GitHub
pubchem-database
Query PubChem via PUG-REST API/PubChemPy (110M+ compounds). Search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics.
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documentation scientific computing AI Skills
Discover documentation scientific computing skills, compare source repositories and read the instructions for each workflow.
Categories: documentation scientific computing
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protocolsio-integration
Integration with protocols.io API for managing scientific protocols. This skill should be used when working with protocols.io to search, create, update, or publish protocols; manage protocol steps and materials...
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GitHub
geniml
This skill should be used when working with genomic interval data (BED files) for machine learning tasks. Use for training region embeddings (Region2Vec, BEDspace), single-cell ATAC-seq analysis (scEmbed), buil...
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GitHub
pydeseq2
Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots, for RNA-seq analysis.
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GitHub
pytdc
Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological prediction.
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GitHub
pysam
Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.
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GitHub
ensembl-database
Query Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, VEP predictions, for genomic research.
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GitHub
scientific-writing
Core skill for the deep research and writing tool. Write scientific manuscripts in full paragraphs (never bullet points). Use two-stage process with (1) section outlines with key points using research-lookup th...
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GitHub
drugbank-database
Access and analyze comprehensive drug information from the DrugBank database including drug properties, interactions, targets, pathways, chemical structures, and pharmacology data. This skill should be used whe...
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GitHub
qutip
Quantum physics simulation library for open quantum systems. Use when studying master equations, Lindblad dynamics, decoherence, quantum optics, or cavity QED. Best for physics research, open system dynamics, a...
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GitHub
kegg-database
Direct REST API access to KEGG (academic use only). Pathway analysis, gene-pathway mapping, metabolic pathways, drug interactions, ID conversion. For Python workflows with multiple databases, prefer bioservices...
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GitHub
scikit-bio
Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.
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GitHub
matchms
Spectral similarity and compound identification for metabolomics. Use for comparing mass spectra, computing similarity scores (cosine, modified cosine), and identifying unknown compounds from spectral libraries...
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GitHub
molfeat
Molecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert SMILES to features, for QSAR and molecular ML.
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GitHub
hypogenic
Automated LLM-driven hypothesis generation and testing on tabular datasets. Use when you want to systematically explore hypotheses about patterns in empirical data (e.g., deception detection, content analysis)....
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GitHub
exploratory-data-analysis
Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats. This skill should be used when analyzing any scientific data file to understand its structure, content, quality...
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GitHub
statistical-analysis
Guided statistical analysis with test selection and reporting. Use when you need help choosing appropriate tests for your data, assumption checking, power analysis, and APA-formatted results. Best for academic...
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GitHub
cellxgene-census
Query the CELLxGENE Census (61M+ cells) programmatically. Use when you need expression data across tissues, diseases, or cell types from the largest curated single-cell atlas. Best for population-scale queries,...
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GitHub
zinc-database
Access ZINC (230M+ purchasable compounds). Search by ZINC ID/SMILES, similarity searches, 3D-ready structures for docking, analog discovery, for virtual screening and drug discovery.
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GitHub
torchdrug
PyTorch-native graph neural networks for molecules and proteins. Use when building custom GNN architectures for drug discovery, protein modeling, or knowledge graph reasoning. Best for custom model development,...
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GitHub
simpy
Process-based discrete-event simulation framework in Python. Use this skill when building simulations of systems with processes, queues, resources, and time-based events such as manufacturing systems, service o...
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GitHub
adaptyv
Cloud laboratory platform for automated protein testing and validation. Use when designing proteins and needing experimental validation including binding assays, expression testing, thermostability measurements...
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GitHub
clinvar-database
Query NCBI ClinVar for variant clinical significance. Search by gene/position, interpret pathogenicity classifications, access via E-utilities API or FTP, annotate VCFs, for genomic medicine.
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GitHub
diffdock
Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design. Not for affinity prediction.
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