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Science Comp.

Simulation and numerical analysis.

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scientific-computing
1

esm

Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C (efficient protein embeddings and representations). Use this skill when working with protein sequences, structures, or function prediction; designing novel proteins; generating protein embeddings; performing inverse folding; or conducting protein engineering tasks. Supports both local model usage and cloud-based Forge API for scalable inference.

hxk622
hxk622
research
open
scientific-computing
1

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.

hxk622
hxk622
research
open
scientific-computing
1

molfeat

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

hxk622
hxk622
research
open
scientific-computing
1

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.

hxk622
hxk622
research
open
scientific-computing
1

rdkit

Modern RDKit workflows for cheminformatics, including molecular fingerprints, drawing, and property calculations. Use when working with molecules, SMILES, molecular fingerprints (Morgan, ECFP, RDKit, atom pairs, topological torsions), molecule visualization/drawing, substructure search, or chemical property calculations. This skill provides up-to-date syntax patterns as RDKit's API evolves.

mcox3406
mcox3406
research
open
scientific-computing
1

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. Use this for direct HTTP/REST work or KEGG-specific control.

hxk622
hxk622
research
open
scientific-computing
1

cosmic-database

Access COSMIC cancer mutation database. Query somatic mutations, Cancer Gene Census, mutational signatures, gene fusions, for cancer research and precision oncology. Requires authentication.

hxk622
hxk622
research
open
scientific-computing
1

scanpy

Standard single-cell RNA-seq analysis pipeline. Use for QC, normalization, dimensionality reduction (PCA/UMAP/t-SNE), clustering, differential expression, and visualization. Best for exploratory scRNA-seq analysis with established workflows. For deep learning models use scvi-tools; for data format questions use anndata.

hxk622
hxk622
research
open
scientific-computing
1

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.

hxk622
hxk622
research
open
scientific-computing
1

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, protein property prediction, retrosynthesis. For pre-trained models and diverse featurizers use deepchem; for benchmark datasets use pytdc.

hxk622
hxk622
research
open
scientific-computing
1

ena-database

Access European Nucleotide Archive via API/FTP. Retrieve DNA/RNA sequences, raw reads (FASTQ), genome assemblies by accession, for genomics and bioinformatics pipelines. Supports multiple formats.

hxk622
hxk622
research
open
scientific-computing
1

rdkit

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 with simpler interface, use datamol (wrapper around RDKit). Use rdkit for advanced control, custom sanitization, specialized algorithms.

hxk622
hxk622
research
open
scientific-computing
1

string-database

Query STRING API for protein-protein interactions (59M proteins, 20B interactions). Network analysis, GO/KEGG enrichment, interaction discovery, 5000+ species, for systems biology.

hxk622
hxk622
research
open
scientific-computing
1

brenda-database

Access BRENDA enzyme database via SOAP API. Retrieve kinetic parameters (Km, kcat), reaction equations, organism data, and substrate-specific enzyme information for biochemical research and metabolic pathway analysis.

hxk622
hxk622
research
open
scientific-computing
1

bioservices

Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database lookups use gget; for sequence/file manipulation use biopython.

hxk622
hxk622
research
open
scientific-computing
1

metabolomics-workbench-database

Access NIH Metabolomics Workbench via REST API (4,200+ studies). Query metabolites, RefMet nomenclature, MS/NMR data, m/z searches, study metadata, for metabolomics and biomarker discovery.

hxk622
hxk622
research
open
scientific-computing
1

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.

hxk622
hxk622
research
open
scientific-computing
1

pubchem-database

Query PubChem via PUG-REST API/PubChemPy (110M+ compounds). Search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics.

hxk622
hxk622
research
open
scientific-computing
1

comsol-docs

Search COMSOL Multiphysics documentation. Use when asked about COMSOL, mesh refinement, boundary conditions, solvers, physics interfaces, FEM simulation, or COMSOL error messages.

jcdoll
jcdoll
research
open
scientific-computing
1

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 when working with pharmaceutical data, drug discovery research, pharmacology studies, drug-drug interaction analysis, target identification, chemical similarity searches, ADMET predictions, or any task requiring detailed drug and drug target information from DrugBank.

hxk622
hxk622
research
open
scientific-computing
1

comsol-docs

Search COMSOL Multiphysics documentation. Use when asked about COMSOL, mesh refinement, boundary conditions, solvers, physics interfaces, FEM simulation, or COMSOL error messages.

jcdoll
jcdoll
research
open
scientific-computing
1

python-scientific-computing

Python for engineering analysis, numerical computing, and scientific workflows using NumPy, SciPy, SymPy

vamseeachanta
vamseeachanta
research
open
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