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import multiprocessing
import gradio as gr
import torch
from omnigenome import OmniGenomeModelForRNADesign # Assuming this is where the model class is defined
import RNA # ViennaRNA library for RNA structure plotting
import tempfile # For handling temporary files
import os # For file operations
# Initialize the model for RNA design
model = OmniGenomeModelForRNADesign(model_path="anonymous8/OmniGenome-186M")
model.to("cuda" if torch.cuda.is_available() else "cpu")
# RNA Design function with structure plotting
def design_rna(target_structure):
if not 0 < len(target_structure) <= 50:
return "The online demo only supports RNA structures with 1 to 100 characters.", None
# Run the genetic algorithm to design RNA sequences
best_sequences = model.run_rna_design(
structure=target_structure.strip(),
mutation_ratio=0.5,
num_population=50,
num_generation=100
)
# Select the best sequence (assuming it's the first one)
best_sequence = best_sequences[0]
# Generate the RNA secondary structure plot
plot_path = plot_rna_structure(best_sequence, target_structure)
return best_sequence, plot_path
# Function to plot RNA structure and return the path to the SVG image
def plot_rna_structure(sequence, structure):
# Create a temporary file to save the SVG plot
with tempfile.NamedTemporaryFile(delete=False, suffix=".svg") as tmpfile:
plot_path = tmpfile.name
# Plot RNA structure using ViennaRNA
RNA.svg_rna_plot(sequence, structure, plot_path)
return plot_path
# Launch the app
if __name__ == "__main__":
multiprocessing.set_start_method('spawn', force=True)
# Gradio Interface with vertical layout
with gr.Blocks() as iface:
gr.Markdown("# RNA Design with OmniGenome")
gr.Markdown(
"Enter a target RNA secondary structure to generate a designed RNA sequence and visualize its structure. "
"Please note that the online demo only supports RNA structures with 1 to 50 bases due to computational resource shortage."
"For larger structures, please run the model locally."
)
gr.Markdown("""
### Example RNA Structures:
- `(((((......)))))`
- `((((((.((((....))))))).)))..........`
- `((....)).((....))`
- `.(((((((((((...)))))....)))))).`
- `..((((((((.....))))((((.....))))))))..`
""")
with gr.Column():
target_structure_input = gr.Textbox(
label="Target RNA Secondary Structure",
placeholder="Enter RNA structure here, e.g., (((((......)))))"
)
output_sequence = gr.Textbox(label="Designed RNA Sequence")
output_plot = gr.Image(type="filepath", label="RNA Structure Plot")
# Defining the function call on input
submit_button = gr.Button("Submit")
submit_button.click(
design_rna,
inputs=target_structure_input,
outputs=[output_sequence, output_plot]
)
iface.launch()
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