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Research

Scientific computing and academic tools.

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computational-chemistry
950

biomni

Autonomous biomedical AI agent framework for executing complex research tasks across genomics, drug discovery, molecular biology, and clinical analysis. Use this skill when conducting multi-step biomedical research including CRISPR screening design, single-cell RNA-seq analysis, ADMET prediction, GWAS interpretation, rare disease diagnosis, or lab protocol optimization. Leverages LLM reasoning with code execution and integrated biomedical databases.

wu-yc
wu-yc
research
open
computational-chemistry
950

deepchem

Molecular ML with diverse featurizers and pre-built datasets. Use for property prediction (ADMET, toxicity) with traditional ML or GNNs when you want extensive featurization options and MoleculeNet benchmarks. Best for quick experiments with pre-trained models, diverse molecular representations. For graph-first PyTorch workflows use torchdrug; for benchmark datasets use pytdc.

wu-yc
wu-yc
research
open
computational-chemistry
950

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. Best for metabolite identification, spectral matching, library searching. For full LC-MS/MS proteomics pipelines use pyopenms.

wu-yc
wu-yc
research
open
computational-chemistry
950

tooluniverse-drug-research

Generates comprehensive drug research reports with compound disambiguation, evidence grading, and mandatory completeness sections. Covers identity, chemistry, pharmacology, targets, clinical trials, safety, pharmacogenomics, and ADMET properties. Use when users ask about drugs, medications, therapeutics, or need drug profiling, safety assessment, or clinical development research.

wu-yc
wu-yc
research
open
computational-chemistry
950

drugbank-search

Search DrugBank comprehensive drug database with natural language queries. Drug mechanisms, interactions, and safety data powered by Valyu.

wu-yc
wu-yc
research
open
computational-chemistry
950

tooluniverse-drug-drug-interaction

Comprehensive drug-drug interaction (DDI) prediction and risk assessment. Analyzes interaction mechanisms (CYP450, transporters, pharmacodynamic), severity classification, clinical evidence grading, and provides management strategies. Supports single drug pairs, polypharmacy analysis (3+ drugs), and alternative drug recommendations. Use when users ask about drug interactions, medication safety, polypharmacy risks, or need DDI assessment for clinical decision support.

wu-yc
wu-yc
research
open
computational-chemistry
950

tooluniverse-drug-repurposing

Identify drug repurposing candidates using ToolUniverse for target-based, compound-based, and disease-driven strategies. Searches existing drugs for new therapeutic indications by analyzing targets, bioactivity, safety profiles, and literature evidence. Use when exploring drug repurposing opportunities, finding new indications for approved drugs, or when users mention drug repositioning, off-label uses, or therapeutic alternatives.

wu-yc
wu-yc
research
open
computational-chemistry
950

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.

wu-yc
wu-yc
research
open
computational-chemistry
950

open-targets-search

Search Open Targets drug-disease associations with natural language queries. Target validation powered by Valyu semantic search.

wu-yc
wu-yc
research
open
computational-chemistry
950

tooluniverse-rare-disease-diagnosis

Provide differential diagnosis for patients with suspected rare diseases based on phenotype and genetic data. Matches symptoms to HPO terms, identifies candidate diseases from Orphanet/OMIM, prioritizes genes for testing, interprets variants of uncertain significance. Use when clinician asks about rare disease diagnosis, unexplained phenotypes, or genetic testing interpretation.

wu-yc
wu-yc
research
open
computational-chemistry
950

chembl-database

Query ChEMBL bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioactivity data (IC50, Ki), find inhibitors, perform SAR studies, for medicinal chemistry.

wu-yc
wu-yc
research
open
computational-chemistry
950

pdb-database

Access RCSB PDB for 3D protein/nucleic acid structures. Search by text/sequence/structure, download coordinates (PDB/mmCIF), retrieve metadata, for structural biology and drug discovery.

wu-yc
wu-yc
research
open
computational-chemistry
950

tooluniverse-infectious-disease

Rapid pathogen characterization and drug repurposing analysis for infectious disease outbreaks. Identifies pathogen taxonomy, essential proteins, predicts structures, and screens existing drugs via docking. Use when facing novel pathogens, emerging infections, or needing rapid therapeutic options during outbreaks.

wu-yc
wu-yc
research
open
computational-chemistry
950

molfeat

Molecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert SMILES to features, for QSAR and molecular ML.

wu-yc
wu-yc
research
open
computational-chemistry
950

datamol

Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, parallel processing. Returns native rdkit.Chem.Mol objects. For advanced control or custom parameters, use rdkit directly.

wu-yc
wu-yc
research
open
computational-chemistry
950

fda-database

Query openFDA API for drugs, devices, adverse events, recalls, regulatory submissions (510k, PMA), substance identification (UNII), for FDA regulatory data analysis and safety research.

wu-yc
wu-yc
research
open
computational-chemistry
950

torch-geometric

Graph Neural Networks (PyG). Node/graph classification, link prediction, GCN, GAT, GraphSAGE, heterogeneous graphs, molecular property prediction, for geometric deep learning.

wu-yc
wu-yc
research
open
computational-chemistry
950

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.

wu-yc
wu-yc
research
open
computational-chemistry
950

tooluniverse-pharmacovigilance

Analyze drug safety signals from FDA adverse event reports, label warnings, and pharmacogenomic data. Calculates disproportionality measures (PRR, ROR), identifies serious adverse events, assesses pharmacogenomic risk variants. Use when asked about drug safety, adverse events, post-market surveillance, or risk-benefit assessment.

wu-yc
wu-yc
research
open
lab-tools
950

detect-common-wetlab-errors

Detects common wet-lab procedural and safety errors from XR or fixed-camera lab video. Identifies pipette volume deviations, forgotten reagent additions, uncapped tubes, contamination risks, sample mix-ups, and other observable hazards. Outputs structured JSON with error type, timestamp, severity, and corrective action suggestions for real-time alerts or post-hoc audit.

wu-yc
wu-yc
research
open
lab-tools
950

handtracking

Real-time hand detection in egocentric videos using victordibia/handtracking. Outputs bounding boxes for hands, specifically trained on EgoHands dataset. Supports video input/output with labeled hand boxes. Lightweight and fast for egocentric view applications.

wu-yc
wu-yc
research
open
lab-tools
950

iso-13485-certification

Comprehensive toolkit for preparing ISO 13485 certification documentation for medical device Quality Management Systems. Use when users need help with ISO 13485 QMS documentation, including (1) conducting gap analysis of existing documentation, (2) creating Quality Manuals, (3) developing required procedures and work instructions, (4) preparing Medical Device Files, (5) understanding ISO 13485 requirements, or (6) identifying missing documentation for medical device certification. Also use when users mention medical device regulations, QMS certification, FDA QMSR, EU MDR, or need help with quality system documentation.

wu-yc
wu-yc
research
open
lab-tools
950

extract-experiment-data-from-video

General-purpose experimental data extractor from lab video streams. Ingests footage from XR headsets or fixed cameras and extracts typed, timestamped measurements — liquid volume levels, color/turbidity shifts, cell and colony counts, pipette readouts, instrument display values, gel band intensities — emitting a time-series JSON or CSV table ready for downstream analysis, charting, or ELN attachment.

wu-yc
wu-yc
research
open
scientific-computing
950

tooluniverse-gwas-finemapping

Identify and prioritize causal variants at GWAS loci using statistical fine-mapping and locus-to-gene predictions. Computes posterior probabilities for causal variants, links variants to genes via L2G predictions, annotates functional consequences, and suggests validation strategies. Use when asked to fine-map GWAS loci, prioritize causal variants, identify credible sets, or link GWAS signals to causal genes.

wu-yc
wu-yc
research
open
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