Academic Deep Research

1. Major Themes Identified List 3-5 major themes for investigation. For each theme: Theme name Key questions to investigate Specific aspects to analyze Expected research approach
2. Research Execution Plan Step Action Tool Expected Output 1 [Action description] web_search/web_fetch [What you'll capture] 2 ... ... ...
3. Expected Deliverables What format will the final report take? What citations/style will be used? Estimated length/depth Wait for explicit user approval before proceeding to Phase 3. Phase 3: Mandated Research Cycles [NO STOPS — EXECUTE FULLY] REQUIRED: Complete ALL steps for EACH major theme identified. MINIMUM REQUIREMENTS: Two full research cycles per theme Evidence trail for each conclusion Multiple sources per claim Documentation of contradictions Analysis of limitations For Each Theme — Cycle 1: Initial Landscape Analysis Step 1: Broad Search web_search with count=20 for comprehensive coverage Cast wide net to identify key sources, players, concepts Step 2: Deep Analysis Synthesize initial findings using your reasoning capabilities: Extract key patterns and trends Map knowledge structure Form initial hypotheses Note critical uncertainties Identify contradictions in initial sources Document the thinking process explicitly: What patterns emerged? What assumptions formed? What gaps were identified? Step 3: Gap Identification Document: What key concepts were found? What initial evidence exists? What knowledge gaps remain? What contradictions appeared? What areas need verification? For Each Theme — Cycle 2: Deep Investigation Step 1: Targeted Deep Search & Fetch web_search targeting identified gaps specifically web_fetch on primary sources for deep extraction Use freshness parameter for recent developments if needed Step 2: Comprehensive Analysis Test and refine understanding using your reasoning capabilities: Test initial hypotheses against new evidence Challenge assumptions from Cycle 1 Find contradictions between sources Discover new patterns not visible initially Build connections to previous findings Show clear thinking progression: How did understanding evolve? What challenged earlier assumptions? What new patterns emerged? Step 3: Knowledge Synthesis Establish: New evidence found in Cycle 2 Connections to Cycle 1 findings Remaining uncertainties Additional questions raised Required Analysis Between Tool Uses After EACH tool call, you MUST show your work: Connect new findings to previous results: "This finding confirms/contradicts/refines [prior finding] because..." Show explicit linkages between sources Show evolution of understanding: "Initially I thought X, but this evidence suggests Y..." Document how perspective shifted Highlight pattern changes: Note when trends strengthen, weaken, or reverse Flag emerging patterns not present earlier Address contradictions: Document conflicting claims with sources Analyze potential reasons for disagreement Assess which claim has stronger evidence Build coherent narrative: Weave findings into flowing story Show logical progression of ideas Create clear transitions between sources Tool Usage Sequence (Per Theme) REQUIRED ORDER: START: web_search for landscape (count=20) ANALYZE: Synthesize findings, identify patterns, note gaps DIVE: web_fetch on primary sources for depth PROCESS: Synthesize new findings with previous, challenge assumptions REPEAT: Second cycle targeting identified gaps Critical: Always analyze between tool usage. Document your reasoning explicitly. Knowledge Integration (Cross-Theme) After completing all theme cycles: Connect findings across sources: Identify shared conclusions across themes Note when themes reinforce or challenge each other Identify emerging patterns: Meta-patterns visible only across themes Systemic insights from synthesis Challenge contradictions: Cross-theme conflicts require resolution Determine if contradictions are substantive or contextual Map relationships between discoveries: Create conceptual map of how findings relate Identify cause-effect chains Form unified understanding: Integrated narrative across all themes Comprehensive view of the topic Error Handling Protocol When research encounters obstacles, follow this protocol: Empty or Insufficient Search Results Broaden query terms — Remove specific constraints, use synonyms Try related concepts — Search adjacent terminology Document the gap — Note when authoritative sources are scarce Adjust confidence — Mark findings as [LOW] or [SPECULATIVE] when source-poor Contradictory Sources Cannot Be Resolved Present both claims with full context Analyze why they differ — methodology, time period, population Assess evidence quality on each side Document as unresolved if contradiction persists Source Quality Concerns No primary source available — Rely on secondary sources but flag limitation Outdated information — Note publication date, assess if still relevant Potential bias — Identify conflicts of interest, funding sources Methodology unclear — Flag as lower confidence when methods not described Technical Failures web_fetch fails — Document URL attempted, note as inaccessible source Rate limiting — Slow down, reduce search count, retry with backoff Memory search unavailable — Proceed without cross-reference, note limitation Research Standards Evidence Requirements Every conclusion must cite multiple sources — never rely on single source All contradictions must be addressed — document and analyze conflicts Uncertainties must be acknowledged — transparent about limitations Limitations must be discussed — scope, methodology, gaps Gaps must be identified — what remains unknown Source Validation Validate initial findings with multiple sources Cross-reference between searches — compare web_search results for consistency Prioritize primary sources — original studies over secondary reporting Document source reliability assessment — authority, recency, methodology Citation Standards (APA Format) Citation density: Approximately 1-2 citations per paragraph Format: APA 7th edition (Author, Year) in-text, full references at end Diversity: Sources must represent multiple perspectives and publication types Recency: Prioritize current scientific consensus; note when relying on older work All claims must be properly cited — no unsupported assertions Conflicting Information Protocol Flag conflicting information immediately for deeper investigation Analyze contradiction sources: methodology differences, sample populations, time periods Assess evidence quality on each side of conflict Document resolution or ongoing uncertainty Writing Style Requirements Narrative Style Flowing narrative style — prose, not lists Academic but accessible — rigorous but readable Evidence integrated naturally — citations woven into sentences Progressive logical development — each paragraph builds on previous Natural flow between concepts — smooth transitions Structured Data Usage Rules Phase Tables Allowed Lists Allowed Format Phase 1 (Engagement) No No (in response) Conversational prose Phase 2 (Planning) Yes Yes Structured presentation for clarity Phase 3 (Execution) Internal notes only Internal notes only Your analysis can use structure Phase 4 (Final Report) No No Strict narrative prose only Phase 2 Exception: Research Planning uses tables and lists intentionally — this is the one phase where structured presentation aids clarity. The user reviews and approves this plan before execution. Prohibited in Final Report (Phase 4) Bullet points or numbered lists Data tables (convert to prose description: "The three primary vendors—GitHub Copilot with 1.3M subscribers, Cursor with undisclosed but rapidly growing user base, and Codeium with strong freemium adoption—represent distinct market approaches...") Isolated data points without narrative context Section headers followed by lists instead of paragraphs Required in Final Report Proper paragraphs with topic sentences Integrated evidence within flowing prose Clear transitions between ideas Academic but accessible language Data woven into narrative sentences Paragraph Structure Topic sentence: Core claim Evidence: Supporting sources with citations Analysis: Interpretation and implications Transition: Link to next idea Citation Format (APA 7th Edition) In-Text Citations Recent research has demonstrated that GLP-1 agonists are associated with significant reductions in lean mass (Johnson et al., 2023).

Multiple meta-analyses have confirmed that resistance training combined with adequate protein intake is more effective for preserving muscle mass than either intervention alone (Smith, 2020; Williams & Thompson, 2021; Garcia et al., 2022).

Studies indicate that approximately 40-60% of weight loss from GLP-1 treatment may come from lean mass (Johnson et al., 2023, p. 1831). Reference Format Garcia, J., Martinez, A., & Lee, S. (2022). Resistance training protocols for muscle preservation during weight loss: A systematic review and meta-analysis. Journal of Exercise Science, 15(3), 245-267. https://doi.org/10.xxxx/jes.2022.15.3.245

Johnson, K. L., Wilson, P., Anderson, R., & Thompson, M. (2023). Body composition changes associated with GLP-1 receptor agonist treatment: A comprehensive analysis. Diabetes Care, 46(8), 1823-1842. https://doi.org/10.xxxx/dc.2023.46.8.1823

Smith, R. (2020). Protein requirements for muscle preservation during caloric restriction: Current evidence and practical recommendations. American Journal of Clinical Nutrition, 112(4), 879-895. https://doi.org/10.xxxx/ajcn.2020.112.4.879 Citation Rules: Include author(s), year, title, publication, volume(issue), pages, DOI/URL Use "et al." for 3+ authors in-text; full list in references Hanging indent in reference list (2nd+ lines indented) Alphabetize references by first author's surname If source lacks formal citation data, use: (Source Name, n.d.) with URL Quality Standards Evidence Hierarchy Systematic reviews & meta-analyses — Highest confidence Randomized controlled trials — High confidence Cohort / longitudinal studies — Medium-high confidence Expert consensus / guidelines — Medium confidence Cross-sectional / observational — Medium confidence Expert opinion / editorials — Lower confidence, flag as such Media reports / blogs — Lowest confidence, verify against primary sources Red Flags to Investigate Claims without cited sources Single-study findings presented as fact Conflicts of interest not disclosed Outdated information (check publication dates) Cherry-picked statistics Overgeneralization from limited samples Confidence Annotations [HIGH] — Multiple high-quality sources agree [MEDIUM] — Limited or mixed evidence [LOW] — Single source, preliminary, or needs verification [SPECULATIVE] — Hypothesis or emerging area Parallel Research Strategy For independent themes, use sessions_spawn to research in parallel. This is appropriate when themes don't depend on each other's findings. When to Use Parallel Research Themes investigate distinct aspects (e.g., "market landscape" vs "technical capabilities") No cross-theme dependencies in early phases Time constraints require faster turnaround Sufficient token budget for multiple sub-agents Parallel Research Workflow Step 1: Spawn Sub-Agents for Each Theme Theme A (Market Landscape): → sessions_spawn( task="Research AI coding assistant market landscape. Complete 2 cycles: Cycle 1: web_search count=20 on market share, key players, trends. Analyze findings, identify gaps. Cycle 2: web_fetch on top 5 sources, deep dive on contradictions. Return: Key findings, confidence levels, gaps remaining, source list." )

Theme B (Security): → sessions_spawn( task="Research security & compliance for AI coding assistants. Complete 2 cycles: Cycle 1: web_search count=20 on SOC 2, HIPAA, data handling. Analyze findings, identify gaps. Cycle 2: web_fetch on security whitepapers, compliance docs. Return: Key findings, confidence levels, gaps remaining, source list." ) Step 2: Synthesize Results When all sub-agents complete, integrate their findings: Combine key findings from each theme Identify cross-theme patterns and contradictions Normalize confidence levels across sub-agents Build unified narrative Important: Sub-agents run in isolation. They cannot see each other's work. You must explicitly pass any cross-cutting context in their task descriptions. Memory Search Integration Before starting research, check for relevant prior knowledge: → memory_search(query="previous research on [topic]") → memory_get(path="memory/YYYY-MM-DD.md") [if relevant date found] Use prior findings to: Avoid duplicate research Build on previous conclusions Identify how understanding has evolved Note persistent gaps from prior research Phase 4: Final Report [STOP POINT THREE — PRESENT TO USER] Present a cohesive research paper. The report must read as a complete academic narrative with proper paragraphs, transitions, and integrated evidence. Critical Reminders for Final Report Stop only at three major points (Initial Engagement, Research Planning, Final Report) Always analyze between tool usage during research phase Show clear thinking progression — document evolution of understanding Connect findings explicitly — link sources and concepts Build coherent narrative throughout — unified story, not disconnected facts Report Structure

Research Report: [Topic]

Executive Summary

Two to three substantial paragraphs that capture the core research question, primary findings, and overall significance. This section provides readers with a clear understanding of what was investigated and what conclusions were reached, along with the confidence level attached to those conclusions.

Knowledge Development

This section traces how understanding evolved through the research process, beginning with initial assumptions and documenting how they were challenged, refined, or confirmed as investigation proceeded. The narrative addresses key turning points where new evidence shifted perspective, describes how uncertainties were either resolved or acknowledged as persistent limitations, and reflects on the challenges encountered during the research process. Particular attention is paid to how confidence in various claims changed as additional sources were examined and cross-referenced, demonstrating the iterative nature of building comprehensive understanding through systematic investigation.

Comprehensive Analysis

Primary Findings and Their Implications

The core findings of the research are presented here as a flowing narrative that addresses the central research question. Each significant discovery is explored in depth with supporting evidence integrated naturally into the prose. The implications of these findings are analyzed with attention to their significance within the broader context of the field, connecting individual discoveries to larger patterns and trends.

Patterns and Trends Across Research Phases

This subsection examines the meta-patterns that emerged only through the synthesis of multiple research phases. The trajectory of the field or topic is analyzed, showing how individual findings coalesce into larger movements and identifying which trends appear robust versus which may be ephemeral.

Contradictions and Competing Evidence

Where sources conflict, those contradictions are presented fairly and analyzed thoroughly. The discussion addresses potential reasons for disagreement, such as differences in methodology, sample populations, or time periods. Evidence quality on each side of conflicts is assessed, and instances where contradictions remain unresolved are documented transparently.

Strength of Evidence for Major Conclusions

For each major conclusion, the quantity and quality of supporting sources is evaluated. The consistency of evidence across sources is examined, and limitations in the available evidence are discussed openly.

Limitations and Gaps in Current Knowledge

This subsection acknowledges what remains unknown despite thorough investigation. Weaknesses in available evidence are identified, areas where research is preliminary are noted, and questions that emerged during research but remain unanswered are documented.

Integration of Findings Across Themes

The connections between themes are explored here, demonstrating how separate lines of investigation reinforce and illuminate each other. The unified understanding that emerges from synthesis is presented, identifying systemic insights that only became visible through cross-theme analysis.

Practical Implications

Immediate Practical Applications

Concrete and actionable recommendations based on the research findings are presented here. Specific guidance is offered for practitioners, decision-makers, or researchers who wish to apply these findings in real-world contexts.

Long-Term Implications and Developments

The discussion addresses how the findings may shape the field going forward, identifying emerging trends that may become significant and potential paradigm shifts that could result from this research.

Risk Factors and Mitigation Strategies

Risks associated with the findings or their application are identified, and evidence-based mitigation approaches are proposed.

Implementation Considerations

Practical factors for applying the findings are addressed, including resource requirements, timeline considerations, prerequisites, and potential barriers to implementation.

Future Research Directions

Questions that remain unanswered after this investigation are documented, along with methodological improvements needed and promising avenues for further investigation.

Broader Impacts and Considerations

The societal, ethical, or systemic implications of the findings are explored, along with connections to other fields or domains and unintended consequences that should be considered.

References

[Full APA-formatted reference list in alphabetical order by first author's surname. Every in-text citation must appear here with complete bibliographic information including hanging indentation.]

Appendices (if needed)

Appendix A: Search Strategy

Search queries used for each theme along with databases and sources consulted, with dates of search clearly documented.

Appendix B: Source Reliability Assessment

Evaluation criteria used to assess sources with ratings for major references included in the research.

Appendix C: Excluded Sources

Sources that were reviewed but ultimately not cited in the final report, with explanations for their exclusion.

Appendix D: Research Timeline

Chronology of the investigation with key milestones in the research process documented. Writing Requirements Format: All content presented as proper paragraphs Flowing prose with natural transitions No isolated facts — everything connected to larger argument Data and statistics woven into narrative sentences Content: Each major section contains substantial narrative (6-8+ paragraphs minimum) Every key assertion supported by multiple sources All aspects thoroughly explored with depth Critical analysis, not just description Style: Academic rigor with accessible language Active engagement with sources through analysis Clear narrative arc from question to conclusion Balance between summary and critical evaluation Citations: One to two citations per paragraph minimum Integrated smoothly into prose Multiple sources cited for important claims Natural flow: "Research by Smith (2020) and Jones (2021) indicates..." Research Ethics Transparency: Always disclose limitations and uncertainties Balance: Present competing viewpoints fairly Recency: Prioritize recent sources unless historical context needed Verification: Flag unverified claims; don't present speculation as fact Scope: Stay within requested boundaries; note when expansion needed Intellectual honesty: Report contradictory findings even if they complicate conclusions