# Cope Labs Medicine
## End-to-End Reference Spec (Rough Draft v0.1)

Status: Rough draft for inspection and alignment.
Last updated: 2026-04-12

## Purpose
This document shows one full example of:
1. What a client submits at project start.
2. What Cope Labs returns at delivery.

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## Part A - Example Client Submittal

### 1) Intake Summary
- Project code: EX-TB-001
- Team type: Small biotech preclinical team
- Primary objective: Identify a short list of TB compounds for review.
- Requested timeline: 7 calendar days

### 2) Required Fields
- Target identifier (example: InhA_mtb)
- Desired output type (screening only, or screening + FTO, etc.)
- Hard constraints (budget, compute cap, jurisdiction, safety filters)
- Review deadline and primary decision date
- Preferred communication channel for clarifications

### 3) Input Materials Submitted
- Target note (1-2 pages)
- Known compounds or seed list (CSV)
- Optional structure references (PDB IDs, if available)
- Internal constraints note (allowed chemotypes, excluded classes)

### 4) Scope Lock Checklist
- [x] Deliverable name agreed
- [x] Delivery date agreed
- [x] Inclusion/exclusion constraints documented
- [x] Optional add-on lanes confirmed (FTO, clinical evidence)

### 5) Example Submittal Payload (Plain Text)
Project: EX-TB-001
Target: InhA_mtb
Deliverable Requested: Contract Screening Deliverable + Optional FTO Rapid Risk Report
Decision Date: 2026-04-20
Constraints:
- Keep MW under 500 where possible
- Flag known high-risk patent zones in US/EU
- Include caveats explicitly

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## Part B - Example Return Package

### 1) Delivery Summary (What Client Gets)
- One packaged folder with versioned outputs
- One short executive summary for non-technical reviewers
- One detailed artifact manifest for technical review

### 2) Example Package Layout
run_id: 20260412_cope_example_tb_inha

files:
- executive_summary.md
  purpose: Plain-language summary of what was run and what to do next.

- ranked_candidates_top50.csv
  purpose: Main ranked output table for decision review.

- findings_brief.md
  purpose: Key observations, likely signals, and practical caveats.

- run_config_snapshot.yaml
  purpose: Frozen settings used for reproducibility.

- provenance_manifest.json
  purpose: Source references, timestamps, and ownership metadata.

- optional_fto_risk_report.md
  purpose: Preliminary patent-risk view with cited records.

### 3) Example Return Summary (Client-Facing)
- Shortlist generated: 50 compounds
- Recommended immediate review set: Top 10
- Optional FTO layer: Included
- Main caveat: Computational ranking is decision support; wet-lab confirmation still required.

### 4) Review Questions Included In Return
- Which top candidates match current assay feasibility?
- Which candidates are blocked by internal exclusions?
- Which candidates require legal review due to patent-risk flags?

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## Part C - Inspection And Acceptance

### 1) Minimum Acceptance Checks
- Every output file is present and named in the manifest.
- Run settings are frozen and attached.
- Caveats are explicit and easy to find.
- Output can be reviewed by both technical and non-technical stakeholders.

### 2) Pass / Fail Standard
Pass:
- Package is understandable, traceable, and decision-ready.

Fail:
- Missing files, hidden assumptions, or no clear reproducibility path.

### 3) Known Limits
- This package does not replace legal, medical, or regulatory sign-off.
- This package is a prioritization tool, not a final clinical claim.

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## Revision Note
This is a rough draft reference specimen intended to make the process inspectable.
Final commercial templates can be tightened after review feedback.