones, and deliverables
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- - Task structure aligned with budget
202
- - Quarterly or annual milestones
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- - Deliverables for each task
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- - Responsible parties
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206
- #### Letters of Commitment
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-
208
- **Required for**:
209
- - Cost share partners
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- - Collaborating institutions
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- - National laboratory partnerships
212
- - Industry partners
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- - Access to facilities or resources
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215
- **Must Include**:
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- - Specific commitment (funding, personnel, equipment)
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- - Signed by authorized representative
218
- - On institutional letterhead
219
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220
- #### Facilities and Equipment
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-
222
- **Describe**:
223
- - Available facilities relevant to project
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- - Major equipment accessible
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- - Computational resources
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- - Unique capabilities
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228
- #### Data Management Plan (DMP)
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-
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- **Increasingly Required**:
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- - Types of data to be generated
232
- - Standards and formats
233
- - Access and sharing policies
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- - Long-term preservation
235
- - Compliance with DOE policies
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-
237
- ## Review Criteria
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239
- ### Office of Science (SC) General Criteria
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241
- Proposals typically evaluated on:
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243
- 1. **Scientific and/or Technical Merit** (35-40%)
244
- - Importance and relevance of research
245
- - Appropriateness of proposed method or approach
246
- - Scientific or technical innovation
247
- - Clarity of objectives and expected outcomes
248
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249
- 2. **Appropriateness of Proposed Method or Approach** (25-30%)
250
- - Technical feasibility
251
- - Likelihood of success
252
- - Adequacy of project design
253
- - Rigor of technical approach
254
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255
- 3. **Competency of Personnel and Adequacy of Facilities** (20-25%)
256
- - Qualifications of PI and team
257
- - Track record in relevant areas
258
- - Access to necessary facilities and equipment
259
- - Institutional support
260
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261
- 4. **Reasonableness and Appropriateness of Budget** (10-15%)
262
- - Budget aligned with proposed work
263
- - Appropriate allocation of resources
264
- - Cost effectiveness
265
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266
- 5. **Relevance to DOE Mission and Program Goals** (10-15%)
267
- - Alignment with program priorities
268
- - Contribution to DOE mission
269
- - Potential impact on energy/environment
270
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271
- ### ARPA-E Review Criteria
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273
- **ARPA-E uses concept paper → full application process**
274
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275
- **Concept Paper Review** (typically 3-5 pages):
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- - Technical innovation and impact
277
- - Potential for transformative advance
278
- - Relevance to energy applications
279
- - Feasibility (team, approach)
280
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281
- **Full Application Review** (if invited):
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283
- 1. **Impact** (40%)
284
- - Potential to dramatically improve energy technology
285
- - Energy and economic impact
286
- - Transformative vs. incremental
287
- - Pathway to market adoption
288
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289
- 2. **Innovation/Technical Merit** (30%)
290
- - Novel approach or technology
291
- - Technical rigor and feasibility
292
- - Likelihood of meeting targets
293
- - Risk and risk mitigation
294
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295
- 3. **Qualifications** (20%)
296
- - Team expertise and experience
297
- - Resources and capabilities
298
- - Management plan
299
- - Track record
300
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- 4. **Workplan** (10%)
302
- - Clear milestones and go/no-go points
303
- - Realistic timeline
304
- - Appropriate budget
305
- - Risk management
306
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307
- ### Technology-to-Market (T2M) Evaluation (ARPA-E)
308
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- **Critical Component**: Path to commercialization
310
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- **Assessed**:
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- - Market opportunity and size
313
- - Competitive landscape
314
- - Barriers to adoption
315
- - Go-to-market strategy
316
- - Partnership and commercialization plan
317
- - Economic viability
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319
- **Common Mistakes**:
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- - Underestimating time to market
321
- - Ignoring competing technologies
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- - Unrealistic cost projections
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- - No clear adoption pathway
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- ## DOE-Specific Considerations
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- ### National Laboratory Collaboration
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- **Benefits**:
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- - Access to unique facilities and expertise
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- - Leveraging world-class capabilities
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- - Credibility and track record
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- **Mechanisms**:
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- - **Subcontract**: Lab is subcontractor to university/company
336
- - **Cooperative Research and Development Agreement (CRADA)**: Partnership with industry
337
- - **User Facility Proposal**: Access to major DOE user facilities
338
- - **Strategic Partnership Project (SPP)**: Formal collaboration
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- **Process**:
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- - Identify appropriate lab partner early
342
- - Contact lab scientist to discuss collaboration
343
- - Develop work scope and budget together
344
- - Obtain lab approval (can take 2-3 months)
345
- - Include letter of commitment
346
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347
- **Major National Labs**:
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- - Argonne (ANL), Brookhaven (BNL), Lawrence Berkeley (LBNL)
349
- - Oak Ridge (ORNL), Pacific Northwest (PNNL), SLAC
350
- - Sandia (SNL), Los Alamos (LANL), Lawrence Livermore (LLNL)
351
- - National Renewable Energy Lab (NREL), Idaho (INL), Fermilab
352
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353
- ### User Facilities
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- **DOE operates 28 major user facilities** open to researchers
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- **Types**:
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- - **Light Sources**: X-ray and neutron scattering (APS, NSLS-II, ALS, etc.)
359
- - **Nanoscale Science Centers**: Fabrication and characterization
360
- - **High-Performance Computing**: Supercomputing centers (OLCF, NERSC, ALCF)
361
- - **Genomic Science**: JGI, EMSL
362
- - **Accelerators and Detectors**: Particle and nuclear physics facilities
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- **Access**:
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- - Submit user proposal (separate from research proposal)
366
- - Peer-reviewed allocation of beam time or computing hours
367
- - No cost for non-proprietary research
368
- - Can include user facility access in grant proposals
369
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370
- ### Cost Sharing Requirements
371
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372
- **Varies by Program**:
373
- - **Office of Science**: Generally not required (except specific FOAs)
374
- - **ARPA-E**: Required (typically 20% universities, 50%+ industry)
375
- - **EERE**: Often required (varies by program)
376
- - **FECM**: Often required
377
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378
- **Types**:
379
- - **Cash**: Direct contribution of funds
380
- - **In-kind**: Personnel time, equipment use, materials
381
- - **Third-party**: Contribution from collaborator or sponsor
382
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383
- **Requirements**:
384
- - Must be documented and verifiable
385
- - Cannot be used for other federal awards
386
- - Must be from non-federal sources (generally)
387
- - Need letters of commitment
388
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389
- ### Technology Readiness Levels (TRLs)
390
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391
- **DOE uses TRL scale 1-9** for technology development programs
392
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393
- **TRL Definitions**:
394
- - **TRL 1-3**: Basic research (idea → proof of concept)
395
- - **TRL 4-6**: Development (component → system prototype)
396
- - **TRL 7-9**: Demonstration and deployment (prototype → commercial)
397
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398
- **Funding by TRL**:
399
- - **Office of Science**: TRL 1-3 (basic research)
400
- - **ARPA-E**: TRL 2-5 (proof of concept → prototype)
401
- - **EERE**: TRL 4-8 (development → demonstration)
402
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403
- **Specify in Proposal**:
404
- - Current TRL of technology
405
- - Target TRL at project end
406
- - Path from current to target
407
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408
- ### Intellectual Property and Data Rights
409
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410
- **Standard Terms**:
411
- - Awardee generally retains IP rights
412
- - Government retains license for government purposes
413
- - Must report inventions to DOE
414
- - May have data sharing requirements
415
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416
- **Industry Partners**:
417
- - Negotiate IP and data rights in advance
418
- - Protected CRADA information (5 years)
419
- - Background IP vs. foreground IP
420
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421
- ### Teaming and Partnerships
422
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423
- **Encouraged for**:
424
- - University-national lab partnerships
425
- - University-industry partnerships
426
- - Multi-institutional teams
427
- - International collaborations (with approval)
428
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429
- **Teaming Partner Lists**: ARPA-E and other programs often provide teaming lists or events
430
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431
- ## Submission Process
432
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433
- ### Finding Opportunities
434
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435
- **Sources**:
436
- - **EERE Exchange**: https://eere-exchange.energy.gov
437
- - **ARPA-E OPEN**: https://arpa-e.energy.gov
438
- - **Office of Science FOAs**: https://science.osti.gov/grants/Funding-Opportunities
439
- - **Grants.gov**: Federal grants database
440
- - **FedConnect**: Subscribe to FOA announcements
441
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442
- ### Application Systems
443
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444
- **Varies by Office**:
445
- - **EERE Exchange**: EERE programs
446
- - **PAMS (Portfolio Analysis and Management System)**: Office of Science
447
- - **ARPA-E OPEN**: ARPA-E submissions
448
- - **Grants.gov**: Some programs
449
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450
- **Registration Required** (can take 2-4 weeks):
451
- - SAM.gov (System for Award Management)
452
- - Grants.gov
453
- - DOE program-specific systems
454
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455
- ### Proposal Development Timeline
456
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457
- **Recommended Timeline**:
458
- - **3-6 months before deadline**: Identify FOA, assemble team, contact lab partners
459
- - **2-3 months**: Develop technical approach, secure commitments
460
- - **1-2 months**: Draft proposal, prepare budget
461
- - **2-4 weeks**: Internal review, revisions
462
- - **1 week**: Final preparation, institutional approvals
463
- - **48 hours early**: Submit (don't wait for deadline)
464
-
465
- ### Required Registrations
466
-
467
- **Before First Submission**:
468
- 1. **SAM.gov**: System for Award Management (2-3 weeks)
469
- 2. **Grants.gov**: Account and authorization (1 week)
470
- 3. **FedConnect**: Optional, for notifications
471
- 4. **PAMS/EERE Exchange**: Program-specific (immediate)
472
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473
- **Institutional Requirements**:
474
- - Authorized Organizational Representative (AOR)
475
- - Institutional approvals
476
- - Cost accounting systems
477
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478
- ## Review and Award Process
479
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480
- ### Timeline
481
-
482
- **Varies by Program**:
483
- - **Office of Science**: 3-6 months
484
- - **ARPA-E**: 4-6 months (after full application invitation)
485
- - **EERE**: 3-6 months
486
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487
- **Steps**:
488
- 1. Administrative compliance check
489
- 2. Peer review (external reviewers)
490
- 3. Program manager evaluation
491
- 4. Selection for award negotiation
492
- 5. Budget negotiation
493
- 6. Award issuance
494
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495
- ### Reviewer Feedback
496
-
497
- **Provided**:
498
- - Reviewer comments (often anonymized)
499
- - Strengths and weaknesses
500
- - Scores by criterion
501
-
502
- **Not Always Provided**: Some programs provide limited feedback
503
-
504
- ### Success Rates
505
-
506
- **Varies Widely**:
507
- - **Office of Science Early Career**: ~10-15%
508
- - **ARPA-E OPEN**: ~2-5% (concept papers → awards)
509
- - **EERE FOAs**: 10-30% (depends on program)
510
- - **Office of Science FOAs**: 20-40% (varies)
511
-
512
- ## Writing Tips for Competitive DOE Proposals
513
-
514
- ### Do's
515
-
516
- ✅ **Align with DOE mission** - Energy, environment, or national security relevance
517
- ✅ **Emphasize impact** - How will this advance energy technology or science?
518
- ✅ **Quantify outcomes** - Energy savings, efficiency gains, cost reductions
519
- ✅ **Show pathway to deployment** - For applied programs, how will technology reach market?
520
- ✅ **Leverage DOE capabilities** - National labs, user facilities, unique resources
521
- ✅ **Include strong management plan** - Milestones, go/no-go, risk mitigation
522
- ✅ **Demonstrate team qualifications** - Track record in relevant area
523
- ✅ **Be specific about innovation** - What's new and why it matters
524
- ✅ **Address technology readiness** - Current TRL and path forward
525
- ✅ **Secure cost share commitments** - If required, get letters early
526
-
527
- ### Don'ts
528
-
529
- ❌ **Don't ignore FOA requirements** - Each FOA is different, read carefully
530
- ❌ **Don't underestimate timeline** - Allow time for registrations and approvals
531
- ❌ **Don't forget cost share** - If required, must be documented
532
- ❌ **Don't overlook lab partnerships** - Can strengthen proposal significantly
533
- ❌ **Don't be vague about impact** - Need quantitative energy/economic metrics
534
- ❌ **Don't ignore commercialization** - For applied programs, market path is critical
535
- ❌ **Don't submit without institutional approval** - Need AOR sign-off
536
- ❌ **Don't wait for deadline** - Systems crash, submit 48 hours early
537
- ❌ **Don't propose basic science to ARPA-E** - Or applied research to Office of Science
538
- ❌ **Don't forget TRL discussion** - Important for technology programs
539
-
540
- ### Common Mistakes
541
-
542
- 1. **Wrong Program**: Proposing to inappropriate office or program
543
- 2. **Insufficient Energy Relevance**: Not clearly tied to DOE mission
544
- 3. **Weak Commercialization Plan**: For ARPA-E and EERE, lack of market strategy
545
- 4. **Unrealistic Milestones**: Overly optimistic timelines
546
- 5. **Poor Budget Justification**: Budget doesn't align with technical plan
547
- 6. **Missing Cost Share**: If required, not documented properly
548
- 7. **Weak Team**: Insufficient expertise or track record
549
- 8. **Ignoring Competing Technologies**: Not addressing competitive landscape
550
-
551
- ## Recent DOE Priorities (2024-2025)
552
-
553
- ### Key Focus Areas
554
-
555
- - **Clean Energy Transition**: Renewable energy, storage, grid modernization
556
- - **Carbon Management**: Carbon capture, utilization, storage, removal
557
- - **Critical Materials**: Supply chain security, recycling, substitutes
558
- - **Advanced Manufacturing**: Energy-efficient processes, sustainable materials
559
- - **Quantum Information Science**: Computing, sensing, communications
560
- - **Fusion Energy**: Accelerating fusion development
561
- - **Hydrogen Economy**: Production, storage, utilization
562
- - **Nuclear Energy**: Advanced reactors, microreactors, fuel cycle
563
- - **Climate Adaptation**: Climate modeling, resilience, impacts
564
- - **Energy Equity**: Environmental justice, workforce development
565
-
566
- ### Major Initiatives
567
-
568
- - **Energy Earthshots**: Ambitious R&D goals (Hydrogen Shot, Long Duration Storage, Carbon Negative, etc.)
569
- - **Bipartisan Infrastructure Law**: $62B for DOE programs
570
- - **Inflation Reduction Act**: Clean energy tax credits and programs
571
- - **CHIPS and Science Act**: Microelectronics, quantum, clean energy manufacturing
572
-
573
- ## Resources
574
-
575
- - **DOE Office of Science**: https://science.osti.gov
576
- - **ARPA-E**: https://arpa-e.energy.gov
577
- - **EERE**: https://www.energy.gov/eere
578
- - **DOE National Laboratories**: https://www.energy.gov/national-laboratories
579
- - **EERE Exchange**: https://eere-exchange.energy.gov
580
- - **Grants.gov**: https://www.grants.gov
581
- - **SAM.gov**: https://sam.gov
582
-
583
- ---
584
-
585
- **Key Takeaway**: DOE proposals require strong alignment with energy and national security missions, clear pathway to impact (especially for applied programs), and often benefit from partnerships with national laboratories or industry. Cost sharing, technology readiness levels, and commercialization strategies are critical considerations for competitive proposals.
586
-