Discover business computational chemistry skills, compare source repositories and read the instructions for each workflow.
WikiPathways enrichment using clusterProfiler and rWikiPathways. Performs over-representation analysis and GSEA on community-curated biological pathways. WikiPathways is an open, collaborative platform with pat...
Calculate alignment statistics including sequence identity, conservation scores, substitution matrices, and similarity metrics. Use for comparing alignment quality, measuring sequence divergence, and analyzing...
Create restriction maps showing enzyme cut positions on DNA sequences using Biopython Bio.Restriction. Visualize cut sites, calculate distances between sites, and generate text or graphical maps.
Find patterns, motifs, and subsequences in biological sequences using Biopython. Use when searching for transcription factor binding sites, regulatory elements, or any sequence pattern. For restriction enzyme a...
Modify protein structures using Biopython Bio.PDB. Use for transforming coordinates, removing atoms or residues, adding new entities, modifying B-factors and occupancies, renumbering residues, and building stru...
Metabolite identification from m/z and retention time. Covers database matching, MS/MS spectral matching, and confidence level assignment. Use when assigning compound identities to detected features in untarget...
Find cross-references between NCBI databases using Biopython Bio.Entrez. Use for navigating from genes to proteins, sequences to publications, finding related records, and discovering database relationships.
Search NCBI databases using Biopython Bio.Entrez. Use for finding records by keyword, building search queries, discovering database structure, and getting global query counts across databases.
Detect sample contamination and cross-species reads using FastQ Screen. Screen reads against multiple reference genomes to identify bacterial, viral, adapter, or sample swap contamination. Use when suspecting c...
End-to-end CRISPR screen analysis from FASTQ to hit genes. Orchestrates guide counting, QC, statistical analysis with MAGeCK, and hit calling with multiple methods.
Create circular genome visualizations with Circos and pyCircos. Display multi-track data including ideograms, genes, variants, CNVs, and interaction arcs.
Perform pairwise sequence alignment using Biopython Bio.Align.PairwiseAligner. Use for comparing two sequences, finding optimal alignments, scoring similarity, and identifying local or global matches between DN...
Annotate CNVs with genes, pathways, and clinical significance. Use to interpret CNV calls and identify affected genes.
Differential binding analysis using DiffBind. Compare ChIP-seq peaks between conditions with statistical rigor. Requires replicate samples. Outputs differentially bound regions with fold changes and p-values.
Calculate PI/PID controller gains using Internal Model Control (IMC) tuning rules for first-order systems.
Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows w...
Query PubChem via PUG-REST API/PubChemPy (110M+ compounds). Search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics.
Build comprehensive attack trees to visualize threat paths. Use when mapping attack scenarios, identifying defense gaps, or communicating security risks to stakeholders.
Python computations in science and engineering (pycse) - helps with scientific computing tasks including nonlinear regression, uncertainty quantification, design of experiments (DOE), Latin hypercube sampling,...
Weather and pollen reports for any location using free APIs. Get current conditions, forecasts, and pollen data.
Perform complex, long-running research tasks using Gemini Deep Research Agent. Use when asked to research topics requiring multi-source synthesis, competitive analysis, market research, or comprehensive technic...
Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data. Use when analyzing RNA-seq, WGS/WES, or ATAC-seq data—either local FASTQs or public datasets from GEO/SRA. Triggers on nf-core,...
Generate clinical trial protocols for medical devices or drugs. This skill should be used when users say "Create a clinical trial protocol", "Generate protocol for [device/drug]", "Help me design a clinical stu...
Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) JSON format or flattened 2D CSV. Use this skill when scientists need to standardize instrument data for LIMS sys...
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