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Embeds sequential information into mass spectrum m/z-intensity pairs for transformer-based MS/MS interpretation in IDSL_MINT.
This skill implements positional encoding to embed ordinal and sequential information into mass spectrum data. This allows transformer self-attention layers to distinguish the position of peaks in a spectrum, which is critical for accurate MS/MS interpretation.
Use this skill specifically when preparing mass spectrum input tensors for transformer encoder layers within the IDSL_MINT framework. It should be applied after vectorizing m/z and intensity features but before the multi-head self-attention blocks.
Scientific AI agents equipped with PyTorch and RDKit, specifically those targeted at bioinformatics, cheminformatics, and metabolomics research.
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GitHub Actions Workflow Inspector
Verify and locally reproduce GitHub Actions CI workflows to validate badge status and build integrity.
Injection Sequence Annotation
Identifies and validates QCpool sample spacing in Sciex Multiquant metabolomics/lipidomics exports.
PyTorch Pretrained Weight Loader
Load pretrained PyTorch model checkpoints to rank candidate molecules or score spectra in metabolomics without retraining.
Record Field Transformation & Collation
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Fragmentation Spectrum Extraction
Extract and deconvolve individual fragmentation spectra from composite mass spectrometry data for metabolomics and exposomics annotation.
Metabolomics QC Report Generation
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Proteomics Spectral Quality Assurance
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GNPS Molecular Network Metadata Organization
Fetch, extract, and standardize GNPS molecular networking job archives for NPLinker integration.
Metabolomic Feature Table Imputation
Replace zero and missing values in LC-MS metabolomics feature tables using minimum-value-based interpolation.
LC Gradient Vector Encoding & Decoding
Convert LC gradient parameters into normalized numerical vectors for Bayesian optimization and GP regression.
Seq Wrangler
Sequence data QC, trimming, alignment, and BAM processing pipeline helper — wraps FastQC, fastp/Trimmomatic, BWA/Bowtie2/Minimap2, and SAMtools for automated re
ToolUniverse Gateway
Unified agent gateway to 1000+ scientific tools (bioinformatics, drug discovery, genomics) via Harvard's ToolUniverse, returning JSON for downstream workflows.
MatchMS (mass spectrometry processing)
Mass spectrometry data processing: import/export mzML/MGF/MSP, filter and normalize spectra, compute spectral similarity (cosine/modified cosine), and build rep
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Python library skill for importing, filtering, and comparing mass spectra (mzML/MGF/MSP); builds reproducible preprocessing pipelines and computes spectral simi
MatchMS — Mass Spectrometry Utilities
Import, process and compare mass spectrometry spectra (mzML/MGF/MSP) with filters, similarity metrics and reproducible pipelines for metabolomics workflows.
KEGG Pathway Enrichment (clusterProfiler)
Run KEGG pathway and module enrichment using clusterProfiler (enrichKEGG/enrichMKEGG) to find metabolic and signaling pathways over-represented in a gene list.
Network Toxicology & Docking Research Planner
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Bizard — Biomedical Visualization Atlas
A comprehensive atlas of biomedical data visualization tutorials and examples (R/Python/Julia) that provides reproducible code and guidance for plots used in bi