scientific-problem-selection

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Tool: LICENSE.txt [1/2] Description: Apache License Version 2.0, January 2004 http://www.apache.org/licenses/ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION 1.

Tool: LICENSE.txt [2/2] Description: this License.

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Tool: SKILL.md [1/2] Description: --- name: scientific-problem-selection description: This skill should be used when scientists need help with research problem selection, project ideation, troubleshooting stuck projects, or strategic scientific decisions. Use this skill when users ask to pitch a new research idea, work through a project problem, evaluate project risks, plan research strategy, navigate decision trees, or get help choosing what scientific problem to work on.

Tool: SKILL.md [2/2] Description: Parameter Strategy Document | 2-3 days | | 5.

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Tool: references/01-intuition-pumps.md [1/2] Description: # SKILL: Intuition Pumps for Scientific Problem Ideation ## Overview This skill helps scientists generate high-quality research ideas by providing systematic prompts ("intuition pumps") and identifying common ideation traps. Based on the framework that most biological and chemical science projects involve **perturbing a system, measuring it, and analyzing the data**, this skill guides users through structured ideation that can significant

Tool: references/01-intuition-pumps.md [2/2] Description: valuable but risks crowding and incrementalism. **When It Works:** The user is enabling a field that truly needs this capability **When It Fails:** The tool is already widely applied; the contribution will be incremental **Self-Check:** Will this tool application open new biological questions, or just extend existing observations? Claude should help the user evaluate this honestly.

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Tool: references/02-risk-assessment.md [1/2] Description: # SKILL 2: Risk Assessment and Assumption Analysis ## Overview This skill helps scientists systematically identify, quantify, and manage project risk through rigorous assumption analysis. The goal is not to eliminate risk—risk-free projects tend to be incremental—but to name it, quantify it, and work steadily to chip away at it. This skill builds directly on the Problem Ideation Document from Skill 1.

Tool: references/02-risk-assessment.md [2/2] Description: specify:** 1. **The Question:** Exactly what is being tested? 2.

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Tool: references/03-optimization-function.md [1/3] Description: # SKILL 3: Optimization Function Selection ## Overview This skill helps scientists articulate HOW their project should be evaluated and define what success means. While Skill 2 focused on likelihood of success (the X-axis), this skill focuses on impact if successful (the Y-axis). The key insight: **value is in the eye of a belief system**—the value creation framework must be explicitly stated and led with.

Tool: references/03-optimization-function.md [2/3] Description: Y-Axis Score | Overall | |---------|-----------|--------------|--------------|---------| | Yours | [Type] | [L/M/H] + reasoning | [L/M/H] + reasoning | [Assessment] | | Alt 1 | [Type] | [L/M/H] + reasoning | [L/M/H] + reasoning | [Assessment] | | Alt 2 | [Type] | [L/M/H] + reasoning | [L/M/H] + reasoning | [Assessment] | **Comparative Questions:** - Which would be most impactful if they all work? - Which has the best risk-adjusted i

Tool: references/03-optimization-function.md [3/3] Description: [How to frame to avoid it] 2.

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Tool: references/04-parameter-strategy.md [1/3] Description: # SKILL 4: Parameter Fixation Strategy ## Overview This skill helps scientists strategically decide which parameters to fix and which to keep flexible in their project. The paradox: too many fixed parameters creates brittleness, but too few causes paralysis. The key is fixing ONE parameter thoughtfully and letting others float—constraints engender creativity.

Tool: references/04-parameter-strategy.md [2/3] Description: - Enables: Trying multiple approaches, testing in different models - Example: "I want to treat disease X; I'm open to any validated approach" ### Phase 6: Parameter Flexibility Matrix For your project, let's create a flexibility assessment: | Parameter | Currently | Should Be? | If Problem Arises, Could This Float?

Tool: references/04-parameter-strategy.md [3/3] Description: sounds like: "Use X to study Y in Z" - When one assumption fails, everything fails - You're attached to HOW more than WHAT - Forcing a technique-application match **Under-Constrained (Too Few/Vague):** - Statement is incredibly broad ("impactful work in...") - Feeling paralyzed about where to start - Avoiding commitment due to infinite options - No clear next experimental step **Well-Constrained:** - One clear fixed parameter with good

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Tool: references/05-decision-tree.md Description: # SKILL 5: Decision Tree Navigation ("The Altitude Dance") ## Overview This skill teaches you to move fluidly between execution (Level 1: getting stuff done) and strategic evaluation (Level 2: critical thinking). Projects rarely unfold linearly—they require frequent course correction.

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Tool: references/06-adversity-planning.md Description: # SKILL 6: Adversity Response Planning ("The Adversity Feature") ## Overview This skill helps you prepare for inevitable crises and reframe them as opportunities.

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Tool: references/07-problem-inversion.md Description: # SKILL 7: Problem Inversion Strategies ("Turn It On Its Head") ## Overview This skill provides three concrete strategies for navigating around obstacles by reframing problems. When stuck, instead of pushing harder on the current approach, try inverting the problem.

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Tool: references/08-integration-synthesis.md Description: # SKILL 8: Integration and Synthesis ## Overview This final individual skill synthesizes all previous skills into a coherent project plan and communication strategy.

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Tool: references/09-meta-framework.md [1/3] Description: # SKILL 9: Meta-Framework - Complete Problem Selection Workflow ## Overview This meta-skill orchestrates the complete problem selection process, guiding users through Skills 1-8 in a systematic, iterative way. This skill should be used when comprehensive support is needed from ideation through execution planning, with integrated literature searches and coherent documentation. ## When to Use This Skill **Use Skill 9 (Complete Workflow) when

Tool: references/09-meta-framework.md [2/3] Description: others capitalize on adversity? - What second-generation projects emerged from failures?

Tool: references/09-meta-framework.md [3/3] Description: Success Metrics ### How Do You Know This Worked? **Immediate Indicators:** - Clearer project vision than before - Honest assessment of risks - Contingency plans for failures - Compelling communication materials - Alignment between project and values - Confidence in problem choice **6-Month Indicators:** - Major decisions made faster (have framework) - Adversity handled productively (used playbook) - No existential crises (risks were mitiga