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Update app.py
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app.py
CHANGED
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@@ -1,6 +1,6 @@
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"""
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DNA-Diffusion Gradio Application
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"""
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import gradio as gr
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@@ -33,7 +33,7 @@ except ImportError:
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return func
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return decorator
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#
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CODON_TABLE = {
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'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L',
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'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S',
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@@ -53,28 +53,21 @@ CODON_TABLE = {
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'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G'
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}
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# Mock DNA model for demonstration
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class DNAModel:
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"""Mock DNA generation model"""
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def generate(self, cell_type: str, num_sequences: int = 1, length: int = 200, guidance_scale: float = 1.0):
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"""Generate DNA sequences with cell-type specific patterns"""
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sequences = []
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for _ in range(num_sequences):
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# Base generation
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sequence = ''.join(random.choice(['A', 'T', 'C', 'G']) for _ in range(length))
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# Add cell-type specific patterns
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if cell_type == "K562":
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# Add GC-rich regions for K562
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for i in range(0, length-8, 50):
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sequence = sequence[:i] + 'GCGCGCGC' + sequence[i+8:]
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elif cell_type == "GM12878":
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# Add AT-rich regions for GM12878
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for i in range(10, length-8, 60):
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sequence = sequence[:i] + 'ATATATAT' + sequence[i+8:]
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elif cell_type == "HepG2":
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# Add mixed patterns for HepG2
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for i in range(20, length-12, 70):
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sequence = sequence[:i] + 'GCGATCGATCGC' + sequence[i+12:]
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return sequences[0] if num_sequences == 1 else sequences
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# Initialize model
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model = DNAModel()
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# Main application class
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class DNADiffusionApp:
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"""Main application with GPU-accelerated functions"""
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def __init__(self):
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self.current_sequence = ""
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self.current_analysis = {}
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@spaces.GPU(duration=60)
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def generate_with_gpu(self, cell_type: str, guidance_scale: float = 1.0, use_enhanced: bool = True):
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"""GPU-accelerated sequence generation"""
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logger.info(f"Generating sequence on GPU for cell type: {cell_type}")
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try:
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time.sleep(2) # Simulated GPU processing
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# Generate sequence
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sequence = model.generate(cell_type, length=200, guidance_scale=guidance_scale)
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# If enhanced mode, do additional processing
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if use_enhanced:
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sequence = self.enhance_sequence(sequence, cell_type)
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raise
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def enhance_sequence(self, sequence: str, cell_type: str) -> str:
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"""Enhance sequence with additional patterns"""
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# Add enhancer sequences based on cell type
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enhancers = {
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"K562": "GGGACTTTCC",
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"GM12878": "TGACGTCA",
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"HepG2": "TGTTGGTGG"
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}
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if cell_type in enhancers:
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# Insert enhancer at a reasonable position
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pos = len(sequence) // 4
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enhancer = enhancers[cell_type]
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sequence = sequence[:pos] + enhancer + sequence[pos+len(enhancer):]
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return sequence
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def analyze_sequence(self, sequence: str) -> Dict[str, Any]:
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"""Analyze DNA sequence properties"""
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if not sequence:
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return {}
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# GC content
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gc_count = sequence.count('G') + sequence.count('C')
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gc_content = (gc_count / len(sequence)) * 100
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# Melting temperature
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if len(sequence) < 14:
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tm = 4 * (sequence.count('G') + sequence.count('C')) + 2 * (sequence.count('A') + sequence.count('T'))
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else:
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tm = 81.5 + 0.41 * gc_content - 675 / len(sequence)
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# Find restriction sites
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restriction_sites = {}
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enzymes = {
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'EcoRI': 'GAATTC',
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if positions:
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restriction_sites[enzyme] = positions
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# Translate to protein
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protein = self.translate_to_protein(sequence)
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return {
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}
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def translate_to_protein(self, dna_sequence: str) -> str:
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"""Translate DNA to protein sequence"""
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protein = []
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# Find start codon
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start_pos = dna_sequence.find('ATG')
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if start_pos == -1:
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start_pos = 0
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# Translate from start position
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for i in range(start_pos, len(dna_sequence) - 2, 3):
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codon = dna_sequence[i:i+3]
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if len(codon) == 3:
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amino_acid = CODON_TABLE.get(codon, 'X')
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if amino_acid == '*':
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break
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protein.append(amino_acid)
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return ''.join(protein)
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'cell_type': cell_type,
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'sequence': sequence,
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'analysis': analysis
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})
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-
# Create the Gradio interface
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def create_demo():
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"""Create the Gradio interface"""
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# Custom CSS
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css = """
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.gradio-container {
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font-family: 'Arial', sans-serif;
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padding: 10px;
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border-radius: 5px;
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}
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"""
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with gr.Blocks(css=css, title="DNA-Diffusion") as demo:
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# Header
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gr.Markdown(
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"""
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# 🧬 DNA-Diffusion: AI-Powered Sequence Generation
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Generate cell-type specific DNA sequences
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This app uses GPU acceleration for optimal performance.
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"""
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)
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# GPU status indicator
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gpu_status = gr.Markdown(
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f"🖥️ **GPU Status**: {'✅ Available' if SPACES_AVAILABLE else '❌ Not Available (CPU mode)'}"
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)
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with gr.Tabs():
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# Tab 1:
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with gr.TabItem("🎯
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with gr.Row():
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with gr.Column(scale=1):
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cell_type = gr.Dropdown(
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analysis_output = gr.JSON(
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label="Sequence Analysis"
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)
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-
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# Examples
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gr.Examples(
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examples=[
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["K562", 1.0, True],
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["GM12878", 5.0, True],
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["HepG2", 3.0, False]
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],
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inputs=[cell_type, guidance_scale, enhanced_mode]
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)
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# Tab 2:
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with gr.TabItem("📦 Batch Generation"):
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with gr.Row():
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with gr.Column():
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headers=["ID", "Cell Type", "Length", "GC%", "Tm(°C)"],
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label="Batch Results"
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)
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download_btn = gr.Button("💾 Download Results")
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# Tab 3: Analysis Tools
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with gr.TabItem("🔬 Analysis Tools"):
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gr.Markdown("### Paste or generate a sequence to analyze")
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analysis_input = gr.Textbox(
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label="DNA Sequence",
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placeholder="Paste your DNA sequence here...",
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lines=3
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)
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analyze_btn = gr.Button("🔍 Analyze")
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with gr.Row():
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gc_plot = gr.Plot(label="GC Content Distribution")
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restriction_plot = gr.Plot(label="Restriction Sites")
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detailed_analysis = gr.JSON(label="Detailed Analysis")
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# Status bar
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status_text = gr.Textbox(
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label="Status",
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value="Ready to generate sequences...",
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# Event handlers
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def generate_single(cell_type, guidance_scale, enhanced):
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"""Handle single sequence generation"""
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try:
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status_text.value = "🔄 Generating sequence on GPU..."
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# Generate sequence using GPU
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sequence = app.generate_with_gpu(cell_type, guidance_scale, enhanced)
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# Analyze the sequence
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analysis = app.analyze_sequence(sequence)
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status_text.value = f"✅ Successfully generated sequence for {cell_type}"
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logger.error(error_msg)
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return "", {}, error_msg
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def generate_batch(cell_types, count):
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"""Handle batch generation"""
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if not cell_types:
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return None, "❌ Please select at least one cell type"
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try:
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status_text.value = "🔄 Generating batch on GPU..."
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])
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status_text.value = f"✅ Generated {len(results)} sequences"
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return
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except Exception as e:
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error_msg = f"❌ Error: {str(e)}"
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logger.error(error_msg)
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return None, error_msg
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-
def analyze_sequence(sequence):
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"""Analyze a given sequence"""
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if not sequence:
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return None, None, {}
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-
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analysis = app.analyze_sequence(sequence.upper())
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# Create GC content plot
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import matplotlib.pyplot as plt
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-
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| 431 |
-
fig1, ax1 = plt.subplots(figsize=(6, 4))
|
| 432 |
-
gc = analysis['gc_content']
|
| 433 |
-
at = 100 - gc
|
| 434 |
-
ax1.bar(['GC%', 'AT%'], [gc, at], color=['#4CAF50', '#2196F3'])
|
| 435 |
-
ax1.set_ylabel('Percentage')
|
| 436 |
-
ax1.set_title('Nucleotide Composition')
|
| 437 |
-
|
| 438 |
-
# Create restriction site plot
|
| 439 |
-
fig2, ax2 = plt.subplots(figsize=(8, 3))
|
| 440 |
-
if analysis['restriction_sites']:
|
| 441 |
-
y_pos = 0
|
| 442 |
-
colors = plt.cm.tab10(range(len(analysis['restriction_sites'])))
|
| 443 |
-
|
| 444 |
-
for (enzyme, positions), color in zip(analysis['restriction_sites'].items(), colors):
|
| 445 |
-
for pos in positions:
|
| 446 |
-
ax2.vlines(pos, y_pos - 0.4, y_pos + 0.4, color=color, linewidth=3)
|
| 447 |
-
ax2.text(-10, y_pos, enzyme, ha='right', va='center')
|
| 448 |
-
y_pos += 1
|
| 449 |
-
|
| 450 |
-
ax2.set_xlim(-50, len(sequence))
|
| 451 |
-
ax2.set_ylim(-0.5, len(analysis['restriction_sites']) - 0.5)
|
| 452 |
-
ax2.set_xlabel('Position (bp)')
|
| 453 |
-
ax2.set_title('Restriction Enzyme Sites')
|
| 454 |
-
ax2.grid(axis='x', alpha=0.3)
|
| 455 |
-
else:
|
| 456 |
-
ax2.text(0.5, 0.5, 'No restriction sites found',
|
| 457 |
-
ha='center', va='center', transform=ax2.transAxes)
|
| 458 |
-
|
| 459 |
-
return fig1, fig2, analysis
|
| 460 |
-
|
| 461 |
# Connect event handlers
|
| 462 |
generate_btn.click(
|
| 463 |
fn=generate_single,
|
|
@@ -465,50 +657,44 @@ def create_demo():
|
|
| 465 |
outputs=[sequence_output, analysis_output, status_text]
|
| 466 |
)
|
| 467 |
|
| 468 |
-
|
| 469 |
-
fn=
|
| 470 |
-
inputs=[
|
| 471 |
-
outputs=[
|
| 472 |
-
)
|
| 473 |
-
|
| 474 |
-
analyze_btn.click(
|
| 475 |
-
fn=analyze_sequence,
|
| 476 |
-
inputs=[analysis_input],
|
| 477 |
-
outputs=[gc_plot, restriction_plot, detailed_analysis]
|
| 478 |
)
|
| 479 |
|
| 480 |
-
# Auto-
|
| 481 |
sequence_output.change(
|
| 482 |
-
fn=
|
| 483 |
inputs=[sequence_output],
|
| 484 |
-
outputs=[
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 485 |
)
|
| 486 |
|
| 487 |
return demo
|
| 488 |
|
| 489 |
-
# Main launch function
|
| 490 |
if __name__ == "__main__":
|
| 491 |
-
# Print startup info
|
| 492 |
logger.info("=" * 50)
|
| 493 |
-
logger.info("DNA-Diffusion App Starting...")
|
| 494 |
logger.info(f"GPU Available: {SPACES_AVAILABLE}")
|
| 495 |
logger.info(f"Environment: {'Hugging Face Spaces' if os.getenv('SPACE_ID') else 'Local'}")
|
| 496 |
logger.info("=" * 50)
|
| 497 |
|
| 498 |
-
# Create and launch the demo
|
| 499 |
demo = create_demo()
|
| 500 |
|
| 501 |
-
# Launch with appropriate settings
|
| 502 |
if os.getenv("SPACE_ID"):
|
| 503 |
-
# Running on Hugging Face Spaces
|
| 504 |
demo.launch(
|
| 505 |
server_name="0.0.0.0",
|
| 506 |
server_port=7860,
|
| 507 |
-
share=False,
|
| 508 |
show_error=True
|
| 509 |
)
|
| 510 |
else:
|
| 511 |
-
# Local development
|
| 512 |
demo.launch(
|
| 513 |
share=True,
|
| 514 |
show_error=True,
|
|
|
|
| 1 |
"""
|
| 2 |
+
DNA-Diffusion Gradio Application with Integrated 3D Viewer
|
| 3 |
+
Combines Gradio interface with HTML-based 3D molecular visualization
|
| 4 |
"""
|
| 5 |
|
| 6 |
import gradio as gr
|
|
|
|
| 33 |
return func
|
| 34 |
return decorator
|
| 35 |
|
| 36 |
+
# DNA Model and genetic code table (same as before)
|
| 37 |
CODON_TABLE = {
|
| 38 |
'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L',
|
| 39 |
'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S',
|
|
|
|
| 53 |
'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G'
|
| 54 |
}
|
| 55 |
|
|
|
|
| 56 |
class DNAModel:
|
| 57 |
"""Mock DNA generation model"""
|
| 58 |
def generate(self, cell_type: str, num_sequences: int = 1, length: int = 200, guidance_scale: float = 1.0):
|
|
|
|
| 59 |
sequences = []
|
| 60 |
|
| 61 |
for _ in range(num_sequences):
|
|
|
|
| 62 |
sequence = ''.join(random.choice(['A', 'T', 'C', 'G']) for _ in range(length))
|
| 63 |
|
|
|
|
| 64 |
if cell_type == "K562":
|
|
|
|
| 65 |
for i in range(0, length-8, 50):
|
| 66 |
sequence = sequence[:i] + 'GCGCGCGC' + sequence[i+8:]
|
| 67 |
elif cell_type == "GM12878":
|
|
|
|
| 68 |
for i in range(10, length-8, 60):
|
| 69 |
sequence = sequence[:i] + 'ATATATAT' + sequence[i+8:]
|
| 70 |
elif cell_type == "HepG2":
|
|
|
|
| 71 |
for i in range(20, length-12, 70):
|
| 72 |
sequence = sequence[:i] + 'GCGATCGATCGC' + sequence[i+12:]
|
| 73 |
|
|
|
|
| 75 |
|
| 76 |
return sequences[0] if num_sequences == 1 else sequences
|
| 77 |
|
|
|
|
| 78 |
model = DNAModel()
|
| 79 |
|
|
|
|
| 80 |
class DNADiffusionApp:
|
|
|
|
|
|
|
| 81 |
def __init__(self):
|
| 82 |
self.current_sequence = ""
|
| 83 |
self.current_analysis = {}
|
|
|
|
| 85 |
|
| 86 |
@spaces.GPU(duration=60)
|
| 87 |
def generate_with_gpu(self, cell_type: str, guidance_scale: float = 1.0, use_enhanced: bool = True):
|
|
|
|
| 88 |
logger.info(f"Generating sequence on GPU for cell type: {cell_type}")
|
| 89 |
|
| 90 |
try:
|
| 91 |
+
time.sleep(2)
|
|
|
|
|
|
|
|
|
|
| 92 |
sequence = model.generate(cell_type, length=200, guidance_scale=guidance_scale)
|
| 93 |
|
|
|
|
| 94 |
if use_enhanced:
|
| 95 |
sequence = self.enhance_sequence(sequence, cell_type)
|
| 96 |
|
|
|
|
| 104 |
raise
|
| 105 |
|
| 106 |
def enhance_sequence(self, sequence: str, cell_type: str) -> str:
|
|
|
|
|
|
|
| 107 |
enhancers = {
|
| 108 |
+
"K562": "GGGACTTTCC",
|
| 109 |
+
"GM12878": "TGACGTCA",
|
| 110 |
+
"HepG2": "TGTTGGTGG"
|
| 111 |
}
|
| 112 |
|
| 113 |
if cell_type in enhancers:
|
|
|
|
| 114 |
pos = len(sequence) // 4
|
| 115 |
enhancer = enhancers[cell_type]
|
| 116 |
sequence = sequence[:pos] + enhancer + sequence[pos+len(enhancer):]
|
|
|
|
| 118 |
return sequence
|
| 119 |
|
| 120 |
def analyze_sequence(self, sequence: str) -> Dict[str, Any]:
|
|
|
|
| 121 |
if not sequence:
|
| 122 |
return {}
|
| 123 |
|
|
|
|
| 124 |
gc_count = sequence.count('G') + sequence.count('C')
|
| 125 |
gc_content = (gc_count / len(sequence)) * 100
|
| 126 |
|
|
|
|
| 127 |
if len(sequence) < 14:
|
| 128 |
tm = 4 * (sequence.count('G') + sequence.count('C')) + 2 * (sequence.count('A') + sequence.count('T'))
|
| 129 |
else:
|
| 130 |
tm = 81.5 + 0.41 * gc_content - 675 / len(sequence)
|
| 131 |
|
|
|
|
| 132 |
restriction_sites = {}
|
| 133 |
enzymes = {
|
| 134 |
'EcoRI': 'GAATTC',
|
|
|
|
| 146 |
if positions:
|
| 147 |
restriction_sites[enzyme] = positions
|
| 148 |
|
|
|
|
| 149 |
protein = self.translate_to_protein(sequence)
|
| 150 |
|
| 151 |
return {
|
|
|
|
| 158 |
}
|
| 159 |
|
| 160 |
def translate_to_protein(self, dna_sequence: str) -> str:
|
|
|
|
| 161 |
protein = []
|
| 162 |
|
|
|
|
| 163 |
start_pos = dna_sequence.find('ATG')
|
| 164 |
if start_pos == -1:
|
| 165 |
start_pos = 0
|
| 166 |
|
|
|
|
| 167 |
for i in range(start_pos, len(dna_sequence) - 2, 3):
|
| 168 |
codon = dna_sequence[i:i+3]
|
| 169 |
if len(codon) == 3:
|
| 170 |
amino_acid = CODON_TABLE.get(codon, 'X')
|
| 171 |
+
if amino_acid == '*':
|
| 172 |
break
|
| 173 |
protein.append(amino_acid)
|
| 174 |
|
| 175 |
return ''.join(protein)
|
| 176 |
+
|
| 177 |
+
app = DNADiffusionApp()
|
| 178 |
+
|
| 179 |
+
# HTML for 3D Viewer
|
| 180 |
+
HTML_3D_VIEWER = """
|
| 181 |
+
<!DOCTYPE html>
|
| 182 |
+
<html>
|
| 183 |
+
<head>
|
| 184 |
+
<meta charset="UTF-8">
|
| 185 |
+
<style>
|
| 186 |
+
body {
|
| 187 |
+
margin: 0;
|
| 188 |
+
padding: 0;
|
| 189 |
+
background: #000;
|
| 190 |
+
font-family: Arial, sans-serif;
|
| 191 |
+
color: #fff;
|
| 192 |
+
height: 100vh;
|
| 193 |
+
overflow: hidden;
|
| 194 |
+
}
|
| 195 |
+
#viewer-container {
|
| 196 |
+
width: 100%;
|
| 197 |
+
height: 100%;
|
| 198 |
+
position: relative;
|
| 199 |
+
}
|
| 200 |
+
#canvas3d {
|
| 201 |
+
width: 100%;
|
| 202 |
+
height: 100%;
|
| 203 |
+
}
|
| 204 |
+
.controls-panel {
|
| 205 |
+
position: absolute;
|
| 206 |
+
top: 20px;
|
| 207 |
+
right: 20px;
|
| 208 |
+
background: rgba(0,0,0,0.8);
|
| 209 |
+
padding: 20px;
|
| 210 |
+
border-radius: 10px;
|
| 211 |
+
border: 2px solid #00ff88;
|
| 212 |
+
max-width: 300px;
|
| 213 |
+
}
|
| 214 |
+
.controls-panel h3 {
|
| 215 |
+
color: #00ff88;
|
| 216 |
+
margin-top: 0;
|
| 217 |
+
}
|
| 218 |
+
.control-btn {
|
| 219 |
+
background: #00ff88;
|
| 220 |
+
color: #000;
|
| 221 |
+
border: none;
|
| 222 |
+
padding: 8px 16px;
|
| 223 |
+
margin: 5px;
|
| 224 |
+
border-radius: 5px;
|
| 225 |
+
cursor: pointer;
|
| 226 |
+
font-weight: bold;
|
| 227 |
+
}
|
| 228 |
+
.control-btn:hover {
|
| 229 |
+
background: #00cc66;
|
| 230 |
+
}
|
| 231 |
+
.info-display {
|
| 232 |
+
position: absolute;
|
| 233 |
+
bottom: 20px;
|
| 234 |
+
left: 20px;
|
| 235 |
+
background: rgba(0,0,0,0.8);
|
| 236 |
+
padding: 15px;
|
| 237 |
+
border-radius: 8px;
|
| 238 |
+
border: 1px solid #0088ff;
|
| 239 |
+
}
|
| 240 |
+
#sequence-display {
|
| 241 |
+
font-family: monospace;
|
| 242 |
+
color: #00ff88;
|
| 243 |
+
word-break: break-all;
|
| 244 |
+
margin-top: 10px;
|
| 245 |
+
}
|
| 246 |
+
</style>
|
| 247 |
+
</head>
|
| 248 |
+
<body>
|
| 249 |
+
<div id="viewer-container">
|
| 250 |
+
<canvas id="canvas3d"></canvas>
|
| 251 |
|
| 252 |
+
<div class="controls-panel">
|
| 253 |
+
<h3>3D View Controls</h3>
|
| 254 |
+
<button class="control-btn" onclick="setViewMode('cartoon')">Cartoon</button>
|
| 255 |
+
<button class="control-btn" onclick="setViewMode('stick')">Stick</button>
|
| 256 |
+
<button class="control-btn" onclick="setViewMode('sphere')">Sphere</button>
|
| 257 |
+
<button class="control-btn" onclick="toggleRotation()">Toggle Rotation</button>
|
| 258 |
+
<button class="control-btn" onclick="resetView()">Reset View</button>
|
| 259 |
+
</div>
|
|
|
|
|
|
|
|
|
|
|
|
|
| 260 |
|
| 261 |
+
<div class="info-display">
|
| 262 |
+
<strong>Current Sequence:</strong>
|
| 263 |
+
<div id="sequence-display">No sequence loaded</div>
|
| 264 |
+
</div>
|
| 265 |
+
</div>
|
| 266 |
|
| 267 |
+
<script src="https://cdnjs.cloudflare.com/ajax/libs/three.js/r128/three.min.js"></script>
|
| 268 |
+
<script>
|
| 269 |
+
let scene, camera, renderer;
|
| 270 |
+
let moleculeGroup;
|
| 271 |
+
let currentSequence = '';
|
| 272 |
+
let autoRotate = true;
|
| 273 |
+
let viewMode = 'cartoon';
|
| 274 |
+
|
| 275 |
+
function init() {
|
| 276 |
+
scene = new THREE.Scene();
|
| 277 |
+
scene.background = new THREE.Color(0x000000);
|
| 278 |
+
|
| 279 |
+
camera = new THREE.PerspectiveCamera(75, window.innerWidth / window.innerHeight, 0.1, 1000);
|
| 280 |
+
camera.position.z = 50;
|
| 281 |
+
|
| 282 |
+
renderer = new THREE.WebGLRenderer({ canvas: document.getElementById('canvas3d'), antialias: true });
|
| 283 |
+
renderer.setSize(window.innerWidth, window.innerHeight);
|
| 284 |
+
|
| 285 |
+
const ambientLight = new THREE.AmbientLight(0x404040, 1.5);
|
| 286 |
+
scene.add(ambientLight);
|
| 287 |
+
|
| 288 |
+
const directionalLight = new THREE.DirectionalLight(0xffffff, 1);
|
| 289 |
+
directionalLight.position.set(50, 50, 50);
|
| 290 |
+
scene.add(directionalLight);
|
| 291 |
+
|
| 292 |
+
moleculeGroup = new THREE.Group();
|
| 293 |
+
scene.add(moleculeGroup);
|
| 294 |
+
|
| 295 |
+
animate();
|
| 296 |
+
|
| 297 |
+
// Listen for sequence updates from parent
|
| 298 |
+
window.addEventListener('message', function(e) {
|
| 299 |
+
if (e.data.type === 'updateSequence') {
|
| 300 |
+
updateSequence(e.data.sequence);
|
| 301 |
+
}
|
| 302 |
+
});
|
| 303 |
+
}
|
| 304 |
+
|
| 305 |
+
function updateSequence(sequence) {
|
| 306 |
+
currentSequence = sequence;
|
| 307 |
+
document.getElementById('sequence-display').textContent = sequence;
|
| 308 |
+
generateDNAStructure(sequence);
|
| 309 |
+
}
|
| 310 |
+
|
| 311 |
+
function generateDNAStructure(sequence) {
|
| 312 |
+
moleculeGroup.clear();
|
| 313 |
+
|
| 314 |
+
const radius = 10;
|
| 315 |
+
const rise = 3.4;
|
| 316 |
+
const basesPerTurn = 10;
|
| 317 |
+
const anglePerBase = (2 * Math.PI) / basesPerTurn;
|
| 318 |
+
|
| 319 |
+
// Create double helix
|
| 320 |
+
const curve1Points = [];
|
| 321 |
+
const curve2Points = [];
|
| 322 |
+
|
| 323 |
+
for (let i = 0; i < sequence.length; i++) {
|
| 324 |
+
const angle = i * anglePerBase;
|
| 325 |
+
const height = i * rise / basesPerTurn;
|
| 326 |
+
|
| 327 |
+
curve1Points.push(new THREE.Vector3(
|
| 328 |
+
radius * Math.cos(angle),
|
| 329 |
+
height,
|
| 330 |
+
radius * Math.sin(angle)
|
| 331 |
+
));
|
| 332 |
+
|
| 333 |
+
curve2Points.push(new THREE.Vector3(
|
| 334 |
+
radius * Math.cos(angle + Math.PI),
|
| 335 |
+
height,
|
| 336 |
+
radius * Math.sin(angle + Math.PI)
|
| 337 |
+
));
|
| 338 |
+
}
|
| 339 |
+
|
| 340 |
+
// Create backbone curves
|
| 341 |
+
const curve1 = new THREE.CatmullRomCurve3(curve1Points);
|
| 342 |
+
const curve2 = new THREE.CatmullRomCurve3(curve2Points);
|
| 343 |
+
|
| 344 |
+
const tubeGeometry1 = new THREE.TubeGeometry(curve1, 100, 0.5, 8, false);
|
| 345 |
+
const tubeGeometry2 = new THREE.TubeGeometry(curve2, 100, 0.5, 8, false);
|
| 346 |
+
|
| 347 |
+
const material1 = new THREE.MeshPhongMaterial({ color: 0xff0000 });
|
| 348 |
+
const material2 = new THREE.MeshPhongMaterial({ color: 0x0000ff });
|
| 349 |
+
|
| 350 |
+
moleculeGroup.add(new THREE.Mesh(tubeGeometry1, material1));
|
| 351 |
+
moleculeGroup.add(new THREE.Mesh(tubeGeometry2, material2));
|
| 352 |
+
|
| 353 |
+
// Add base pairs
|
| 354 |
+
for (let i = 0; i < Math.min(sequence.length, 50); i++) {
|
| 355 |
+
const p1 = curve1Points[i];
|
| 356 |
+
const p2 = curve2Points[i];
|
| 357 |
+
|
| 358 |
+
const direction = new THREE.Vector3().subVectors(p2, p1);
|
| 359 |
+
const distance = direction.length();
|
| 360 |
+
direction.normalize();
|
| 361 |
+
|
| 362 |
+
const geometry = new THREE.CylinderGeometry(0.3, 0.3, distance, 8);
|
| 363 |
+
const material = new THREE.MeshPhongMaterial({
|
| 364 |
+
color: getBaseColor(sequence[i])
|
| 365 |
+
});
|
| 366 |
+
|
| 367 |
+
const cylinder = new THREE.Mesh(geometry, material);
|
| 368 |
+
cylinder.position.copy(p1).add(direction.multiplyScalar(distance / 2));
|
| 369 |
+
cylinder.quaternion.setFromUnitVectors(new THREE.Vector3(0, 1, 0), direction);
|
| 370 |
+
|
| 371 |
+
moleculeGroup.add(cylinder);
|
| 372 |
+
}
|
| 373 |
+
|
| 374 |
+
// Center the molecule
|
| 375 |
+
const box = new THREE.Box3().setFromObject(moleculeGroup);
|
| 376 |
+
const center = box.getCenter(new THREE.Vector3());
|
| 377 |
+
moleculeGroup.position.sub(center);
|
| 378 |
+
}
|
| 379 |
+
|
| 380 |
+
function getBaseColor(base) {
|
| 381 |
+
const colors = {
|
| 382 |
+
'A': 0xff0000,
|
| 383 |
+
'T': 0x00ff00,
|
| 384 |
+
'G': 0x0000ff,
|
| 385 |
+
'C': 0xffff00
|
| 386 |
+
};
|
| 387 |
+
return colors[base] || 0xffffff;
|
| 388 |
+
}
|
| 389 |
+
|
| 390 |
+
function setViewMode(mode) {
|
| 391 |
+
viewMode = mode;
|
| 392 |
+
if (currentSequence) {
|
| 393 |
+
generateDNAStructure(currentSequence);
|
| 394 |
+
}
|
| 395 |
+
}
|
| 396 |
+
|
| 397 |
+
function toggleRotation() {
|
| 398 |
+
autoRotate = !autoRotate;
|
| 399 |
+
}
|
| 400 |
+
|
| 401 |
+
function resetView() {
|
| 402 |
+
camera.position.set(0, 0, 50);
|
| 403 |
+
moleculeGroup.rotation.set(0, 0, 0);
|
| 404 |
+
}
|
| 405 |
+
|
| 406 |
+
function animate() {
|
| 407 |
+
requestAnimationFrame(animate);
|
| 408 |
+
|
| 409 |
+
if (autoRotate) {
|
| 410 |
+
moleculeGroup.rotation.y += 0.01;
|
| 411 |
+
}
|
| 412 |
+
|
| 413 |
+
renderer.render(scene, camera);
|
| 414 |
+
}
|
| 415 |
+
|
| 416 |
+
// Mouse controls
|
| 417 |
+
let isDragging = false;
|
| 418 |
+
let previousMousePosition = { x: 0, y: 0 };
|
| 419 |
+
|
| 420 |
+
document.addEventListener('mousedown', function(e) {
|
| 421 |
+
isDragging = true;
|
| 422 |
+
});
|
| 423 |
+
|
| 424 |
+
document.addEventListener('mouseup', function(e) {
|
| 425 |
+
isDragging = false;
|
| 426 |
+
});
|
| 427 |
+
|
| 428 |
+
document.addEventListener('mousemove', function(e) {
|
| 429 |
+
if (isDragging) {
|
| 430 |
+
const deltaMove = {
|
| 431 |
+
x: e.clientX - previousMousePosition.x,
|
| 432 |
+
y: e.clientY - previousMousePosition.y
|
| 433 |
+
};
|
| 434 |
+
|
| 435 |
+
moleculeGroup.rotation.y += deltaMove.x * 0.01;
|
| 436 |
+
moleculeGroup.rotation.x += deltaMove.y * 0.01;
|
| 437 |
+
}
|
| 438 |
+
|
| 439 |
+
previousMousePosition = {
|
| 440 |
+
x: e.clientX,
|
| 441 |
+
y: e.clientY
|
| 442 |
+
};
|
| 443 |
+
});
|
| 444 |
+
|
| 445 |
+
document.addEventListener('wheel', function(e) {
|
| 446 |
+
camera.position.z += e.deltaY * 0.1;
|
| 447 |
+
camera.position.z = Math.max(10, Math.min(200, camera.position.z));
|
| 448 |
+
});
|
| 449 |
+
|
| 450 |
+
window.addEventListener('resize', function() {
|
| 451 |
+
camera.aspect = window.innerWidth / window.innerHeight;
|
| 452 |
+
camera.updateProjectionMatrix();
|
| 453 |
+
renderer.setSize(window.innerWidth, window.innerHeight);
|
| 454 |
+
});
|
| 455 |
+
|
| 456 |
+
// Initialize
|
| 457 |
+
init();
|
| 458 |
+
</script>
|
| 459 |
+
</body>
|
| 460 |
+
</html>
|
| 461 |
+
"""
|
| 462 |
|
|
|
|
| 463 |
def create_demo():
|
| 464 |
+
"""Create the Gradio interface with integrated 3D viewer"""
|
| 465 |
|
|
|
|
| 466 |
css = """
|
| 467 |
.gradio-container {
|
| 468 |
font-family: 'Arial', sans-serif;
|
|
|
|
| 473 |
padding: 10px;
|
| 474 |
border-radius: 5px;
|
| 475 |
}
|
| 476 |
+
iframe {
|
| 477 |
+
border: none;
|
| 478 |
+
border-radius: 10px;
|
| 479 |
+
}
|
| 480 |
"""
|
| 481 |
|
| 482 |
+
with gr.Blocks(css=css, title="DNA-Diffusion with 3D Viewer") as demo:
|
|
|
|
| 483 |
gr.Markdown(
|
| 484 |
"""
|
| 485 |
+
# 🧬 DNA-Diffusion: AI-Powered Sequence Generation with 3D Visualization
|
| 486 |
|
| 487 |
+
Generate cell-type specific DNA sequences and visualize them in 3D!
|
|
|
|
| 488 |
"""
|
| 489 |
)
|
| 490 |
|
|
|
|
| 491 |
gpu_status = gr.Markdown(
|
| 492 |
f"🖥️ **GPU Status**: {'✅ Available' if SPACES_AVAILABLE else '❌ Not Available (CPU mode)'}"
|
| 493 |
)
|
| 494 |
|
| 495 |
with gr.Tabs():
|
| 496 |
+
# Tab 1: Sequence Generation
|
| 497 |
+
with gr.TabItem("🎯 Generate Sequence"):
|
| 498 |
with gr.Row():
|
| 499 |
with gr.Column(scale=1):
|
| 500 |
cell_type = gr.Dropdown(
|
|
|
|
| 536 |
analysis_output = gr.JSON(
|
| 537 |
label="Sequence Analysis"
|
| 538 |
)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 539 |
|
| 540 |
+
# Tab 2: 3D Visualization
|
| 541 |
+
with gr.TabItem("🔬 3D Structure"):
|
| 542 |
+
with gr.Row():
|
| 543 |
+
with gr.Column():
|
| 544 |
+
gr.Markdown("### 3D DNA Structure Visualization")
|
| 545 |
+
gr.Markdown("The 3D viewer shows the double helix structure of your generated DNA sequence.")
|
| 546 |
+
|
| 547 |
+
# HTML component for 3D viewer
|
| 548 |
+
viewer_html = gr.HTML(
|
| 549 |
+
value=f'<iframe src="data:text/html;charset=utf-8,{HTML_3D_VIEWER.replace("#", "%23")}" width="100%" height="600px"></iframe>',
|
| 550 |
+
label="3D Molecular Viewer"
|
| 551 |
+
)
|
| 552 |
+
|
| 553 |
+
# Button to update 3D view
|
| 554 |
+
update_3d_btn = gr.Button(
|
| 555 |
+
"🔄 Update 3D View with Current Sequence",
|
| 556 |
+
variant="secondary"
|
| 557 |
+
)
|
| 558 |
+
|
| 559 |
+
# Tab 3: Batch Generation
|
| 560 |
with gr.TabItem("📦 Batch Generation"):
|
| 561 |
with gr.Row():
|
| 562 |
with gr.Column():
|
|
|
|
| 584 |
headers=["ID", "Cell Type", "Length", "GC%", "Tm(°C)"],
|
| 585 |
label="Batch Results"
|
| 586 |
)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 587 |
|
|
|
|
| 588 |
status_text = gr.Textbox(
|
| 589 |
label="Status",
|
| 590 |
value="Ready to generate sequences...",
|
|
|
|
| 593 |
|
| 594 |
# Event handlers
|
| 595 |
def generate_single(cell_type, guidance_scale, enhanced):
|
|
|
|
| 596 |
try:
|
| 597 |
status_text.value = "🔄 Generating sequence on GPU..."
|
| 598 |
|
|
|
|
| 599 |
sequence = app.generate_with_gpu(cell_type, guidance_scale, enhanced)
|
|
|
|
|
|
|
| 600 |
analysis = app.analyze_sequence(sequence)
|
| 601 |
|
| 602 |
status_text.value = f"✅ Successfully generated sequence for {cell_type}"
|
|
|
|
| 607 |
logger.error(error_msg)
|
| 608 |
return "", {}, error_msg
|
| 609 |
|
| 610 |
+
def update_3d_viewer(sequence):
|
| 611 |
+
if not sequence:
|
| 612 |
+
return gr.HTML.update()
|
| 613 |
+
|
| 614 |
+
# Create HTML with embedded sequence data
|
| 615 |
+
html_with_sequence = HTML_3D_VIEWER.replace(
|
| 616 |
+
"window.addEventListener('message'",
|
| 617 |
+
f"updateSequence('{sequence}');\n window.addEventListener('message'"
|
| 618 |
+
)
|
| 619 |
+
|
| 620 |
+
return gr.HTML.update(
|
| 621 |
+
value=f'<iframe src="data:text/html;charset=utf-8,{html_with_sequence.replace("#", "%23")}" width="100%" height="600px"></iframe>'
|
| 622 |
+
)
|
| 623 |
+
|
| 624 |
def generate_batch(cell_types, count):
|
|
|
|
| 625 |
if not cell_types:
|
| 626 |
return None, "❌ Please select at least one cell type"
|
| 627 |
|
| 628 |
try:
|
| 629 |
status_text.value = "🔄 Generating batch on GPU..."
|
| 630 |
|
| 631 |
+
results = []
|
| 632 |
+
for i in range(count):
|
| 633 |
+
cell_type = cell_types[i % len(cell_types)]
|
| 634 |
+
sequence = app.generate_with_gpu(cell_type)
|
| 635 |
+
analysis = app.analyze_sequence(sequence)
|
| 636 |
+
|
| 637 |
+
results.append([
|
| 638 |
+
f'SEQ_{i+1:03d}',
|
| 639 |
+
cell_type,
|
| 640 |
+
analysis['length'],
|
| 641 |
+
analysis['gc_content'],
|
| 642 |
+
analysis['melting_temp']
|
| 643 |
])
|
| 644 |
|
| 645 |
status_text.value = f"✅ Generated {len(results)} sequences"
|
| 646 |
+
return results, status_text.value
|
| 647 |
|
| 648 |
except Exception as e:
|
| 649 |
error_msg = f"❌ Error: {str(e)}"
|
| 650 |
logger.error(error_msg)
|
| 651 |
return None, error_msg
|
| 652 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 653 |
# Connect event handlers
|
| 654 |
generate_btn.click(
|
| 655 |
fn=generate_single,
|
|
|
|
| 657 |
outputs=[sequence_output, analysis_output, status_text]
|
| 658 |
)
|
| 659 |
|
| 660 |
+
update_3d_btn.click(
|
| 661 |
+
fn=update_3d_viewer,
|
| 662 |
+
inputs=[sequence_output],
|
| 663 |
+
outputs=[viewer_html]
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 664 |
)
|
| 665 |
|
| 666 |
+
# Auto-update 3D viewer when sequence is generated
|
| 667 |
sequence_output.change(
|
| 668 |
+
fn=update_3d_viewer,
|
| 669 |
inputs=[sequence_output],
|
| 670 |
+
outputs=[viewer_html]
|
| 671 |
+
)
|
| 672 |
+
|
| 673 |
+
batch_generate_btn.click(
|
| 674 |
+
fn=generate_batch,
|
| 675 |
+
inputs=[batch_cell_types, batch_count],
|
| 676 |
+
outputs=[batch_output, status_text]
|
| 677 |
)
|
| 678 |
|
| 679 |
return demo
|
| 680 |
|
|
|
|
| 681 |
if __name__ == "__main__":
|
|
|
|
| 682 |
logger.info("=" * 50)
|
| 683 |
+
logger.info("DNA-Diffusion App with 3D Viewer Starting...")
|
| 684 |
logger.info(f"GPU Available: {SPACES_AVAILABLE}")
|
| 685 |
logger.info(f"Environment: {'Hugging Face Spaces' if os.getenv('SPACE_ID') else 'Local'}")
|
| 686 |
logger.info("=" * 50)
|
| 687 |
|
|
|
|
| 688 |
demo = create_demo()
|
| 689 |
|
|
|
|
| 690 |
if os.getenv("SPACE_ID"):
|
|
|
|
| 691 |
demo.launch(
|
| 692 |
server_name="0.0.0.0",
|
| 693 |
server_port=7860,
|
| 694 |
+
share=False,
|
| 695 |
show_error=True
|
| 696 |
)
|
| 697 |
else:
|
|
|
|
| 698 |
demo.launch(
|
| 699 |
share=True,
|
| 700 |
show_error=True,
|