Skip to content
Flagship · disease-agnostic

# The Therapeutic Program Architect

Give it any disease — common or genetic/rare — and it runs a full, human-in-the-loop drug-development program: from unmet need and patient priorities, through data- and literature-mined target and modality selection, AI/ML design and in-silico pressure-testing, to scientific, regulatory, and commercial strategy. It stops and asks you at every consequential decision.

How to install & use ↓ Repository →

### This is for any disease — not just EoE

The disease, target, and modality are all parameters resolved from data and your decisions, not hard-coded. The same modality router that produced a tolerizing vaccine for eosinophilic esophagitis produces a ligand-trap, antibody, or small molecule for another disease depending on the target biology. If your community has a disease and a question, this is built for you.

How it works

## Ten stages, threaded through one dossier

A single JSON program dossier is the source of truth for a whole run — disease, scope, every decision and who made it, per-stage artifacts, gate status, and open questions. A program can be paused, resumed, and audited.

1. Indication & unmet need Epidemiology, biology, standard of care, and precedent.
2. Patient priorities / PFDD What patients actually want fixed — with an optional community survey.
3. Literature + competitive pipeline Mechanism map plus who is developing what, and why they succeeded or failed.
4. Data mining → targets Omics meta-analysis and single-cell → ranked druggable targets.
5. Target & modality selection The pivotal fork: a scored rubric → you confirm.
6. Design & pressure-test Modality-routed AI/ML design plus in-silico validation.
7. Scientific development plan AI-to-first-in-human assay cascade, CMC, biomarkers.
8. Regulatory strategy FDA / EMA path, designations, endpoints.
9. Commercial & financing TAM/SAM/SOM, whitespace, financial model, and the Ask.
10. Deliverables & synthesis Business plan, scientific plan, deck, manuscript, peer review.

You stay in control

## Human-in-the-loop by design

The pipeline never silently commits a target, modality, endpoint, price, or go/no-go. It stops at named gates and asks a structured question with its recommendation and options.

Hard gates

### Block until you answer

- Scope lock
- Whitespace confirm
- Target / modality lock
- Design go / no-go
- Financing assumptions
- Final review

Soft gates

### It proposes; you can veto

- Priority rank
- Target evidence
- Regulatory assumptions
- Any low-confidence flag becomes a recorded open question — not a confident-sounding assertion

Evidence it generalizes

## Validated beyond EoE

Dry run

### IPF

Idiopathic pulmonary fibrosis. The modality router lands on a ligand-trap / antibody / small molecule path driven by the target biology — not the tolerizing vaccine EoE called for.

Dry run

### SMA (genetic)

Spinal muscular atrophy. Exercises the genetic/rare archetype branch — a monogenic, mechanism-driven program with a different modality decision tree.

Full build

### EoE

Eosinophilic esophagitis. The complete run behind Project Tolera — a personalized pMHC-II tolerance vaccine, end to end.

Get started

## How to install and use it

It comes in two pieces: drug-program-orchestration (the conductor skill) and the Therapeutic Program Architect (a specialist agent that preloads the skill and has full access to the skill catalog and all data/regulatory connectors).

1. Get the repository Clone or download from GitHub:

       git clone https://github.com/ruthannepai-tech/therapeutic-program-architect.git

2. Add it to Claude Science Drop the skill folder into your skills directory, or publish it via the skill SDK. The specialist profile registers the orchestration skill and its connectors.
3. Switch to the specialist In the Claude Science session-config popover, choose the Therapeutic Program Architect specialist (or accept the switch prompt).
4. Run a program Say it in one line:

       Run the drug program for <your disease>.

   The orchestrator initializes a dossier and walks the ten stages, stopping at each gate.

### No specialist switch? Any agent can run it

    Load the drug-program-orchestration skill
    and run the pipeline for <your disease>.

### Requirements & caveats

The design stage (Stage 6) benefits from a GPU compute target — the orchestrator checks for one and runs the CPU-feasible parts or defers design if none is configured. Connector calls (ClinicalTrials.gov, Open Targets, FDA, GEO/PRIDE, ChEMBL) run automatically inside the specialist. All forward-looking scientific, regulatory, and commercial statements are development hypotheses — not established results, medical advice, or guaranteed outcomes.

Open the repository → All repositories