@pikaa-ai/pikaa 0.3.0 → 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 +1170 -602
  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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- # Presentation Structure Guide
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-
3
- ## Overview
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-
5
- Effective scientific presentations follow a clear narrative structure that guides the audience through your research story. This guide provides structure templates for different talk lengths and contexts, helping you organize content for maximum impact and clarity.
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-
7
- ## Core Narrative Structure
8
-
9
- All scientific presentations should follow a story arc that engages, informs, and persuades:
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-
11
- 1. **Hook**: Grab attention immediately (30 seconds - 1 minute)
12
- 2. **Context**: Establish the research area and importance (5-10% of talk)
13
- 3. **Problem/Gap**: Identify what's unknown or problematic (5-10% of talk)
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- 4. **Approach**: Explain your solution or method (15-25% of talk)
15
- 5. **Results**: Present key findings (40-50% of talk)
16
- 6. **Implications**: Discuss meaning and impact (15-20% of talk)
17
- 7. **Closure**: Memorable conclusion and call to action (1-2 minutes)
18
-
19
- This arc mirrors the scientific method while maintaining narrative flow that keeps audiences engaged.
20
-
21
- ## Slide Count Guidelines
22
-
23
- **General Rule**: Approximately 1 slide per minute, with adjustments based on content complexity.
24
-
25
- | Talk Duration | Total Slides | Title/Intro | Methods | Results | Discussion | Conclusion |
26
- |---------------|--------------|-------------|---------|---------|------------|------------|
27
- | 5 minutes (lightning) | 5-7 | 1-2 | 0-1 | 2-3 | 1 | 1 |
28
- | 10 minutes (short) | 10-12 | 2 | 1-2 | 4-5 | 2-3 | 1 |
29
- | 15 minutes (conference) | 15-18 | 2-3 | 2-3 | 6-8 | 3-4 | 1-2 |
30
- | 20 minutes (extended) | 20-24 | 3 | 3-4 | 8-10 | 4-5 | 2 |
31
- | 30 minutes (seminar) | 25-30 | 3-4 | 5-6 | 10-12 | 6-8 | 2 |
32
- | 45 minutes (keynote) | 35-45 | 4-5 | 8-10 | 15-20 | 8-10 | 2-3 |
33
- | 60 minutes (lecture) | 45-60 | 5-6 | 10-12 | 20-25 | 10-12 | 3-4 |
34
-
35
- **Adjustments**:
36
- - **Complex data**: Reduce slide count (spend more time per slide)
37
- - **Simple concepts**: Can increase slide count slightly
38
- - **Heavy animations**: Count as multiple slides if building incrementally
39
- - **Q&A included**: Reduce content slides by 20-30%
40
-
41
- ## Structure by Talk Length
42
-
43
- ### 5-Minute Lightning Talk
44
-
45
- **Purpose**: Communicate one key idea quickly and memorably.
46
-
47
- **Structure** (5-7 slides):
48
- 1. **Title slide** (15 seconds): Title, name, affiliation
49
- 2. **The Problem** (45 seconds): One compelling problem statement with visual
50
- 3. **Your Solution** (60 seconds): Core approach or finding (1 slide or 2 if showing before/after)
51
- 4. **Key Result** (90 seconds): Single most important finding with clear visualization
52
- 5. **Impact** (45 seconds): Why it matters, one key implication
53
- 6. **Closing** (30 seconds): Memorable takeaway, contact info
54
-
55
- **Tips**:
56
- - Focus on ONE message only
57
- - Maximize visuals, minimize text
58
- - Practice exact timing
59
- - No methods details (mention in one sentence)
60
- - Prepare for "tell me more" conversations after
61
-
62
- ### 10-Minute Conference Talk
63
-
64
- **Purpose**: Present a complete research story with key findings.
65
-
66
- **Structure** (10-12 slides):
67
- 1. **Title slide** (30 seconds)
68
- 2. **Hook + Context** (60 seconds): Compelling opening that establishes importance
69
- 3. **Problem Statement** (60 seconds): Knowledge gap or challenge
70
- 4. **Approach Overview** (60-90 seconds): High-level methods (1-2 slides)
71
- 5. **Key Results** (4-5 minutes): Main findings (4-5 slides)
72
- - Result 1: Primary finding
73
- - Result 2: Supporting evidence
74
- - Result 3: Additional validation or application
75
- - (Optional) Result 4: Extension or implication
76
- 6. **Interpretation** (90 seconds): What it means (1-2 slides)
77
- 7. **Conclusions** (45 seconds): Main takeaways
78
- 8. **Acknowledgments** (15 seconds): Funding, collaborators
79
-
80
- **Tips**:
81
- - Spend 40-50% of time on results
82
- - Use build animations to control information flow
83
- - Practice transitions between sections
84
- - Leave 2-3 minutes for questions if Q&A is included
85
- - Have 1-2 backup slides with extra data
86
-
87
- ### 15-Minute Conference Talk (Standard)
88
-
89
- **Purpose**: Comprehensive presentation of a research project with detailed results.
90
-
91
- **Structure** (15-18 slides):
92
- 1. **Title slide** (30 seconds)
93
- 2. **Opening Hook** (45 seconds): Attention-grabbing problem or statistic
94
- 3. **Background/Context** (90 seconds): Why this research area matters (1-2 slides)
95
- 4. **Knowledge Gap** (60 seconds): What's unknown or problematic
96
- 5. **Research Question/Hypothesis** (45 seconds): Clear statement of objectives
97
- 6. **Methods Overview** (2-3 minutes): Experimental design (2-3 slides)
98
- - Study design/participants
99
- - Key procedures or techniques
100
- - Analysis approach
101
- 7. **Results** (6-7 minutes): Detailed findings (6-8 slides)
102
- - Opening: Sample characteristics or validation
103
- - Main finding 1: Primary outcome with statistics
104
- - Main finding 2: Secondary outcome or subgroup
105
- - Main finding 3: Mechanism or extension
106
- - (Optional) Additional analyses or sensitivity tests
107
- 8. **Discussion** (2-3 minutes): Interpretation and context (3-4 slides)
108
- - Relationship to prior work
109
- - Mechanisms or explanations
110
- - Limitations
111
- - Implications
112
- 9. **Conclusions** (60 seconds): Key takeaways (1-2 slides)
113
- 10. **Acknowledgments + Questions** (30 seconds)
114
-
115
- **Tips**:
116
- - Budget time for each section and practice with timer
117
- - Use section dividers or progress indicators
118
- - Spend most time on results (40-45%)
119
- - Anticipate likely questions and prepare backup slides
120
- - Have a "Plan B" for running over (know which slides to skip)
121
-
122
- ### 20-Minute Extended Talk
123
-
124
- **Purpose**: In-depth presentation with room for multiple studies or detailed methodology.
125
-
126
- **Structure** (20-24 slides):
127
-
128
- Similar to 15-minute talk but with:
129
- - More detailed methods (3-4 slides with diagrams)
130
- - Additional result categories or subanalyses
131
- - More extensive discussion of prior work
132
- - Deeper dive into one or two key findings
133
- - More context on limitations and future directions
134
-
135
- **Distribution**:
136
- - Introduction: 3 minutes (3 slides)
137
- - Methods: 4 minutes (3-4 slides)
138
- - Results: 9 minutes (8-10 slides)
139
- - Discussion: 3 minutes (4-5 slides)
140
- - Conclusion: 1 minute (2 slides)
141
-
142
- ### 30-Minute Seminar
143
-
144
- **Purpose**: Comprehensive research presentation with methodological depth.
145
-
146
- **Structure** (25-30 slides):
147
- 1. **Opening** (2-3 minutes): Title, hook, outline (3-4 slides)
148
- 2. **Background** (4-5 minutes): Detailed context and prior work (4-5 slides)
149
- 3. **Research Questions** (1 minute): Clear objectives (1 slide)
150
- 4. **Methods** (5-6 minutes): Detailed methodology (5-6 slides)
151
- - Study design with rationale
152
- - Participants/materials
153
- - Procedures (possibly multiple slides)
154
- - Analysis plan
155
- - Validation or pilot data
156
- 5. **Results** (10-12 minutes): Comprehensive findings (10-12 slides)
157
- - Demographics/baseline
158
- - Primary analyses (multiple slides)
159
- - Secondary analyses
160
- - Subgroup analyses
161
- - Sensitivity analyses
162
- - Summary visualization
163
- 6. **Discussion** (5-6 minutes): Interpretation and implications (6-8 slides)
164
- - Summary of findings
165
- - Comparison to literature (multiple references)
166
- - Mechanisms
167
- - Strengths and limitations (detailed)
168
- - Clinical/practical implications
169
- - Future directions
170
- 7. **Conclusions** (1-2 minutes): Key messages (2 slides)
171
- 8. **Acknowledgments/Questions** (1 minute)
172
-
173
- **Tips**:
174
- - Include an outline slide showing talk structure
175
- - Use section headers to maintain orientation
176
- - Can include animations and builds for complex concepts
177
- - More detailed methods are expected
178
- - Address potential objections proactively
179
- - Leave 5-10 minutes for Q&A
180
-
181
- ### 45-Minute Keynote or Invited Talk
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-
183
- **Purpose**: Comprehensive overview of a research program or major project with broader context.
184
-
185
- **Structure** (35-45 slides):
186
- 1. **Opening** (3-5 minutes): Hook, personal connection, outline (4-5 slides)
187
- 2. **Big Picture** (5-7 minutes): Field overview and importance (5-7 slides)
188
- 3. **Prior Work** (3-5 minutes): Literature review and gaps (4-5 slides)
189
- 4. **Your Research Program** (25-30 minutes):
190
- - Study 1: Question, methods, results (8-10 slides)
191
- - Transition: What we learned and what remained unknown
192
- - Study 2: Question, methods, results (8-10 slides)
193
- - (Optional) Study 3: Extensions or applications (5-7 slides)
194
- 5. **Synthesis** (5-7 minutes): What it all means (5-7 slides)
195
- - Integrated findings
196
- - Theoretical implications
197
- - Practical applications
198
- - Limitations
199
- 6. **Future Directions** (2-3 minutes): Where the field is going (2-3 slides)
200
- 7. **Conclusions** (2 minutes): Key messages (2 slides)
201
- 8. **Acknowledgments** (1 minute)
202
-
203
- **Tips**:
204
- - Tell a story arc across multiple studies
205
- - Show evolution of thinking
206
- - Include more personal elements and humor
207
- - Can discuss failed experiments or pivots
208
- - More philosophical and forward-looking
209
- - Engage audience with rhetorical questions
210
- - Leave 10-15 minutes for discussion
211
-
212
- ### 60-Minute Lecture or Tutorial
213
-
214
- **Purpose**: Educational presentation teaching a concept, method, or field overview.
215
-
216
- **Structure** (45-60 slides):
217
- 1. **Introduction** (5 minutes): Topic importance, learning objectives (5-6 slides)
218
- 2. **Foundations** (10-12 minutes): Essential background (10-12 slides)
219
- 3. **Core Content - Part 1** (15-18 minutes): First major topic (15-20 slides)
220
- 4. **Core Content - Part 2** (15-18 minutes): Second major topic (15-20 slides)
221
- 5. **Applications** (5-7 minutes): Real-world examples (5-7 slides)
222
- 6. **Summary** (3-5 minutes): Key takeaways, resources (3-4 slides)
223
- 7. **Questions/Discussion** (Remaining time)
224
-
225
- **Tips**:
226
- - Include checkpoints: "Are there questions so far?"
227
- - Use examples and analogies liberally
228
- - Build complexity gradually
229
- - Include interactive elements if possible
230
- - Provide resources for further learning
231
- - Repeat key concepts at transitions
232
- - Use consistent visual templates for concept types
233
-
234
- ## Opening Strategies
235
-
236
- ### The Hook (First 30-60 seconds)
237
-
238
- Your opening sets the tone and captures attention. Effective hooks:
239
-
240
- **1. Surprising Statistic**
241
- - "Every year, X million people experience Y, yet only Z% receive effective treatment."
242
- - Works well for applied research with societal impact
243
-
244
- **2. Provocative Question**
245
- - "What if I told you that everything we thought about X is wrong?"
246
- - Engages audience immediately, creates curiosity
247
-
248
- **3. Personal Story**
249
- - "Five years ago, I encountered a patient/problem that changed how I think about..."
250
- - Humanizes research, creates emotional connection
251
-
252
- **4. Visual Puzzle**
253
- - Start with an intriguing image or data visualization
254
- - "Look at this pattern. What could explain it?"
255
-
256
- **5. Contrasting Paradigms**
257
- - "The traditional view says X, but new evidence suggests Y."
258
- - Sets up tension and your contribution
259
-
260
- **6. Scope and Scale**
261
- - "This problem affects X people, costs Y dollars, and has been unsolved for Z years."
262
- - Establishes immediate importance
263
-
264
- ### Title Slide Essentials
265
-
266
- Your title slide should include:
267
- - **Clear, specific title** (not generic)
268
- - **Your name and credentials**
269
- - **Affiliation(s) with logos**
270
- - **Date and venue** (conference name)
271
- - **Optional**: QR code to paper, slides, or resources
272
- - **Optional**: Compelling background image related to research
273
-
274
- **Title Crafting**:
275
- - Be specific: "Machine Learning Predicts Alzheimer's Risk from Retinal Images"
276
- - Not vague: "Applications of AI in Healthcare"
277
- - Include key method and outcome
278
- - Maximum 15 words
279
- - Avoid jargon if presenting to broader audience
280
-
281
- ### Outline Slides
282
-
283
- For talks >20 minutes, include a brief outline slide:
284
- - Shows 3-5 main sections
285
- - Provides roadmap for audience
286
- - Can return to outline as section dividers
287
- - Keep simple and visual (not just bullet list)
288
-
289
- Example outline approach:
290
- ```
291
- [Icon] Background → [Icon] Methods → [Icon] Results → [Icon] Implications
292
- ```
293
-
294
- ## Closing Strategies
295
-
296
- ### Effective Conclusions
297
-
298
- The last 1-2 minutes are most remembered. Strong conclusions:
299
-
300
- **1. Key Takeaways Format**
301
- - 3-5 bullet points summarizing main messages
302
- - Each should be a complete, memorable sentence
303
- - Not just "Results": make claims
304
-
305
- **2. Call-Back Hook**
306
- - Reference your opening hook or question
307
- - "Remember that surprising statistic? Our findings suggest..."
308
- - Creates narrative closure
309
-
310
- **3. Practical Implications**
311
- - "What does this mean for clinicians/researchers/policy?"
312
- - Action-oriented takeaways
313
- - Bridges science to application
314
-
315
- **4. Visual Summary**
316
- - Single powerful figure integrating all findings
317
- - Conceptual model showing relationships
318
- - Before/after comparison
319
-
320
- **5. Future Outlook**
321
- - "These findings open doors to..."
322
- - 1-2 specific next steps
323
- - Inspiration for audience's own work
324
-
325
- ### Acknowledgments Slide
326
-
327
- Essential elements:
328
- - **Funding sources** (with grant numbers)
329
- - **Key collaborators** (with photos if space)
330
- - **Institution/lab** (with logo)
331
- - **Study participants** (appropriate mention)
332
- - Keep brief (15-30 seconds max)
333
- - Optional: Include contact info and QR codes here
334
-
335
- ### Final Slide
336
-
337
- Your final slide stays visible during Q&A. Include:
338
- - **"Thank you" or "Questions?"**
339
- - **Your contact information** (email, Twitter/X)
340
- - **QR code to paper, preprint, or slides**
341
- - **Lab website or GitHub**
342
- - **Key visual from your research** (not just text)
343
-
344
- Avoid ending with "References" or dense acknowledgments—these don't facilitate discussion.
345
-
346
- ## Transition Techniques
347
-
348
- Smooth transitions maintain narrative flow and audience orientation.
349
-
350
- ### Between Major Sections
351
-
352
- **Explicit Transition Slides**:
353
- - Use consistent visual style (color, icon, position)
354
- - Single word or short phrase: "Methods" "Results" "Implications"
355
- - Optional: Return to outline with current section highlighted
356
-
357
- **Verbal Transitions**:
358
- - "Now that we've established X, let's examine how we studied Y..."
359
- - "With that background, I'll turn to our key findings..."
360
- - "This raises the question: How did we measure this?"
361
-
362
- ### Between Related Slides
363
-
364
- **Visual Continuity**:
365
- - Repeat key element (figure, title format) across slides
366
- - Use consistent color coding
367
- - Progressive builds of same figure
368
-
369
- **Verbal Bridges**:
370
- - "Building on this finding..."
371
- - "To test this further..."
372
- - "This pattern was consistent across..."
373
-
374
- ### Signposting Language
375
-
376
- Help audience track progress through talk:
377
- - "First, I'll show... Second... Finally..."
378
- - "There are three key findings to discuss..."
379
- - "Now, let's turn to the most surprising result..."
380
- - "Coming back to our original question..."
381
-
382
- ## Pacing and Timing
383
-
384
- ### Time Budgeting
385
-
386
- **Plan timing for each slide**:
387
- - Simple title/transition slides: 15-30 seconds
388
- - Text content slides: 45-90 seconds
389
- - Complex figures: 2-3 minutes
390
- - Key results: 2-4 minutes each
391
-
392
- **Common Timing Mistakes**:
393
- - ❌ Spending too long on introduction (>15% of talk)
394
- - ❌ Rushing through results (should be 40-50%)
395
- - ❌ Not leaving time for questions
396
- - ❌ Going over time (extremely unprofessional)
397
-
398
- ### Practice Strategies
399
-
400
- **Full Run-Throughs** (Do 3-5 times):
401
- 1. **First run**: Rough timing, identify problem areas
402
- 2. **Second run**: Practice transitions, smooth language
403
- 3. **Third run**: Final timing with backup plans
404
- 4. **Recording**: Video yourself, watch for tics/filler words
405
- 5. **Audience practice**: Present to colleagues for feedback
406
-
407
- **Section Practice**:
408
- - Practice complex result slides multiple times
409
- - Rehearse opening and closing until flawless
410
- - Prepare ad-libs for common questions
411
-
412
- **Timing Techniques**:
413
- - Note target time at bottom of key slides
414
- - Set phone/watch to vibrate at checkpoints
415
- - Have Plan B: know which slides to skip if running over
416
- - Practice with live timer visible
417
-
418
- ### Managing Time During Talk
419
-
420
- **If Running Ahead** (rarely a problem):
421
- - Expand on key points naturally
422
- - Take questions mid-talk if appropriate
423
- - Provide more context or examples
424
- - Slow down slightly (but don't add filler)
425
-
426
- **If Running Behind**:
427
- - Skip backup slides or extra examples (prepare these in advance)
428
- - Summarize rather than detail on secondary points
429
- - Never rush through conclusions—skip earlier content instead
430
- - NEVER say "I'll go quickly through these" (just skip them)
431
-
432
- **Time Checkpoints**:
433
- - 25% through talk = 25% through time
434
- - 50% through talk = 50% through time
435
- - After results = should have 5-10 minutes left
436
- - Start conclusions with 2-3 minutes remaining
437
-
438
- ## Audience Engagement
439
-
440
- ### Reading the Room
441
-
442
- **Visual Cues**:
443
- - **Engaged**: Leaning forward, nodding, taking notes
444
- - **Lost**: Confused expressions, checking phones
445
- - **Bored**: Leaning back, glazed eyes, fidgeting
446
-
447
- **Adjustments**:
448
- - If losing audience: Speed up, add humor, show compelling visual
449
- - If audience confused: Slow down, ask "Does this make sense?", re-explain
450
- - If highly engaged: Can add more detail, encourage questions
451
-
452
- ### Interactive Elements
453
-
454
- For seminars and longer talks:
455
-
456
- **Rhetorical Questions**:
457
- - "Why do you think this pattern occurred?"
458
- - "What would you predict happens next?"
459
- - Pauses for thought (don't immediately answer)
460
-
461
- **Quick Polls** (if appropriate):
462
- - "Raise your hand if you've encountered X..."
463
- - "How many think the result will be A vs. B?"
464
- - Brief, not disruptive
465
-
466
- **Checkpoint Questions**:
467
- - "Before I continue, are there questions about the methods?"
468
- - "Is everyone comfortable with this concept?"
469
- - For longer talks or tutorials
470
-
471
- ### Body Language and Delivery
472
-
473
- **Effective Practices**:
474
- - ✅ Stand to side of screen, facing audience
475
- - ✅ Use pointer deliberately for specific elements
476
- - ✅ Make eye contact with different sections of room
477
- - ✅ Gesture naturally to emphasize points
478
- - ✅ Vary voice pitch and pace
479
- - ✅ Pause after important points
480
-
481
- **Avoid**:
482
- - ❌ Reading slides verbatim
483
- - ❌ Turning back to audience
484
- - ❌ Standing in front of projection
485
- - ❌ Fidgeting with pointer/objects
486
- - ❌ Pacing repetitively
487
- - ❌ Monotone delivery
488
-
489
- ## Special Considerations
490
-
491
- ### Virtual Presentations
492
-
493
- **Technical Setup**:
494
- - Test screen sharing, audio, and video beforehand
495
- - Use presenter mode if available (see notes)
496
- - Ensure good lighting and camera angle
497
- - Minimize background distractions
498
-
499
- **Engagement Challenges**:
500
- - Can't read audience body language as well
501
- - More explicit engagement needed
502
- - Use polls, chat, reactions if platform allows
503
- - Encourage unmuting for questions
504
-
505
- **Pacing**:
506
- - Slightly slower pace (harder to interrupt virtually)
507
- - More explicit transitions and signposting
508
- - Build in planned pauses for questions
509
- - Monitor chat for questions during talk
510
-
511
- ### Handling Questions
512
-
513
- **During Talk**:
514
- - For short talks: "Please hold questions until the end"
515
- - For seminars: "Feel free to interrupt with questions"
516
- - If interrupted: "Great question, let me finish this point and come back to it"
517
-
518
- **Q&A Session**:
519
- - **Listen fully** before answering
520
- - **Repeat or rephrase** question for whole audience
521
- - **Answer concisely** (30-90 seconds max)
522
- - **Be honest** if you don't know: "That's a great question I don't have data on yet"
523
- - **Redirect if off-topic**: "That's interesting but beyond scope. Happy to discuss after."
524
- - **Have backup slides** with extra data/analyses ready
525
-
526
- **Difficult Questions**:
527
- - **Hostile**: Stay calm, acknowledge concern, stick to data
528
- - **Confusing**: Ask for clarification: "Could you rephrase that?"
529
- - **Out of scope**: "I focused on X, but your question about Y is important for future work"
530
-
531
- ### Technical Difficulties
532
-
533
- **Preparation**:
534
- - Have backup: PDF on laptop, cloud, and USB drive
535
- - Test connections and adapters beforehand
536
- - Know how to reset display if needed
537
- - Have printout of slides as absolute backup
538
-
539
- **During Talk**:
540
- - Stay calm and professional
541
- - Fill time with verbal explanation while fixing
542
- - Skip problem slide if necessary
543
- - Apologize briefly but don't dwell on it
544
-
545
- ## Adapting to Different Venues
546
-
547
- ### Conference Presentation
548
-
549
- **Context**:
550
- - Concurrent sessions, some audience may arrive late
551
- - Audience has seen many talks that day
552
- - Strict time limits
553
- - May be recorded
554
-
555
- **Adaptations**:
556
- - Strong hook to capture attention
557
- - Clear, focused message (not trying to show everything)
558
- - Adhere exactly to time limits
559
- - Compelling visuals (tired audiences need visual interest)
560
- - Provide URL or QR code for more information
561
-
562
- ### Department Seminar
563
-
564
- **Context**:
565
- - Familiar audience with domain knowledge
566
- - More relaxed atmosphere
567
- - Can go deeper into methods
568
- - Questions encouraged throughout
569
-
570
- **Adaptations**:
571
- - Can use more technical language
572
- - Show more methodological details
573
- - Discuss failed experiments or challenges
574
- - Engage in back-and-forth discussion
575
- - Less formal style acceptable
576
-
577
- ### Thesis Defense
578
-
579
- **Context**:
580
- - Committee has read dissertation
581
- - Evaluating your mastery of field
582
- - Formal assessment situation
583
- - Extended Q&A expected
584
-
585
- **Adaptations**:
586
- - Comprehensive coverage required
587
- - Show depth of knowledge
588
- - Address limitations proactively
589
- - Demonstrate independent thinking
590
- - More formal, professional tone
591
- - Prepare extensively for questions
592
-
593
- ### Grant Pitch or Industry Talk
594
-
595
- **Context**:
596
- - Audience evaluating feasibility and impact
597
- - Emphasis on applications and outcomes
598
- - May include non-scientists
599
- - Shorter attention for technical details
600
-
601
- **Adaptations**:
602
- - Lead with impact and significance
603
- - Minimal methods details (what, not how)
604
- - Show preliminary data and proof of concept
605
- - Emphasize feasibility and timeline
606
- - Clear, simple language
607
- - Strong business case or societal benefit
608
-
609
- ## Summary Checklist
610
-
611
- Before finalizing your presentation structure:
612
-
613
- **Overall Structure**:
614
- - [ ] Clear narrative arc (hook → context → problem → solution → results → impact)
615
- - [ ] Appropriate slide count for time available (~1 slide/minute)
616
- - [ ] 40-50% of time allocated to results
617
- - [ ] Strong opening and closing
618
- - [ ] Smooth transitions between sections
619
-
620
- **Timing**:
621
- - [ ] Practiced full talk at least 3 times
622
- - [ ] Timing noted for key sections
623
- - [ ] Plan B for running over (slides to skip)
624
- - [ ] Buffer time for questions (if applicable)
625
-
626
- **Engagement**:
627
- - [ ] Opening hook captures attention
628
- - [ ] Clear signposting throughout
629
- - [ ] Conclusion provides memorable takeaways
630
- - [ ] Final slide facilitates discussion
631
-
632
- **Technical**:
633
- - [ ] Slides numbered (for question reference)
634
- - [ ] Backup slides prepared for anticipated questions
635
- - [ ] Contact info and QR codes on final slide
636
- - [ ] Multiple copies of presentation saved
637
-
638
- **Practice**:
639
- - [ ] Comfortable with content (minimal note reliance)
640
- - [ ] Transitions smooth and natural
641
- - [ ] Prepared for likely questions
642
- - [ ] Tested with live audience if possible