Spaces:
Running
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Running
on
Zero
docs: add note about ZeroGPU
Browse files
app.py
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@@ -696,7 +696,7 @@ with gr.Blocks(
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gr.Markdown(
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f"""
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# π _De Novo_ Peptide Sequencing with InstaNovo
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Upload your mass spectrometry data file (.mgf, .mzml, or .mzxml) and get peptide sequence predictions.
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Choose your prediction method and decoding options.
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* **Transformer Decoding Methods:**
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* **Greedy Search:** use this for optimal performance, has similar performance as Knapsack Beam Search at 5% FDR.
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* **Knapsack Beam Search:** use this for the best results and highest peptide recall, but is about 10x slower than Greedy Search.
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* `delta_mass_ppm` shows the lowest absolute precursor mass error (ppm) across isotopes 0-1 for the final sequence.
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* Check logs for progress, especially for large files or slower methods.
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**
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* [InstaNovo enables diffusion-powered de novo peptide sequencing in large-scale proteomics experiments](https://www.nature.com/articles/s42256-025-01019-5), Eloff, Kalogeropoulos et al. 2025, Nature Machine Intelligence.
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* [GitHub Repository for InstaNovo](https://github.com/instadeepai/instanovo)
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""",
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elem_classes="feedback"
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)
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with gr.Accordion("Application Logs", open=True):
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log_display = Log(log_file, dark=True, height=300)
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gr.Markdown(
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value="""
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```bibtex
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@article{eloff_kalogeropoulos_2025_instanovo,
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title = {InstaNovo enables diffusion-powered de novo peptide sequencing in large-scale proteomics experiments},
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author = {Kevin Eloff and Konstantinos Kalogeropoulos and Amandla Mabona and Oliver Morell and Rachel Catzel and
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doi = {10.1038/s42256-025-01019-5},
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url = {https://www.nature.com/articles/s42256-025-01019-5}
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}
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""",
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show_copy_button=True
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label="If you use InstaNovo in your research, please cite:"
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)
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# --- Launch the App ---
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gr.Markdown(
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f"""
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# π _De Novo_ Peptide Sequencing with InstaNovo and InstaNovo+
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Upload your mass spectrometry data file (.mgf, .mzml, or .mzxml) and get peptide sequence predictions.
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Choose your prediction method and decoding options.
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* **Transformer Decoding Methods:**
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* **Greedy Search:** use this for optimal performance, has similar performance as Knapsack Beam Search at 5% FDR.
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* **Knapsack Beam Search:** use this for the best results and highest peptide recall, but is about 10x slower than Greedy Search.
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* Check logs for progress, especially for large files or slower methods.
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This Hugging Face Space is powered by a [ZeroGPU ](https://huggingface.co/docs/hub/en/spaces-zerogpu), which is free but **limited to 5 minutes per day per user**βso if you test with your own files, please use only small files.
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""",
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elem_classes="feedback"
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)
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with gr.Accordion("Application Logs", open=True):
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log_display = Log(log_file, dark=True, height=300)
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gr.Markdown(""" **Links:**
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* [GitHub Repository for InstaNovo](https://github.com/instadeepai/instanovo)
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* [InstaNovo enables diffusion-powered de novo peptide sequencing in large-scale proteomics experiments](https://www.nature.com/articles/s42256-025-01019-5), Eloff, Kalogeropoulos et al. 2025, Nature Machine Intelligence.
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If you use InstaNovo in your research, please cite:""")
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gr.Markdown(
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value="""
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```
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@article{eloff_kalogeropoulos_2025_instanovo,
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title = {InstaNovo enables diffusion-powered de novo peptide sequencing in large-scale proteomics experiments},
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author = {Kevin Eloff and Konstantinos Kalogeropoulos and Amandla Mabona and Oliver Morell and Rachel Catzel and
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doi = {10.1038/s42256-025-01019-5},
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url = {https://www.nature.com/articles/s42256-025-01019-5}
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}
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```
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""",
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show_copy_button=True
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)
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# --- Launch the App ---
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