Assay Profiler

This module builds chemical-assay profiles using PubChem bioactvity data to fill experimental gaps. You can upload up to 500 chemicals (by PubChem CID). Assays with at least one active compound are selected; mutual information identifies informative assays; then Random Forest models (trained on up to 500 actives and 500 inactives per informative assay) impute missing values.

Upload a file containing PubChem CIDs (one per line) to profile by bioactivity data. Accepted formats: .txt or .csv, single column. If you have other identifiers (e.g., SMILES), use PubChem’s batch converter: ID Exchange

Download Sample CSV Download Sample TXT
File must be a single column of CIDs. Empty lines are ignored.
What Each Download Option Means
  • Download Bioprofile: Exports the bioprofile matrix with chemicals as rows and bioassays as columns. Activity values are encoded as 1 (Active/Probe), -1 (Inactive), and 0 (Inconclusive/Unspecified/empty).
  • Download Heatmap: A clustered heatmap of the bioprofile matrix to spot activity patterns across assays and chemicals. Supports up to 2000 assay columns.
  • Download Model Metrics: Detailed performance statistics (accuracy, precision, recall, F1-score, ROC AUC) for Random Forest models on top informative assays.
  • Download Model Metrics Plot: Bar charts summarizing model performance for quick comparison.
  • Download Filled Data Gaps Matrix: Returns the chemical-assay matrix with missing activity values imputed using trained models.
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