ESMscan

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MassimoGregorioTotaro commited on Dec 9, 2024

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8ecc9a8

1 Parent(s): d911c22

instructions reorganisation

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Files changed (5) hide show

LICENSE +1 -1
README.md +1 -1
app.py +60 -57
header.md +5 -0
instructions.md +1 -12

LICENSE CHANGED Viewed

@@ -1,4 +1,4 @@
-Copyright (c) 2023, Massimo G. Totaro All rights reserved.
 Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:


1	+ Copyright (c) 2024, Massimo G. Totaro All rights reserved.
2
3	Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
4

README.md CHANGED Viewed

@@ -7,7 +7,7 @@ sdk: gradio
 sdk_version: 5.5.0
 app_file: app.py
 pinned: false
-license: bsd-2-clause
 ---
 Check out the configuration reference at https://huggingface.co/docs/hub/spaces-config-reference

 sdk_version: 5.5.0
 app_file: app.py
 pinned: false
+license: bsd-3-clause
 ---
 Check out the configuration reference at https://huggingface.co/docs/hub/spaces-config-reference

app.py CHANGED Viewed

@@ -1,4 +1,4 @@
-from gradio import Blocks, Button, Checkbox, DataFrame, DownloadButton, Dropdown, Examples, File, Image, Markdown, Textbox
 from model import get_models
 from data import Data
@@ -27,63 +27,66 @@ def app(*argv):
     return *out, DownloadButton(value=data.csv(), visible=True)
 # Create the Gradio interface
-with open("instructions.md", "r", encoding="utf-8") as md, Blocks() as esm_scan:
     # Define the interface components
-    Markdown(md.read())
-    seq = Textbox(
-        lines=2,
-        label="Sequence",
-        placeholder="FASTA sequence here...",
-        value=''
-    )
-    trg = Textbox(
-        lines=1,
-        label="Substitutions",
-        placeholder="Substitutions here...",
-        value=""
-    )
-    model_name = Dropdown(MODELS, label="Model", value="facebook/esm2_t30_150M_UR50D")
-    scoring_strategy = Checkbox(value=True, label="Use higher accuracy scoring", interactive=True)
-    btn = Button(value="Run", variant="primary")
-    dlb = DownloadButton(label="Download raw data", visible=False)
-    out = Image(visible=False)
-    ouu = DataFrame(visible=False)
-    btn.click(
-        fn=app,
-        inputs=[seq, trg, model_name],
-        outputs=[out, ouu, dlb]
-    )
-    ex = Examples(
-        examples=[
-            [
-                "MVEQYLLEAIVRDARDGITISDCSRPDNPLVFVNDAFTRMTGYDAEEVIGKNCRFLQRGDINLSAVHTIKIAMLTHEPCLVTLKNYRKDGTIFWNELSLTPIINKNGLITHYLGIQKDVSAQVILNQTLHEENHLLKSNKEMLEYLVNIDALTGLHNRRFLEDQLVIQWKLASRHINTITIFMIDIDYFKAFNDTYGHTAGDEALRTIAKTLNNCFMRGSDFVARYGGEEFTILAIGMTELQAHEYSTKLVQKIENLNIHHKGSPLGHLTISLGYSQANPQYHNDQNLVIEQADRALYSAKVEGKNRAVAYREQ",
-                "deep mutational scanning",
-                "facebook/esm2_t6_8M_UR50D"
-             ],
-            [
-                "MVEQYLLEAIVRDARDGITISDCSRPDNPLVFVNDAFTRMTGYDAEEVIGKNCRFLQRGDINLSAVHTIKIAMLTHEPCLVTLKNYRKDGTIFWNELSLTPIINKNGLITHYLGIQKDVSAQVILNQTLHEENHLLKSNKEMLEYLVNIDALTGLHNRRFLEDQLVIQWKLASRHINTITIFMIDIDYFKAFNDTYGHTAGDEALRTIAKTLNNCFMRGSDFVARYGGEEFTILAIGMTELQAHEYSTKLVQKIENLNIHHKGSPLGHLTISLGYSQANPQYHNDQNLVIEQADRALYSAKVEGKNRAVAYREQ",
-                "217 218 219",
-                "facebook/esm2_t12_35M_UR50D"
-             ],
-            [
-                "MVEQYLLEAIVRDARDGITISDCSRPDNPLVFVNDAFTRMTGYDAEEVIGKNCRFLQRGDINLSAVHTIKIAMLTHEPCLVTLKNYRKDGTIFWNELSLTPIINKNGLITHYLGIQKDVSAQVILNQTLHEENHLLKSNKEMLEYLVNIDALTGLHNRRFLEDQLVIQWKLASRHINTITIFMIDIDYFKAFNDTYGHTAGDEALRTIAKTLNNCFMRGSDFVARYGGEEFTILAIGMTELQAHEYSTKLVQKIENLNIHHKGSPLGHLTISLGYSQANPQYHNDQNLVIEQADRALYSAKVEGKNRAVAYREQ",
-                "R218K R218S R218N R218A R218V R218D",
-                "facebook/esm2_t30_150M_UR50D",
-             ],
-            [
-                "MVEQYLLEAIVRDARDGITISDCSRPDNPLVFVNDAFTRMTGYDAEEVIGKNCRFLQRGDINLSAVHTIKIAMLTHEPCLVTLKNYRKDGTIFWNELSLTPIINKNGLITHYLGIQKDVSAQVILNQTLHEENHLLKSNKEMLEYLVNIDALTGLHNRRFLEDQLVIQWKLASRHINTITIFMIDIDYFKAFNDTYGHTAGDEALRTIAKTLNNCFMRGSDFVARYGGEEFTILAIGMTELQAHEYSTKLVQKIENLNIHHKGSPLGHLTISLGYSQANPQYHNDQNLVIEQADRALYSAKVEGKNRAVAYREQ",
-                "MVEQYLLEAIVRDARDGITISDCSRPDNPLVFVNDAFTRMTGYDAEEVIGKNCRFLQRGDINLSAVHTIKIAMLTHEPCLVTLKNYRKDGTIFWNELSLTPIINKNGLITHYLGIQKDVSAQVILNQTLHEENHLLKSNKEMLEYLVNIDALTGLHNRRFLEDQLVIQWKLASRHINTITIFMIDIDYFKAFNDTYGHTAGDEALRTIAKTLNNCFMWGSDFVARYGGEEFTILAIGMTELQAHEYSTKLVQKIENLNIHHKGSPLGHLTISLGYSQANPQYHNDQNLVIEQADRALYSAKVEGKNRAVAYREQ",
-                "facebook/esm2_t33_650M_UR50D",
-             ],
-        ],
-        inputs=[seq,
-                trg,
-                model_name],
-        outputs=[out],
-        fn=app,
-        cache_examples=False
-    )
 # Launch the Gradio interface
 if __name__ == "__main__":

+from gradio import Blocks, Button, Checkbox, DataFrame, DownloadButton, Dropdown, Examples, Image, Markdown, Tab, Textbox
 from model import get_models
 from data import Data
     return *out, DownloadButton(value=data.csv(), visible=True)
 # Create the Gradio interface
+with Blocks() as esm_scan:
+    Markdown("# [ESM-Scan](https://doi.org/10.1002/pro.5221)")
     # Define the interface components
+    with Tab("App"):
+        Markdown(open("header.md", "r", encoding="utf-8").read())
+        seq = Textbox(
+            lines=2,
+            label="Sequence",
+            placeholder="FASTA sequence here...",
+            value=''
+        )
+        trg = Textbox(
+            lines=1,
+            label="Substitutions",
+            placeholder="Substitutions here...",
+            value=""
+        )
+        model_name = Dropdown(MODELS, label="Model", value="facebook/esm2_t30_150M_UR50D")
+        scoring_strategy = Checkbox(value=True, label="Use higher accuracy scoring", interactive=True)
+        btn = Button(value="Run", variant="primary")
+        dlb = DownloadButton(label="Download raw data", visible=False)
+        out = Image(visible=False)
+        ouu = DataFrame(visible=False)
+        btn.click(
+            fn=app,
+            inputs=[seq, trg, model_name],
+            outputs=[out, ouu, dlb]
+        )
+        ex = Examples(
+            examples=[
+                [
+                    "MVEQYLLEAIVRDARDGITISDCSRPDNPLVFVNDAFTRMTGYDAEEVIGKNCRFLQRGDINLSAVHTIKIAMLTHEPCLVTLKNYRKDGTIFWNELSLTPIINKNGLITHYLGIQKDVSAQVILNQTLHEENHLLKSNKEMLEYLVNIDALTGLHNRRFLEDQLVIQWKLASRHINTITIFMIDIDYFKAFNDTYGHTAGDEALRTIAKTLNNCFMRGSDFVARYGGEEFTILAIGMTELQAHEYSTKLVQKIENLNIHHKGSPLGHLTISLGYSQANPQYHNDQNLVIEQADRALYSAKVEGKNRAVAYREQ",
+                    "deep mutational scanning",
+                    "facebook/esm2_t6_8M_UR50D"
+                ],
+                [
+                    "MVEQYLLEAIVRDARDGITISDCSRPDNPLVFVNDAFTRMTGYDAEEVIGKNCRFLQRGDINLSAVHTIKIAMLTHEPCLVTLKNYRKDGTIFWNELSLTPIINKNGLITHYLGIQKDVSAQVILNQTLHEENHLLKSNKEMLEYLVNIDALTGLHNRRFLEDQLVIQWKLASRHINTITIFMIDIDYFKAFNDTYGHTAGDEALRTIAKTLNNCFMRGSDFVARYGGEEFTILAIGMTELQAHEYSTKLVQKIENLNIHHKGSPLGHLTISLGYSQANPQYHNDQNLVIEQADRALYSAKVEGKNRAVAYREQ",
+                    "217 218 219",
+                    "facebook/esm2_t12_35M_UR50D"
+                ],
+                [
+                    "MVEQYLLEAIVRDARDGITISDCSRPDNPLVFVNDAFTRMTGYDAEEVIGKNCRFLQRGDINLSAVHTIKIAMLTHEPCLVTLKNYRKDGTIFWNELSLTPIINKNGLITHYLGIQKDVSAQVILNQTLHEENHLLKSNKEMLEYLVNIDALTGLHNRRFLEDQLVIQWKLASRHINTITIFMIDIDYFKAFNDTYGHTAGDEALRTIAKTLNNCFMRGSDFVARYGGEEFTILAIGMTELQAHEYSTKLVQKIENLNIHHKGSPLGHLTISLGYSQANPQYHNDQNLVIEQADRALYSAKVEGKNRAVAYREQ",
+                    "R218K R218S R218N R218A R218V R218D",
+                    "facebook/esm2_t30_150M_UR50D",
+                ],
+                [
+                    "MVEQYLLEAIVRDARDGITISDCSRPDNPLVFVNDAFTRMTGYDAEEVIGKNCRFLQRGDINLSAVHTIKIAMLTHEPCLVTLKNYRKDGTIFWNELSLTPIINKNGLITHYLGIQKDVSAQVILNQTLHEENHLLKSNKEMLEYLVNIDALTGLHNRRFLEDQLVIQWKLASRHINTITIFMIDIDYFKAFNDTYGHTAGDEALRTIAKTLNNCFMRGSDFVARYGGEEFTILAIGMTELQAHEYSTKLVQKIENLNIHHKGSPLGHLTISLGYSQANPQYHNDQNLVIEQADRALYSAKVEGKNRAVAYREQ",
+                    "MVEQYLLEAIVRDARDGITISDCSRPDNPLVFVNDAFTRMTGYDAEEVIGKNCRFLQRGDINLSAVHTIKIAMLTHEPCLVTLKNYRKDGTIFWNELSLTPIINKNGLITHYLGIQKDVSAQVILNQTLHEENHLLKSNKEMLEYLVNIDALTGLHNRRFLEDQLVIQWKLASRHINTITIFMIDIDYFKAFNDTYGHTAGDEALRTIAKTLNNCFMWGSDFVARYGGEEFTILAIGMTELQAHEYSTKLVQKIENLNIHHKGSPLGHLTISLGYSQANPQYHNDQNLVIEQADRALYSAKVEGKNRAVAYREQ",
+                    "facebook/esm2_t33_650M_UR50D",
+                ],
+            ],
+            inputs=[seq,
+                    trg,
+                    model_name],
+            outputs=[out],
+            fn=app,
+            cache_examples=False
+        )
+    with Tab("Instructions"):
+        Markdown(open("instructions.md", "r", encoding="utf-8").read())
 # Launch the Gradio interface
 if __name__ == "__main__":

header.md ADDED Viewed

	@@ -0,0 +1,5 @@

+Calculate the fitness of single amino acid substitutions on proteins, using a [zero-shot](https://doi.org/10.1101/2021.07.09.450648) [language model predictor](https://github.com/facebookresearch/esm)
+**WARNING:**
+Due to high server traffic, the tool might become slow or unresponsive.
+In this case, it is recommended to duplicate and clone the space in your personal HuggingFace account by clicking the top right menu.

instructions.md CHANGED Viewed

@@ -1,10 +1,3 @@
-# **ESM-Scan**
-Calculate the <u>fitness of single amino acid substitutions</u> on proteins, using a [zero-shot](https://doi.org/10.1101/2021.07.09.450648) [language model predictor](https://github.com/facebookresearch/esm)
-<details>
-  <summary> <b> USAGE INSTRUCTIONS </b> </summary>
 ## Setup
 No setup is required. Simply fill in the input boxes with the necessary data and click the **Run** button.
@@ -54,8 +47,4 @@ The **Download raw data** button lets you download the output in CSV format.
 **If you use this tool in your research, please cite**:
-- Totaro, M.G. (2023). “ESM-Scan - a tool to guide amino acid substitutions.” bioRxiv. [doi.org/10.1101/2023.12.12.571273](https://doi.org/10.1101/2023.12.12.571273)
-- Meier, J. (2021). “Language Models Enable Zero-Shot Prediction of the Effects of Mutations on Protein Function.” bioRxiv (Cold Spring Harbor Laboratory), July. [doi.org/10.1101/2021.07.09.450648](https://doi.org/10.1101/2021.07.09.450648)
-</details>

 ## Setup
 No setup is required. Simply fill in the input boxes with the necessary data and click the **Run** button.
 **If you use this tool in your research, please cite**:
+Totaro MG, Vide U, Zausinger R, Winkler A, Oberdorfer G. ESM-scan—A tool to guide amino acid substitutions. *Protein Science.* 2024; 33(12):e5221. [doi.org/10.1002/pro.5221](https://doi.org/10.1002/pro.5221)