frumu-ai/bio-research-strategy

Scientific Problem Selection Skills

A conversational framework for systematic scientific problem selection based on Fischbach & Walsh's "Problem choice and decision trees in science and engineering" (Cell, 2024).

Getting Started

Present users with three entry points:

1) Pitch an idea for a new project — to work it up together

2) Share a problem in a current project — to troubleshoot together

3) Ask a strategic question — to navigate the decision tree together

This conversational entry meets scientists where they are and establishes a collaborative tone.

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Option 1: Pitch an Idea

Initial Prompt

Ask: "Tell me the short version of your idea (1-2 sentences)."

Response Approach

After the user shares their idea, return a quick summary (no more than one paragraph) demonstrating understanding. Note the general area of research and rephrase the idea in a way that highlights its kernel—showing alignment and readiness to dive into details.

Follow-up Prompt

Then ask for more detail: "Now give me a bit more detail. You might include, however briefly or even say where you are unsure:

1. What exactly you want to do
2. How you currently plan to do it
3. If it works, why will it be a big deal
4. What you think are the major risks"

Workflow

From there, guide the user through the early stages of problem selection and evaluation:

• Skill 1: Intuition Pumps - Refine and strengthen the idea
• Skill 2: Risk Assessment - Identify and manage project risks
• Skill 3: Optimization Function - Define success metrics
• Skill 4: Parameter Strategy - Determine what to fix vs. keep flexible

I can access detailed guidance in the references/ folder of this skill.

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Option 2: Troubleshoot a Problem

Initial Prompt

Ask: "Tell me a short version of your problem (1-2 sentences or whatever is easy)."

Response Approach

After the user shares their problem, return a quick summary (no more than one paragraph) demonstrating understanding. Note the context of the project where the problem occurred and rephrase the problem—highlighting its core essence—so the user knows the situation is understood. Also raise additional questions that seem important to discuss.

Follow-up Prompt

Then ask: "Now give me a bit more detail. You might include, however briefly:

1. The overall goal of your project (if we have not talked about it before)
2. What exactly went wrong
3. Your current ideas for fixing it"

Workflow

From there, guide the user through troubleshooting and decision tree navigation:

• Skill 5: Decision Tree Navigation - Plan decision points and navigate between execution and strategic thinking
• Skill 4: Parameter Strategy - Fix one parameter at a time, let others float
• Skill 6: Adversity Response - Frame problems as opportunities for growth
• Skill 7: Problem Inversion - Strategies for navigating around obstacles

Always include workarounds that might be useful whether or not the problem can be fixed easily.

I can access detailed guidance in the references/ folder of this skill.

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Option 3: Ask a Strategic Question

Initial Prompt

Ask: "Tell me the short version of your question (1-2 sentences)."

Response Approach

After the user shares their question, return a quick summary (no more than one paragraph) demonstrating understanding. Note the broader context and rephrase the question—highlighting its crux—to confirm alignment with their thinking.

Follow-up Prompt

Then ask: "Now give me a bit more detail. You might include, however briefly:

1. The setting (i.e., is this about a current or future project)
2. A bit more detail about what you're thinking"

Workflow

From there, draw on the specific modules from the problem choice framework most appropriate to the question:

• Skills 1-4 for future project planning (ideation, risk, optimization, parameters)
• Skills 5-7 for current project navigation (decision trees, adversity, inversion)
• Skill 8 for communication and synthesis
• Skill 9 for comprehensive workflow orchestration

See the complete reference materials in the references/ folder.