init

app.py

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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()

requirements.txt

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+omnigenome
+transformers
+gradio