Upload 5 files

.env.example

@@ -0,0 +1,20 @@
+OPENAI_API_KEY=
+UMLS_API_KEY=
+NCBI_API_KEY=
+NCBI_EMAIL=
+BIOPORTAL_API_KEY=
+HF_TOKEN=
+GEMINI_API_KEY=
+ELEVEN_LABS_API_KEY=
+NEO4J_URI=bolt://neo4j:7687
+NEO4J_USER=neo4j
+NEO4J_PASSWORD=
+
+GENESIS_DISABLE_TRACING=1
+GENESIS_DEEP_MODEL=o3-deep-research
+GENESIS_DEEP_FAST_MODEL=o4-mini-deep-research
+GENESIS_INSTRUCTION_MODEL=gpt-4o-mini
+GENESIS_TRIAGE_MODEL=gpt-4o-mini
+GENESIS_CLARIFY_MODEL=gpt-4o-mini
+GENESIS_SAFETY_MODEL=gpt-4o-mini
+GENESIS_MCP_URL=

README.md

@@ -1,12 +1,23 @@
----
-title: SCEINCE
-emoji: 📊
-colorFrom: green
-colorTo: red
-sdk: gradio
-sdk_version: 5.42.0
-app_file: app.py
-pinned: false
----
-
-Check out the configuration reference at https://huggingface.co/docs/hub/spaces-config-reference
+# GENESIS-AI — Synthetic Biology Deep Research (Hugging Face Space)
+
+A production-grade, safety-first **agentic research Space** for high-level literature synthesis in synthetic biology.
+Integrates **OpenAI Deep Research + Agents SDK**, optional **Gemini**/**DeepSeek-compatible** models for summaries,
+and domain tools (UMLS/BioPortal/NCBI/PDBe). **No wet‑lab/operational protocols** are generated.
+
+## Deploy on Spaces
+1) Create a new Space (SDK: Gradio).  
+2) Upload this zip.  
+3) Add secrets in Space settings matching `.env.example`.  
+4) Run — open the Research tab.
+
+## Local Dev
+```
+python -m venv .venv && source .venv/bin/activate
+pip install -r requirements.txt
+cp .env.example .env  # fill values
+python app.py
+```
+
+## Safety
+- The app refuses to output step-by-step lab instructions or growth conditions.
+- Use this for **high-level literature review, synthesis, citations, and knowledge graphs** only.

README.space.yaml

@@ -0,0 +1,8 @@
+title: GENESIS-AI — Synthetic Biology Deep Research (Safety-First)
+emoji: 🧬
+colorFrom: teal
+colorTo: blue
+sdk: gradio
+sdk_version: 4.44.0
+python_version: 3.10
+license: apache-2.0

app.py

@@ -0,0 +1,40 @@
+
+from __future__ import annotations
+import os, asyncio, json
+import gradio as gr
+from dotenv import load_dotenv
+
+load_dotenv()
+
+from genesis.pipeline import research_once
+
+APP_TITLE = "GENESIS-AI — Synthetic Biology Deep Research (Safety-First)"
+APP_DESC = "High-level synthetic biology literature synthesis with citations. This app **never** produces operational protocols."
+
+async def run_research(query: str, fast: bool):
+    out = await research_once(query, fast=fast)
+    final_text = out.get("final_output") or "_No output_"
+    cites = out.get("citations", [])
+    cites_md = "\n".join([f"- [{c.get('title','link')}]({c.get('url','')})" for c in cites]) or "_None detected_"
+    return final_text, cites_md, json.dumps(out, indent=2)
+
+with gr.Blocks(theme=gr.themes.Soft(), fill_height=True) as demo:
+    gr.Markdown(f"# {APP_TITLE}")
+    gr.Markdown(APP_DESC)
+
+    query = gr.Textbox(label="Your high-level research request", lines=4, placeholder="e.g., High-level synthesis of CRISPR base-editing trends in oncology (last 2 years).")
+    fast = gr.Checkbox(label="Fast mode (o4-mini-deep-research)", value=False)
+    go = gr.Button("Run Deep Research", variant="primary")
+
+    with gr.Tabs():
+        with gr.Tab("Research Report"):
+            report = gr.Markdown()
+        with gr.Tab("Citations"):
+            citations = gr.Markdown()
+        with gr.Tab("JSON Export"):
+            json_out = gr.Code(language="json")
+
+    go.click(fn=run_research, inputs=[query, fast], outputs=[report, citations, json_out])
+
+if __name__ == "__main__":
+    demo.launch()

requirements.txt

@@ -0,0 +1,12 @@
+openai>=1.88
+openai-agents>=0.0.19
+gradio>=4.44.0
+httpx>=0.27.0
+pydantic>=2.7.0
+python-dotenv>=1.0.1
+neo4j>=5.25.0
+rich>=13.7.1
+pandas>=2.2.2
+networkx>=3.3
+pyvis>=0.3.2
+google-generativeai>=0.7.2