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.gitattributes

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.gitignore

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+__pycache__/
+*.pyc
+.env

Dockerfile

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+FROM python:3.11-slim
+
+WORKDIR /app
+
+COPY requirements.txt .
+RUN pip install --no-cache-dir -r requirements.txt
+
+COPY . .
+
+EXPOSE 7860
+
+ENV PORT=7860
+CMD ["python", "app.py"]

README.md

@@ -1,12 +1,12 @@
 ---
 title: ProtoPure
-emoji: 🏃
-colorFrom: red
-colorTo: purple
-sdk: gradio
-sdk_version: 6.11.0
-app_file: app.py
+emoji: 🧬
+colorFrom: blue
+colorTo: green
+sdk: docker
 pinned: false
 ---
 
-Check out the configuration reference at https://huggingface.co/docs/hub/spaces-config-reference
+# ProtoPure Dashboard
+
+Interactive dashboard for exploring LLM-extracted protein purification conditions.

cleanup_clustering.sh

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+#!/bin/bash
+# Removes unused clustering files (pkl, png, svg, distribution htmls, individual field CSVs)
+# Keeps only: *_cluster.html, *_ALL_FIELDS.csv, *_FIELD_CLUSTER_METRICS.csv
+
+set -e
+cd /data/ralmadamonter/llm_dashboard/data/clustering
+
+for model in model=*/; do
+    for min in "$model"min=*/; do
+        rm -f "$min"*.pkl
+        rm -f "$min"*.png
+        rm -f "$min"*.svg
+        rm -f "$min"*_clusters_distribution_*.html
+        for f in "$min"*.csv; do
+            [[ "$f" == *_ALL_FIELDS.csv ]] && continue
+            [[ "$f" == *_FIELD_CLUSTER_METRICS.csv ]] && continue
+            rm -f "$f"
+        done
+        for d in "$min"t=*/; do
+            [ -d "$d" ] && rm -rf "$d"
+        done
+    done
+done
+
+echo "Done. Final size:"
+du -sh /data/ralmadamonter/llm_dashboard/data/clustering/

data/clustering/model=NeuML__pubmedbert-base-embeddings/min=10/t=0.5_ALL_FIELDS.csv.gz

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+version https://git-lfs.github.com/spec/v1
+oid sha256:d6c1bf6381a8c562433b69b528ed90ed931074d81662ce673e9189b2ca596eca
+size 1628215

data/clustering/model=NeuML__pubmedbert-base-embeddings/min=10/t=0.5_FIELD_CLUSTER_METRICS.csv

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+field,n_total,n_used,n_clusters,silhouette_cosine,davies_bouldin,min_community_size,threshold
+organism_source,6292,6031,43,0.7171725630760193,1.3300621518094844,10,0.5
+strain,2444,2267,26,0.6957342028617859,1.684334598182741,10,0.5
+expression_strain,5677,5602,12,0.6700806617736816,1.2064563826678447,10,0.5
+molecular_weight,295,285,2,0.4025617241859436,1.8648349615568287,10,0.5
+induction_temperature,3656,3641,13,0.3743528425693512,1.9030132841502945,10,0.5
+lysis_buffer,3714,3681,13,0.3627944886684418,2.5478526370321384,10,0.5
+elution_buffer,3530,3502,13,0.2114894688129425,2.4060399023229584,10,0.5
+inducer,7889,7829,14,0.14916038513183594,2.5754939251632427,10,0.5
+desalting_process,3720,3686,19,0.143924742937088,2.628677276959593,10,0.5
+plasmid,5480,5300,60,-0.013144510798156261,3.421050857693413,10,0.5
+enzyme_name,7975,7044,205,-0.019518611952662468,3.352876814222691,10,0.5
+medium_name,4806,4692,50,-0.03975028917193413,2.837953092993161,10,0.5
+source_key,8021,8021,1,,,10,0.5

data/clustering/model=NeuML__pubmedbert-base-embeddings/min=10/t=0.5_molecular_weight_cluster.html

@@ -0,0 +1,7 @@
+<html>
+<head><meta charset="utf-8" /></head>
+<body>
+    <div>                        <script type="text/javascript">window.PlotlyConfig = {MathJaxConfig: 'local'};</script>
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71,170 Da (dimer)","~100 kDa",0],["24737322",0,"molecular_weight","18.34 kDa","~100 kDa",0],["8617763",0,"molecular_weight","33 kDa","~100 kDa",0],["15701515",0,"molecular_weight","~20 kDa (including His-tag)","~100 kDa",0],["15701515",1,"molecular_weight","~20 kDa (including His-tag)","~100 kDa",0],["20103719",0,"molecular_weight","20,743 Da (including His6-tag)","~100 kDa",0],["20103719",1,"molecular_weight","20,275 Da (including His6-tag)","~100 kDa",0],["16468985",0,"molecular_weight","∼730 kDa (measured); 750 kDa (predicted)","~100 kDa",0],["29174965",0,"molecular_weight","37 kDa","~100 kDa",0],["21283666",0,"molecular_weight","22.8 kDa (experimental); 19.6 kDa (theoretical)","~100 kDa",0],["22023140",0,"molecular_weight","17.5 kDa","~100 kDa",0],["18461140",0,"molecular_weight","27.5 kDa","~100 kDa",0],["18461140",1,"molecular_weight","93.0 kDa","~100 kDa",0],["18461140",2,"molecular_weight","61.0 kDa","~100 kDa",0],["18461140",3,"molecular_weight","89.0 kDa","~100 kDa",0],["18461140",4,"molecular_weight","31.0 kDa","~100 kDa",0],["20188740",0,"molecular_weight","29.9 kDa","~100 kDa",0],["20188740",1,"molecular_weight","34.1 kDa","~100 kDa",0],["28082125",0,"molecular_weight","23,874 Da (subunit)","~100 kDa",0],["37747938",1,"molecular_weight","~37 kDa (expected for variants; 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With ATP\u002fUTP: 337,000–347,000 Da. 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