0A.3: Stage 1 Science Research and Basic Project Infrastructure

[LanYang430]

Sprint: 0A (Jan 20-26)
Story Points: 5
Labels: science, research, sprint-0A

Description

Research and identify methods for CG model quality assessment (prepare for Stage 1 development).
Add essential project files for open source best practices.

Tasks

• Literature review: CG model validation methods
  • Sampling coverage metrics (RMSD distributions, PCA)
  • Convergence analysis (block averaging, autocorrelation)
  • Dynamics validation (timescales, contact maps)
• Review existing tools: PyEmma, MDTraj, MDAnalysis capabilities
• Document candidate metrics in docs/stage1_research_notes.md
• Identify 2-3 CG force fields for testing (e.g., MARTINI, SIRAH)
• Draft Stage 1 API design (input/output format)
• Update .gitignore (Python, Jupyter, IDEs)
• Create CONTRIBUTING.md with development workflow
• Add CODE_OF_CONDUCT.md (Contributor Covenant)
• Create issue templates:
  • Bug report
  • Feature request
  • Question
• Update README with fellowship acknowledgment

Acceptance Criteria

• Research notes document created
• At least 5 papers reviewed
• List of metrics to implement (ranked by priority)
• API design sketch ready for mentor review

Estimated Time

3-4 days