@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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@@ -1,220 +0,0 @@
1
- # Responsible AI in Research Ideation
2
-
3
- AI can supply prompts, reframings, counterarguments, or organizational help.
4
- It is not an expert panel, evidence source, author, ethics reviewer, or
5
- scientific decision maker. Capabilities and policies change; follow current
6
- institutional, funder, publisher, legal, and community requirements.
7
-
8
- ## Default sequence
9
-
10
- 1. **Classify information.** Decide whether the prompt would include personal,
11
- patient, confidential, unpublished, proprietary, export-controlled,
12
- security-sensitive, or otherwise restricted information.
13
- 2. **Generate human ideas first.** Freeze an independent human-only round
14
- before showing AI suggestions.
15
- 3. **Define the AI role.** Examples: produce orthogonal questions, challenge an
16
- assumption, list search terms, or reformat an already approved record.
17
- 4. **Use only an approved tool and data class.** Do not assume a paid or
18
- “private” interface satisfies institutional controls.
19
- 5. **Capture provenance.** Record tool/model or service, date, purpose, material
20
- prompt constraints, output IDs used, and human editor. Avoid storing
21
- restricted prompt text in the session register.
22
- 6. **Verify externally.** Check factual claims and every citation against
23
- authoritative sources. Search for contradictory and null evidence.
24
- 7. **Run a second independent human round.** Ask for ideas outside the AI's
25
- frames and for harms or stakeholders the output omitted.
26
- 8. **Disclose as required.** The accountable humans retain authorship,
27
- responsibility, and final judgment.
28
-
29
- AI use is optional. The bundled CLIs make no network or LLM calls.
30
-
31
- ## Suitable bounded roles
32
-
33
- - Generate alternative phrasings of a non-sensitive focal question.
34
- - Suggest dimensions for a morphological matrix, followed by human review.
35
- - Produce counterexamples or alternative mechanisms for registered ideas.
36
- - Identify ambiguous terms or missing assumptions.
37
- - Generate candidate search vocabulary, not references presented as real.
38
- - Convert an approved, non-sensitive record between formats.
39
- - Act as one disclosed adversarial prompt after human-first ideation.
40
-
41
- Avoid using AI to:
42
-
43
- - decide which scientific claim is true;
44
- - certify novelty, safety, ethics, legality, or regulatory compliance;
45
- - invent or complete missing data;
46
- - rank people, patients, communities, or protected groups;
47
- - replace stakeholder participation or domain expertise;
48
- - generate actionable harmful or dual-use procedures;
49
- - review confidential manuscripts, grants, or peer-review material in systems
50
- where confidentiality is not assured.
51
-
52
- ## Hallucination and source verification
53
-
54
- Generative systems can produce plausible but false claims, references,
55
- methods, statistics, and quotations. A 2023 study found fabricated and
56
- substantively erroneous bibliographic citations in outputs from the tested
57
- GPT-3.5 and GPT-4 versions; model-specific rates are not timeless estimates.
58
-
59
- For every AI-suggested source:
60
-
61
- 1. locate the work in a trusted index or publisher site;
62
- 2. match title, authors, venue, year, DOI, and version;
63
- 3. read the relevant primary text;
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- 4. confirm the cited result, population, design, and limitations;
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- 5. record the stable source identifier;
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- 6. delete unsupported claims rather than laundering them as “AI suggested.”
67
-
68
- Never cite the model as evidence for a scientific claim.
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-
70
- ## Anchoring and homogenization
71
-
72
- AI output can anchor users on examples and compress a group's idea diversity.
73
- In a preregistered short-story experiment, access to GPT-4 ideas improved
74
- average evaluated creativity for some writers while making outputs more
75
- similar in aggregate. The task was short creative writing, not scientific
76
- ideation, so treat homogenization as a credible risk to test—not a universal
77
- effect size.
78
-
79
- Controls:
80
-
81
- - human-only generation before any AI output;
82
- - different participants receive no AI, or distinct prompt frames, when the
83
- comparison is methodologically justified;
84
- - ask for mechanisms that contradict the AI's dominant frame;
85
- - compare assumptions, predictions, and causal structure—not only wording;
86
- - preserve pre-AI ideas and record which ideas changed after exposure;
87
- - include non-AI domain, methods, stakeholder, ethics, and safety perspectives;
88
- - do not infer independent support from many outputs of the same model.
89
-
90
- Multiple AI samples are correlated products of a system, not independent
91
- experts or replications.
92
-
93
- ## Automation bias and false authority
94
-
95
- Fluent language, technical detail, and confident formatting are not evidence.
96
- To reduce deference:
97
-
98
- - hide model branding during idea review when feasible;
99
- - evaluate ideas against the same predeclared criteria;
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- - require a human rationale and uncertainty statement;
101
- - assign a non-originating human challenger;
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- - verify with primary evidence and domain experts;
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- - retain a “no decision / insufficient evidence” outcome;
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- - prohibit automatic advancement based only on an AI or matrix score.
105
-
106
- Do not ask an AI system to assign a probability it cannot calibrate and then
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- treat the number as measured uncertainty.
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-
109
- ## Confidentiality, privacy, and intellectual property
110
-
111
- Do not submit the following to an external AI service unless an authorized
112
- policy and agreement explicitly permit that data class:
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-
114
- - patient, participant, employee, student, or other personal information;
115
- - unpublished manuscripts, peer reviews, grants, invention disclosures, or
116
- partner materials;
117
- - proprietary protocols, source code, compounds, sequences, or business data;
118
- - controlled unclassified, export-controlled, classified, or
119
- security-sensitive information;
120
- - credentials, tokens, private links, or internal system details;
121
- - community-governed or Indigenous data outside agreed governance.
122
-
123
- Data minimization and abstraction are still required with an approved tool.
124
- Check retention, training use, access, location, deletion, audit, and incident
125
- terms. If the work cannot be safely abstracted, use an approved local/closed
126
- process or do not use AI.
127
-
128
- ## Bias, representation, and participation
129
-
130
- AI output may reproduce gaps and stereotypes in training data and overrepresent
131
- well-indexed, English-language, high-resource perspectives. It cannot consent
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- on behalf of affected communities.
133
-
134
- - Ask which populations, languages, geographies, disciplines, and negative
135
- findings are missing.
136
- - Involve relevant people directly and compensate them where applicable.
137
- - Distinguish biological variables from social identities and avoid
138
- essentialist mechanisms.
139
- - Examine whether a proposed measurement or intervention transfers across
140
- settings.
141
- - Treat accessibility, equity, and distribution of benefits and burdens as
142
- review criteria and possible gates.
143
-
144
- ## Research integrity and disclosure
145
-
146
- Humans remain responsible for accuracy, attribution, originality, permissions,
147
- and the research record. AI systems should not be listed as authors. Record and
148
- disclose AI use at the level required by the institution, funder, venue, and
149
- applicable guidance.
150
-
151
- A useful internal disclosure includes:
152
-
153
- ```text
154
- Tool/service and model or version (if exposed):
155
- Date used:
156
- Purpose:
157
- Information classification and approved environment:
158
- Human-first idea set frozen before use: yes/no
159
- Outputs retained or used:
160
- Verification performed:
161
- Material changes made by humans:
162
- Known limitations:
163
- ```
164
-
165
- Disclosure does not cure inappropriate data sharing, plagiarism, fabricated
166
- citations, or unverified content.
167
-
168
- ## Dual-use and misuse review
169
-
170
- AI can make technical ideation faster and more accessible. Screen both the
171
- research idea and the AI interaction for misuse potential.
172
-
173
- Escalate before generating operational detail when an idea could materially
174
- enable:
175
-
176
- - pathogen enhancement, immune evasion, host-range change, or harmful delivery;
177
- - synthesis, acquisition, concealment, scaling, or dissemination of hazardous
178
- agents or toxins;
179
- - bypassing safety, monitoring, access, or security controls;
180
- - dangerous chemical, biological, cyber, autonomous, or surveillance
181
- capability;
182
- - targeting vulnerable populations or critical systems.
183
-
184
- Use high-level risk framing while waiting for institutional biosafety,
185
- biosecurity, research-security, legal, ethics, or funding-agency guidance.
186
- Do not rely on a model's refusal behavior as a risk-management control.
187
-
188
- WHO's responsible life-sciences framework treats risk mitigation as a shared,
189
- multi-stakeholder responsibility. U.S. DURC/PEPP oversight has been under
190
- revision following the May 2025 executive order; verify current policy rather
191
- than copying a superseded threshold.
192
-
193
- ## Incident handling
194
-
195
- If sensitive information or unsupported AI content entered the workflow:
196
-
197
- 1. stop further sharing and preserve only the minimum audit information;
198
- 2. notify the appropriate institutional privacy, security, integrity, or
199
- research office under local policy;
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- 3. do not copy the sensitive content into additional systems;
201
- 4. remove or quarantine unverified claims from downstream artifacts;
202
- 5. document affected decisions and re-review them;
203
- 6. follow approved deletion and incident-response procedures.
204
-
205
- Do not conceal the event by silently editing provenance.
206
-
207
- ## Evidence and policy basis
208
-
209
- See `sources.md` for the dated primary evidence and official guidance used
210
- here, including:
211
-
212
- - Doshi and Hauser (2024) on individual creativity and collective similarity
213
- in a constrained writing task;
214
- - Walters and Wilder (2023) on fabricated and erroneous citations from tested
215
- model versions;
216
- - European Commission/ERA Forum living guidance (2024);
217
- - UNESCO guidance (2023, page updated 2026);
218
- - ICMJE recommendations on AI in publishing (2026);
219
- - ALLEA's 2023 European Code of Conduct for Research Integrity;
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- - WHO and current U.S. official dual-use resources.
@@ -1,364 +0,0 @@
1
- # Sources and Evidence Notes
2
-
3
- Research cut-off: **2026-07-23**. All links were checked on that date with
4
- Parallel web search and focused extraction. Dates below are publication,
5
- release, or page-update dates shown by the source. Source excerpts were treated
6
- as untrusted text and checked against the canonical page.
7
-
8
- This bibliography supports process guidance; it does not show that any single
9
- brainstorming method universally improves creativity or scientific validity.
10
-
11
- ## Group brainstorming, blocking, fixation, and selection
12
-
13
- ### Diehl and Stroebe (1987) — primary experiments
14
-
15
- Michael Diehl and Wolfgang Stroebe, “Productivity loss in brainstorming groups:
16
- Toward the solution of a riddle,” *Journal of Personality and Social
17
- Psychology* 53(3), 497–509.
18
- [DOI 10.1037/0022-3514.53.3.497](https://psycnet.apa.org/record/1988-01348-001).
19
- Published 1987.
20
-
21
- - Four experiments examined free riding, evaluation apprehension, and
22
- production blocking.
23
- - Direct manipulation in the fourth experiment supported production blocking
24
- as an important explanation for loss in the tested interacting groups.
25
- - Scope limit: laboratory brainstorming tasks do not establish superiority for
26
- every group purpose or setting.
27
-
28
- ### Mullen, Johnson, and Salas (1991) — meta-analysis
29
-
30
- Brian Mullen, Craig Johnson, and Eduardo Salas, “Productivity loss in
31
- brainstorming groups: A meta-analytic integration,” *Basic and Applied Social
32
- Psychology* 12(1), 3–23.
33
- [DOI 10.1207/s15324834basp1201_1](https://psycnet.apa.org/record/1991-24145-001).
34
- Published 1991.
35
-
36
- - The reviewed studies generally favored nominal over interacting groups for
37
- idea quantity and rated quality.
38
- - Loss varied with conditions such as group size and vocal versus written
39
- contribution.
40
- - Historical tasks, methods, and outcome definitions limit direct transfer to
41
- modern scientific teams.
42
-
43
- ### Rietzschel, Nijstad, and Stroebe (2006) — primary experiment
44
-
45
- Eric F. Rietzschel, Bernard A. Nijstad, and Wolfgang Stroebe, “Productivity is
46
- not enough: A comparison of interactive and nominal brainstorming groups on
47
- idea generation and selection,” *Journal of Experimental Social Psychology*
48
- 42(2), 244–251.
49
- [DOI 10.1016/j.jesp.2005.04.005](https://www.sciencedirect.com/science/article/abs/pii/S0022103105000600).
50
- Published March 2006.
51
-
52
- - In 42 analyzed three-person student groups, nominal groups generated more
53
- ideas; their ideas were more original and less feasible.
54
- - Selected-idea quality did not differ among conditions, and selection was not
55
- significantly better than chance.
56
- - Strictly separating generation and selection did not establish a universal
57
- selection advantage in this experiment.
58
-
59
- ### Rietzschel, Nijstad, and Stroebe (2010) — primary experiments
60
-
61
- Eric F. Rietzschel, Bernard A. Nijstad, and Wolfgang Stroebe, “The selection of
62
- creative ideas after individual idea generation: Choosing between creativity
63
- and impact,” *British Journal of Psychology* 101(1), 47–68.
64
- [DOI 10.1348/000712609X414204](https://pubmed.ncbi.nlm.nih.gov/19267959/).
65
- Published February 2010.
66
-
67
- - Explicit selection criteria improved selection on the named originality
68
- dimension in the reported studies, with trade-offs in satisfaction or rated
69
- effectiveness.
70
- - This supports explicit criteria, not a claim that a single composite score
71
- identifies the scientifically best idea.
72
-
73
- ### Smith, Ward, and Schumacher (1993) — primary experiments
74
-
75
- Steven M. Smith, Thomas B. Ward, and Jay S. Schumacher, “Constraining effects
76
- of examples in a creative generation task,” *Memory & Cognition* 21, 837–845.
77
- [DOI 10.3758/BF03202751](https://pubmed.ncbi.nlm.nih.gov/8289661/).
78
- Published November 1993.
79
-
80
- - Across three creative-generation experiments, participants exposed to
81
- examples were more likely to reproduce example features.
82
- - The specific drawing/design tasks support an anchoring or fixation risk; they
83
- do not quantify the effect for scientific ideation.
84
-
85
- ### Esser (1998) — review
86
-
87
- James K. Esser, “Alive and Well after 25 Years: A Review of Groupthink
88
- Research,” *Organizational Behavior and Human Decision Processes* 73(2–3),
89
- 116–141.
90
- [DOI 10.1006/obhd.1998.2758](https://pubmed.ncbi.nlm.nih.gov/9705799/).
91
- Published February 1998.
92
-
93
- - Reviews the evidence and evolution of Janis's groupthink model.
94
- - The broader literature includes substantial debate over the model and its
95
- antecedents; this skill therefore uses “groupthink” as a risk prompt, not a
96
- definitive diagnosis.
97
-
98
- ## Nominal groups, Delphi, and structured elicitation
99
-
100
- ### Van de Ven and Delbecq (1972) — early NGT paper
101
-
102
- Andrew H. Van de Ven and André L. Delbecq, “The nominal group as a research
103
- instrument for exploratory health studies,” *American Journal of Public
104
- Health* 62(3), 337–342.
105
- [DOI 10.2105/AJPH.62.3.337](https://pmc.ncbi.nlm.nih.gov/articles/PMC1530096/).
106
- Published March 1972.
107
-
108
- - Primary early account of the nominal-group approach in exploratory health
109
- research.
110
- - Historical evidence should be combined with current, context-specific
111
- reporting guidance.
112
-
113
- ### Harb et al. (2021) — NGT scoping review
114
-
115
- Sami I. Harb et al., “Methodological options of the nominal group technique for
116
- survey item elicitation in health research: A scoping review,” *Journal of
117
- Clinical Epidemiology* 139, 140–148.
118
- [DOI 10.1016/j.jclinepi.2021.08.008](https://www.sciencedirect.com/science/article/abs/pii/S0895435621002535).
119
- Published November 2021.
120
-
121
- - Included 57 studies and identified 30 process decision points across five
122
- broad stages.
123
- - Supports documenting actual choices and their rationale rather than treating
124
- NGT as one invariant protocol.
125
- - Scope is health-survey item elicitation, not every use of NGT.
126
-
127
- ### Jünger et al. (2017) — CREDES systematic review and guidance
128
-
129
- Saskia Jünger et al., “Guidance on Conducting and REporting DElphi Studies
130
- (CREDES) in palliative care,” *Palliative Medicine* 31(8), 684–706.
131
- [DOI 10.1177/0269216317690685](https://pubmed.ncbi.nlm.nih.gov/28190381/).
132
- E-published 13 February 2017.
133
-
134
- - A methodological systematic review of 30 palliative-care Delphi studies
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- found substantial variation in conduct, terminology, and reporting.
136
- - CREDES is reporting and conduct guidance developed in a palliative-care
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- context, not proof that Delphi consensus is correct.
138
-
139
- ### RAND (2023) — official Delphi methods guidance
140
-
141
- Dmitry Khodyakov, Sean Grant, Jack Kroger, and Melissa Bauman,
142
- [*RAND Methodological Guidance for Conducting and Critically Appraising Delphi
143
- Panels*](https://www.rand.org/pubs/tools/TLA3082-1.html).
144
- RAND Corporation, 29 December 2023.
145
- [DOI 10.7249/TLA3082-1](https://doi.org/10.7249/TLA3082-1).
146
-
147
- - Defines Delphi as iterative, anonymous, structured group communication under
148
- uncertainty and provides a design/appraisal tool.
149
- - RAND explicitly notes a lack of consistent methodological guidance across
150
- the many Delphi variants.
151
-
152
- ### EFSA (2014) — official expert-knowledge elicitation guidance
153
-
154
- European Food Safety Authority, “Guidance on Expert Knowledge Elicitation in
155
- Food and Feed Safety Risk Assessment,” *EFSA Journal* 12(6):3734.
156
- [DOI 10.2903/j.efsa.2014.3734](https://efsa.onlinelibrary.wiley.com/doi/10.2903/j.efsa.2014.3734).
157
- Adopted 22 May and published 19 June 2014.
158
-
159
- - Covers problem definition, preparation, expert/method selection, elicitation,
160
- uncertainty, aggregation, and documentation.
161
- - Developed for EFSA food/feed risk assessment; apply domain-specific guidance
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- elsewhere.
163
-
164
- ### Cooke, Mendel, and Thijs (1988) — structured judgment method
165
-
166
- Roger Cooke, Max Mendel, and Wim Thijs, “Calibration and information in expert
167
- resolution; a classical approach,” *Automatica* 24(1), 87–94.
168
- [DOI 10.1016/0005-1098(88)90011-8](https://www.sciencedirect.com/science/article/abs/pii/0005109888900118).
169
- Published 1988.
170
-
171
- - Presents calibration and information concepts for combining expert
172
- judgments and an experiment with descriptive value.
173
- - Using a “calibration” label without the method's elicitation, seed questions,
174
- and validation requirements would be misleading.
175
-
176
- ## Rigor, reproducibility, and sex as a biological variable
177
-
178
- ### NIH rigor and reproducibility guidance
179
-
180
- NIH Office of Extramural Research,
181
- [*Guidance: Rigor and Reproducibility in Grant Applications*](https://grants.nih.gov/policy-and-compliance/policy-topics/reproducibility/guidance).
182
- Page dated 16 October 2024.
183
-
184
- - Identifies rigor of prior research, rigorous experimental design, relevant
185
- biological variables, and authentication of key resources.
186
- - This is grant guidance. It does not validate an idea or substitute for a
187
- protocol, statistical review, or field-specific reporting standard.
188
-
189
- ### NIH SABV policy and current ORWH guidance
190
-
191
- NIH Office of Research on Women's Health,
192
- [*Sex as a Biological Variable*](https://orwh.od.nih.gov/sex-as-biological-variable).
193
- Page last updated 17 October 2025.
194
-
195
- - NIH expects sex to be considered in design, analysis, and reporting for
196
- vertebrate animal and human studies and requests strong justification for a
197
- single-sex scope.
198
- - The page links the governing
199
- [NOT-OD-15-102](https://grants.nih.gov/grants/guide/notice-files/not-od-15-102.html),
200
- released 9 June 2015 and effective for relevant applications from 2016.
201
- - Scope is NIH policy; other funders and jurisdictions may differ.
202
-
203
- ## Preregistration and open science
204
-
205
- ### Nosek et al. (2018) — preregistration perspective
206
-
207
- Brian A. Nosek et al., “The preregistration revolution,” *Proceedings of the
208
- National Academy of Sciences* 115(11), 2600–2606.
209
- [DOI 10.1073/pnas.1708274114](https://pubmed.ncbi.nlm.nih.gov/29531091/).
210
- Published 13 March 2018.
211
-
212
- - Frames preregistration as a way to distinguish prediction from postdiction
213
- by specifying questions and analyses before observing outcomes.
214
- - It is a methodological perspective, not evidence that registration alone
215
- guarantees rigor or reproducibility.
216
-
217
- ### Nosek et al. (2015) — TOP Guidelines
218
-
219
- Brian A. Nosek et al., “Promoting an open research culture,” *Science*
220
- 348(6242), 1422–1425.
221
- [DOI 10.1126/science.aab2374](https://www.science.org/doi/10.1126/science.aab2374).
222
- Published 26 June 2015.
223
-
224
- - Proposes modular journal-policy standards for transparency and openness.
225
- - A policy framework does not itself establish that a specific study is valid
226
- or ethically shareable.
227
-
228
- ### COS/OSF — current operational guidance
229
-
230
- Center for Open Science,
231
- [*Preregistration*](https://www.cos.io/initiatives/prereg) and
232
- [*Preregistration: A Plan, Not a Prison*](https://www.cos.io/blog/preregistration-plan-not-prison).
233
- Current pages accessed 23 July 2026.
234
-
235
- - Explicitly values both exploratory and confirmatory research, recommends
236
- transparent labeling, and explains how to report deviations.
237
-
238
- Center for Open Science,
239
- [*Registered Reports*](https://www.cos.io/initiatives/registered-reports).
240
- Current page accessed 23 July 2026.
241
-
242
- - Describes Stage 1 protocol review and in-principle acceptance before results,
243
- with exploratory analyses reported separately.
244
- - COS states that Registered Reports are not a panacea for every field or
245
- design.
246
-
247
- ## Responsible AI and research integrity
248
-
249
- ### Doshi and Hauser (2024) — primary randomized experiment
250
-
251
- Anil R. Doshi and Oliver P. Hauser, “Generative AI enhances individual
252
- creativity but reduces the collective diversity of novel content,” *Science
253
- Advances* 10(28):eadn5290.
254
- [DOI 10.1126/sciadv.adn5290](https://www.science.org/doi/10.1126/sciadv.adn5290).
255
- Published 12 July 2024.
256
-
257
- - Preregistered online experiment: 293 analyzed UK participants wrote
258
- eight-sentence stories with no, one, or up to five GPT-4 ideas.
259
- - AI access improved average evaluated novelty/usefulness, especially for
260
- lower-scoring writers, while outputs became more similar in aggregate.
261
- - Constrained short-story writing is not scientific ideation; the study
262
- supports a risk hypothesis, not a universal creativity claim.
263
-
264
- ### Walters and Wilder (2023) — primary citation audit
265
-
266
- William H. Walters and Esther Isabelle Wilder, “Fabrication and errors in the
267
- bibliographic citations generated by ChatGPT,” *Scientific Reports* 13.
268
- [DOI 10.1038/s41598-023-41032-5](https://www.nature.com/articles/s41598-023-41032-5).
269
- Published 7 September 2023.
270
-
271
- - Audited 84 texts produced in April 2023 by tested GPT-3.5 and GPT-4 versions
272
- and documented fabricated and substantive citation errors.
273
- - Results are model-, prompt-, task-, and date-specific; they justify direct
274
- source verification rather than a timeless error rate.
275
-
276
- ### European Commission / ERA Forum (2024) — official living guidance
277
-
278
- European Commission Directorate-General for Research and Innovation,
279
- [*Guidelines on the responsible use of generative AI in
280
- research*](https://research-and-innovation.ec.europa.eu/news/all-research-and-innovation-news/guidelines-responsible-use-generative-ai-research-developed-european-research-area-forum-2024-03-20_en).
281
- Published 20 March 2024.
282
-
283
- - Emphasizes transparency, responsibility, privacy, confidentiality,
284
- intellectual property, bias awareness, and avoiding AI in sensitive
285
- evaluation activities when confidentiality is not assured.
286
- - The Commission describes the guidance as living and subject to updates.
287
-
288
- ### UNESCO (2023; updated 2026) — official guidance
289
-
290
- Fengchun Miao and Wayne Holmes,
291
- [*Guidance for generative AI in education and research*](https://www.unesco.org/en/articles/guidance-generative-ai-education-and-research).
292
- Published 7 September 2023; page last updated 16 January 2026.
293
-
294
- - Uses a human-centered framing and addresses privacy, ethical validation,
295
- inclusion, equity, and institutional capacity.
296
- - Much of the document concerns education; apply research-specific provisions
297
- with local policy.
298
-
299
- ### ICMJE (2026) — official publishing recommendations
300
-
301
- International Committee of Medical Journal Editors,
302
- [*Use of Artificial Intelligence in Publishing*](https://www.icmje.org/recommendations/browse/artificial-intelligence).
303
- Recommendations page dated 2026.
304
-
305
- - Humans remain responsible for accuracy, attribution, permissions,
306
- confidentiality, and disclosure; AI tools are not authors.
307
- - Publishing guidance does not replace institutional research policy.
308
-
309
- ### ALLEA (2023) — research-integrity code
310
-
311
- ALLEA,
312
- [*The European Code of Conduct for Research Integrity, 2023 Revised
313
- Edition*](https://allea.org/portfolio-item/european-code-of-conduct-2023).
314
- [DOI 10.26356/ECOC](https://doi.org/10.26356/ECOC). Published 2023.
315
-
316
- - Cross-disciplinary self-regulatory framework recognized as a reference for
317
- EU-funded research.
318
- - General principles require translation into institutional and
319
- discipline-specific procedures.
320
-
321
- ## Dual-use and responsible life sciences
322
-
323
- ### WHO global framework and current program
324
-
325
- World Health Organization,
326
- [*Ensuring responsible use of life sciences research*](https://www.who.int/activities/ensuring-responsible-use-of-life-sciences-research).
327
- Program page accessed 23 July 2026; it indexes the 13 September 2022 Global
328
- Guidance Framework and materials through a 15 June 2026 meeting report.
329
-
330
- - Frames dual-use risk mitigation as individual and collective,
331
- multi-stakeholder work across life sciences and relevant emerging
332
- technologies.
333
- - Global guidance must be applied with jurisdictional and institutional rules.
334
-
335
- ### Current U.S. policy-status notice
336
-
337
- U.S. Department of Health and Human Services, Administration for Strategic
338
- Preparedness and Response,
339
- [*Dual Use Research of Concern Oversight Policy Framework*](https://aspr.hhs.gov/S3/Pages/Dual-Use-Research-of-Concern-Oversight-Policy-Framework.aspx).
340
- Current-status notice accessed 23 July 2026.
341
-
342
- - The page states that federal departments and agencies will revise or replace
343
- the 2024 DURC/PEPP policy in response to the 5 May 2025 executive order and
344
- that the page will be updated when revised policy is available.
345
- - Therefore this skill does not present the 2024 policy as a stable current
346
- checklist; researchers should consult their institution and current agency
347
- materials.
348
-
349
- ## Research method
350
-
351
- Parallel CLI searches used focused academic and official-domain queries for:
352
-
353
- - interactive versus nominal brainstorming and productivity blocking;
354
- - NGT, Delphi, and structured expert elicitation;
355
- - divergent/convergent idea generation and selection;
356
- - NIH rigor, reproducibility, and SABV;
357
- - preregistration, Registered Reports, and open-science guidance;
358
- - responsible AI, hallucinated citations, homogenization, confidentiality,
359
- research integrity, and disclosure;
360
- - WHO and U.S. dual-use policy status.
361
-
362
- Canonical sources were then fetched with `parallel-cli extract` using focused
363
- objectives for bibliographic metadata, methods, findings, limitations, and
364
- current policy status. No research JSON artifacts were saved in the skill.