opencode-knowledge-work 0.0.0-stage → 0.1.0

package/content/bio-research/skills/bio-research-scientific-problem-selection/LICENSE.txt

@@ -0,0 +1,201 @@
+Apache License
+Version 2.0, January 2004
+http://www.apache.org/licenses/
+
+TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+1. Definitions.
+
+"License" shall mean the terms and conditions for use, reproduction,
+and distribution as defined by Sections 1 through 9 of this document.
+
+"Licensor" shall mean the copyright owner or entity authorized by
+the copyright owner that is granting the License.
+
+"Legal Entity" shall mean the union of the acting entity and all
+other entities that control, are controlled by, or are under common
+control with that entity. For the purposes of this definition,
+"control" means (i) the power, direct or indirect, to cause the
+direction or management of such entity, whether by contract or
+otherwise, or (ii) ownership of fifty percent (50%) or more of the
+outstanding shares, or (iii) beneficial ownership of such entity.
+
+"You" (or "Your") shall mean an individual or Legal Entity
+exercising permissions granted by this License.
+
+"Source" form shall mean the preferred form for making modifications,
+including but not limited to software source code, documentation
+source, and configuration files.
+
+"Object" form shall mean any form resulting from mechanical
+transformation or translation of a Source form, including but
+not limited to compiled object code, generated documentation,
+and conversions to other media types.
+
+"Work" shall mean the work of authorship, whether in Source or
+Object form, made available under the License, as indicated by a
+copyright notice that is included in or attached to the work
+(an example is provided in the Appendix below).
+
+"Derivative Works" shall mean any work, whether in Source or Object
+form, that is based on (or derived from) the Work and for which the
+editorial revisions, annotations, elaborations, or other modifications
+represent, as a whole, an original work of authorship. For the purposes
+of this License, Derivative Works shall not include works that remain
+separable from, or merely link (or bind by name) to the interfaces of,
+the Work and Derivative Works thereof.
+
+"Contribution" shall mean any work of authorship, including
+the original version of the Work and any modifications or additions
+to that Work or Derivative Works thereof, that is intentionally
+submitted to Licensor for inclusion in the Work by the copyright owner
+or by an individual or Legal Entity authorized to submit on behalf of
+the copyright owner. For the purposes of this definition, "submitted"
+means any form of electronic, verbal, or written communication sent
+to the Licensor or its representatives, including but not limited to
+communication on electronic mailing lists, source code control systems,
+and issue tracking systems that are managed by, or on behalf of, the
+Licensor for the purpose of discussing and improving the Work, but
+excluding communication that is conspicuously marked or otherwise
+designated in writing by the copyright owner as "Not a Contribution."
+
+"Contributor" shall mean Licensor and any individual or Legal Entity
+on behalf of whom a Contribution has been received by Licensor and
+subsequently incorporated within the Work.
+
+2. Grant of Copyright License. Subject to the terms and conditions of
+this License, each Contributor hereby grants to You a perpetual,
+worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+copyright license to reproduce, prepare Derivative Works of,
+publicly display, publicly perform, sublicense, and distribute the
+Work and such Derivative Works in Source or Object form.
+
+3. Grant of Patent License. Subject to the terms and conditions of
+this License, each Contributor hereby grants to You a perpetual,
+worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+(except as stated in this section) patent license to make, have made,
+use, offer to sell, sell, import, and otherwise transfer the Work,
+where such license applies only to those patent claims licensable
+by such Contributor that are necessarily infringed by their
+Contribution(s) alone or by combination of their Contribution(s)
+with the Work to which such Contribution(s) was submitted. If You
+institute patent litigation against any entity (including a
+cross-claim or counterclaim in a lawsuit) alleging that the Work
+or a Contribution incorporated within the Work constitutes direct
+or contributory patent infringement, then any patent licenses
+granted to You under this License for that Work shall terminate
+as of the date such litigation is filed.
+
+4. Redistribution. You may reproduce and distribute copies of the
+Work or Derivative Works thereof in any medium, with or without
+modifications, and in Source or Object form, provided that You
+meet the following conditions:
+
+(a) You must give any other recipients of the Work or
+Derivative Works a copy of this License; and
+
+(b) You must cause any modified files to carry prominent notices
+stating that You changed the files; and
+
+(c) You must retain, in the Source form of any Derivative Works
+that You distribute, all copyright, patent, trademark, and
+attribution notices from the Source form of the Work,
+excluding those notices that do not pertain to any part of
+the Derivative Works; and
+
+(d) If the Work includes a "NOTICE" text file as part of its
+distribution, then any Derivative Works that You distribute must
+include a readable copy of the attribution notices contained
+within such NOTICE file, excluding those notices that do not
+pertain to any part of the Derivative Works, in at least one
+of the following places: within a NOTICE text file distributed
+as part of the Derivative Works; within the Source form or
+documentation, if provided along with the Derivative Works; or,
+within a display generated by the Derivative Works, if and
+wherever such third-party notices normally appear. The contents
+of the NOTICE file are for informational purposes only and
+do not modify the License. You may add Your own attribution
+notices within Derivative Works that You distribute, alongside
+or as an addendum to the NOTICE text from the Work, provided
+that such additional attribution notices cannot be construed
+as modifying the License.
+
+You may add Your own copyright statement to Your modifications and
+may provide additional or different license terms and conditions
+for use, reproduction, or distribution of Your modifications, or
+for any such Derivative Works as a whole, provided Your use,
+reproduction, and distribution of the Work otherwise complies with
+the conditions stated in this License.
+
+5. Submission of Contributions. Unless You explicitly state otherwise,
+any Contribution intentionally submitted for inclusion in the Work
+by You to the Licensor shall be under the terms and conditions of
+this License, without any additional terms or conditions.
+Notwithstanding the above, nothing herein shall supersede or modify
+the terms of any separate license agreement you may have executed
+with Licensor regarding such Contributions.
+
+6. Trademarks. This License does not grant permission to use the trade
+names, trademarks, service marks, or product names of the Licensor,
+except as required for reasonable and customary use in describing the
+origin of the Work and reproducing the content of the NOTICE file.
+
+7. Disclaimer of Warranty. Unless required by applicable law or
+agreed to in writing, Licensor provides the Work (and each
+Contributor provides its Contributions) on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+implied, including, without limitation, any warranties or conditions
+of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+PARTICULAR PURPOSE. You are solely responsible for determining the
+appropriateness of using or redistributing the Work and assume any
+risks associated with Your exercise of permissions under this License.
+
+8. Limitation of Liability. In no event and under no legal theory,
+whether in tort (including negligence), contract, or otherwise,
+unless required by applicable law (such as deliberate and grossly
+negligent acts) or agreed to in writing, shall any Contributor be
+liable to You for damages, including any direct, indirect, special,
+incidental, or consequential damages of any character arising as a
+result of this License or out of the use or inability to use the
+Work (including but not limited to damages for loss of goodwill,
+work stoppage, computer failure or malfunction, or any and all
+other commercial damages or losses), even if such Contributor
+has been advised of the possibility of such damages.
+
+9. Accepting Warranty or Additional Liability. While redistributing
+the Work or Derivative Works thereof, You may choose to offer,
+and charge a fee for, acceptance of support, warranty, indemnity,
+or other liability obligations and/or rights consistent with this
+License. However, in accepting such obligations, You may act only
+on Your own behalf and on Your sole responsibility, not on behalf
+of any other Contributor, and only if You agree to indemnify,
+defend, and hold each Contributor harmless for any liability
+incurred by, or claims asserted against, such Contributor by reason
+of your accepting any such warranty or additional liability.
+
+END OF TERMS AND CONDITIONS
+
+APPENDIX: How to apply the Apache License to your work.
+
+To apply the Apache License to your work, attach the following
+boilerplate notice, with the fields enclosed by brackets "[]"
+replaced with your own identifying information. (Don't include
+the brackets!) The text should be enclosed in the appropriate
+comment syntax for the file format. We also recommend that a
+file or class name and description of purpose be included on the
+same "printed page" as the copyright notice for easier
+identification within third-party archives.
+
+Copyright [yyyy] [name of copyright owner]
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.

package/content/bio-research/skills/bio-research-scientific-problem-selection/SKILL.md

@@ -0,0 +1,269 @@
+---
+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. Typical requests include "I have an idea for a project", "I'm stuck on my research", "help me evaluate this project", "what should I work on", or "I need strategic advice about my research".
+---
+
+# 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.
+
+---
+
+## 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
+
+See `references/01-intuition-pumps.md`, `references/02-risk-assessment.md`, `references/03-optimization-function.md`, and `references/04-parameter-strategy.md` for detailed guidance.
+
+---
+
+## 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.
+
+See `references/05-decision-tree.md`, `references/06-adversity-planning.md`, `references/07-problem-inversion.md`, and `references/04-parameter-strategy.md` for detailed guidance.
+
+---
+
+## 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.
+
+---
+
+## Core Framework Concepts
+
+### The Central Insight
+**Problem Choice >> Execution Quality**
+
+Even brilliant execution of a mediocre problem yields incremental impact. Good execution of an important problem yields substantial impact.
+
+### The Time Paradox
+Scientists typically spend:
+- **Days** choosing a problem
+- **Years** solving it
+
+This imbalance limits impact. These skills help invest more time choosing wisely.
+
+### Evaluation Axes
+**For Evaluating Ideas:**
+- **X-axis:** Likelihood of success
+- **Y-axis:** Impact if successful
+
+Skills help move ideas rightward (more feasible) and upward (more impactful).
+
+### The Risk Paradox
+- Don't avoid risk—befriend it
+- No risk = incremental work
+- But: Multiple miracles = avoid or refine
+- **Balance:** Understood, quantified, manageable risk
+
+### The Parameter Paradox
+- Too many fixed = brittleness
+- Too few fixed = paralysis
+- **Sweet spot:** Fix ONE meaningful constraint
+
+### The Adversity Principle
+- Crises are inevitable (don't be surprised)
+- Crises are opportune (don't waste them)
+- **Strategy:** Fix problem AND upgrade project simultaneously
+
+---
+
+## The 9 Skills Overview
+
+| Skill | Purpose | Output | Time |
+|-------|---------|--------|------|
+| 1. Intuition Pumps | Generate high-quality research ideas | Problem Ideation Document | ~1 week |
+| 2. Risk Assessment | Identify and manage project risks | Risk Assessment Matrix | 3-5 days |
+| 3. Optimization Function | Define success metrics | Impact Assessment Document | 2-3 days |
+| 4. Parameter Strategy | Decide what to fix vs. keep flexible | Parameter Strategy Document | 2-3 days |
+| 5. Decision Tree Navigation | Plan decision points and altitude dance | Decision Tree Map | 2 days |
+| 6. Adversity Response | Prepare for crises as opportunities | Adversity Playbook | 2 days |
+| 7. Problem Inversion | Navigate around obstacles | Problem Inversion Analysis | 1 day |
+| 8. Integration & Synthesis | Synthesize into coherent plan | Project Communication Package | 3-5 days |
+| 9. Meta-Framework | Orchestrate complete workflow | Complete Project Package | 1-6 weeks |
+
+---
+
+## Skill Workflow
+
+```
+SKILL 1: Intuition Pumps
+         | (generates idea)
+         v
+SKILL 2: Risk Assessment
+         | (evaluates feasibility)
+         v
+SKILL 3: Optimization Function
+         | (defines success metrics)
+         v
+SKILL 4: Parameter Strategy
+         | (determines flexibility)
+         v
+SKILL 5: Decision Tree
+         | (plans execution and evaluation)
+         v
+SKILL 6: Adversity Planning
+         | (prepares for failure modes)
+         v
+SKILL 7: Problem Inversion
+         | (provides pivot strategies)
+         v
+SKILL 8: Integration & Communication
+         | (synthesizes into coherent plan)
+         v
+SKILL 9: Meta-Skill
+         (orchestrates complete workflow)
+```
+
+---
+
+## Key Design Principles
+
+1. **Conversational Entry** - Meet users where they are with three clear starting points
+2. **Thoughtful Interaction** - Ask clarifying questions; low confidence prompts additional input
+3. **Literature Integration** - Use PubMed searches at strategic points for validation
+4. **Concrete Outputs** - Every skill produces tangible 1-2 page documents
+5. **Building Specificity** - Progressive detail emerges through targeted questions
+6. **Flexibility** - Skills work independently, sequentially, or iteratively
+7. **Scientific Rigor** - Claims about generality and feasibility should be evidence-based
+
+---
+
+## Who Should Use These Skills
+
+### Graduate Students (Primary Audience)
+- **When:** Choosing thesis projects, qualifying exams, committee meetings
+- **Focus:** Skills 1-3 (ideation, risk, impact) + Skill 9 (complete workflow)
+- **Timeline:** 2-4 weeks for comprehensive planning
+
+### Postdocs
+- **When:** Starting new position, planning independent projects, fellowship applications
+- **Focus:** All skills, emphasizing independence and risk management
+- **Timeline:** 1-2 weeks intensive planning
+
+### Principal Investigators
+- **When:** New lab, new direction, mentoring trainees, grant cycles
+- **Focus:** Skills 1, 3, 4, 6 (ideation, impact, parameters, adversity)
+- **Timeline:** Ongoing, integrate into lab culture
+
+### Startup Founders
+- **When:** Company inception, pivot decisions, investor pitches
+- **Focus:** Skills 1-4 (ideation through parameters) + Skill 8 (communication)
+- **Timeline:** 1-2 weeks for initial planning, revisit quarterly
+
+---
+
+## Reference Materials
+
+Detailed skill documentation is available in the `references/` folder:
+
+| File | Content | Search Patterns |
+|------|---------|-----------------|
+| `01-intuition-pumps.md` | Generate research ideas | `Intuition Pump #`, `Trap #`, `Phase [0-9]` |
+| `02-risk-assessment.md` | Risk identification | `Risk.*1-5`, `go/no-go`, `assumption` |
+| `03-optimization-function.md` | Success metrics | `Generality.*Learning`, `optimization`, `impact` |
+| `04-parameter-strategy.md` | Parameter fixation | `fixed.*float`, `constraint`, `parameter` |
+| `05-decision-tree.md` | Decision tree navigation | `altitude`, `Level [0-9]`, `decision` |
+| `06-adversity-planning.md` | Adversity response | `adversity`, `crisis`, `ensemble` |
+| `07-problem-inversion.md` | Problem inversion strategies | `Strategy [0-9]`, `inversion`, `goal` |
+| `08-integration-synthesis.md` | Integration and synthesis | `narrative`, `communication`, `story` |
+| `09-meta-framework.md` | Complete workflow | `Phase`, `workflow`, `orchestrat` |
+
+---
+
+## Expected Outcomes
+
+### Immediate (After Completing Workflow)
+- Clear project vision
+- Honest risk assessment
+- Contingency plans
+- Communication materials ready
+- Confidence in problem choice
+
+### 6-Month
+- Faster decisions (have framework)
+- Productive adversity handling
+- No existential crises (risks mitigated)
+
+### 2-Year
+- Published results or strong progress
+- Avoided dead-end projects
+- Career aligned with goals
+- **Time well-spent** (ultimate measure)
+
+---
+
+## Foundational Reference
+
+**Fischbach, M.A., & Walsh, C.T. (2024).** "Problem choice and decision trees in science and engineering." *Cell*, 187, 1828-1833.
+
+Based on course BIOE 395 taught at Stanford University.