Spaces:
Sleeping
Sleeping
File size: 4,842 Bytes
e589553 81d9b6a 2f85a76 81d9b6a e589553 81d9b6a |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 |
# app.py
import os
import gradio as gr
from genesis.pipeline import (
run_literature_review,
run_molecule_lookup,
run_pathway_analysis,
run_funding_analysis,
run_image_analysis
)
from genesis.visualization import generate_pathway_graph, generate_funding_network
from genesis.utils.pdf_export import export_to_pdf
# Load custom CSS
with open("genesis/static/style.css", "r") as f:
custom_css = f.read()
# App Title
APP_TITLE = "🧬 GENESIS-AI — The Synthetic Biology OS"
APP_DESCRIPTION = """
Your **multi-modal synthetic biology intelligence suite**.
Explore molecules, pathways, funding, literature, and images — with real-time AI insights.
"""
# =========================
# TAB FUNCTIONS
# =========================
def literature_tab(query):
"""Run literature review (PubMed, ChEMBL, BioPortal, UMLS)"""
summary, citations = run_literature_review(query)
pdf_path = export_to_pdf(summary, citations, filename="literature_report.pdf")
return summary, citations, pdf_path
def molecule_tab(molecule_name):
"""Fetch molecule data from ChEMBL/NCBI & visualize"""
mol_data, mol_img = run_molecule_lookup(molecule_name)
pdf_path = export_to_pdf(mol_data, None, filename="molecule_report.pdf")
return mol_data, mol_img, pdf_path
def pathway_tab(pathway_name):
"""Run pathway analysis & generate graph"""
analysis = run_pathway_analysis(pathway_name)
graph_fig = generate_pathway_graph(pathway_name)
pdf_path = export_to_pdf(analysis, None, filename="pathway_report.pdf")
return analysis, graph_fig, pdf_path
def funding_tab(keyword):
"""Run funding analysis & generate investor graph"""
funding_info = run_funding_analysis(keyword)
funding_graph = generate_funding_network(keyword)
pdf_path = export_to_pdf(funding_info, None, filename="funding_report.pdf")
return funding_info, funding_graph, pdf_path
def image_tab(image_file):
"""Run microscopy/image analysis"""
analysis_text = run_image_analysis(image_file)
pdf_path = export_to_pdf(analysis_text, None, filename="image_report.pdf")
return analysis_text, pdf_path
# =========================
# GRADIO UI
# =========================
with gr.Blocks(css=custom_css, theme="default") as demo:
gr.HTML(f"<h1>{APP_TITLE}</h1><p>{APP_DESCRIPTION}</p>")
with gr.Tabs():
# Literature Tab
with gr.Tab("📚 Literature Review"):
lit_query = gr.Textbox(label="Enter research question")
lit_summary = gr.Textbox(label="Summary", lines=8)
lit_citations = gr.Textbox(label="Citations", lines=5)
lit_pdf = gr.File(label="Download PDF")
lit_btn = gr.Button("Run Literature Review", variant="primary")
lit_btn.click(literature_tab, inputs=lit_query, outputs=[lit_summary, lit_citations, lit_pdf])
# Molecule Lookup
with gr.Tab("🧪 Molecule Viewer"):
mol_name = gr.Textbox(label="Enter molecule name / ChEMBL ID")
mol_info = gr.Textbox(label="Molecule Information", lines=8)
mol_img = gr.Image(label="Structure")
mol_pdf = gr.File(label="Download PDF")
mol_btn = gr.Button("Lookup Molecule", variant="primary")
mol_btn.click(molecule_tab, inputs=mol_name, outputs=[mol_info, mol_img, mol_pdf])
# Pathway Analysis
with gr.Tab("🔬 Pathway Analysis"):
path_name = gr.Textbox(label="Enter pathway name")
path_analysis = gr.Textbox(label="Pathway Analysis", lines=8)
path_graph = gr.Plot(label="Pathway Graph")
path_pdf = gr.File(label="Download PDF")
path_btn = gr.Button("Analyze Pathway", variant="primary")
path_btn.click(pathway_tab, inputs=path_name, outputs=[path_analysis, path_graph, path_pdf])
# Funding Network
with gr.Tab("💰 Funding Explorer"):
fund_keyword = gr.Textbox(label="Enter biotech keyword")
fund_info = gr.Textbox(label="Funding Information", lines=8)
fund_graph = gr.Plot(label="Funding Network")
fund_pdf = gr.File(label="Download PDF")
fund_btn = gr.Button("Analyze Funding", variant="primary")
fund_btn.click(funding_tab, inputs=fund_keyword, outputs=[fund_info, fund_graph, fund_pdf])
# Image Analysis
with gr.Tab("🖼️ Image Analysis"):
img_upload = gr.Image(type="filepath", label="Upload microscopy or bio-image")
img_analysis = gr.Textbox(label="Image Analysis", lines=8)
img_pdf = gr.File(label="Download PDF")
img_btn = gr.Button("Analyze Image", variant="primary")
img_btn.click(image_tab, inputs=img_upload, outputs=[img_analysis, img_pdf])
demo.queue().launch(server_name="0.0.0.0", server_port=7860)
|