k-dense-ai

name: k-dense-ai description: '- alphafold-database - Protein structure prediction'

K-Dense-AI Scientific Computing Bundle

Provenance: K-Dense-AI / Codex scientific skills GF(3) Trit: +1 (PLUS) - Generative/Synthetic Mutual Awareness: trailofbits-security bundle (MINUS -1)

Skills (37)

Bioinformatics Core

• alphafold-database - Protein structure prediction
• biopython - Biological computation toolkit
• esm - Evolutionary Scale Modeling
• scanpy - Single-cell analysis
• anndata - Annotated data matrices
• cellxgene-census - Cell atlas queries

Databases

• chembl-database - Bioactive molecules
• pubchem-database - Chemical compounds
• uniprot-database - Protein sequences
• pdb-database - Protein structures
• kegg-database - Pathway maps
• reactome-database - Biological pathways
• brenda-database - Enzyme data
• drugbank-database - Drug information
• gene-database - Gene annotations
• biorxiv-database - Preprints
• clinicaltrials-database - Clinical studies

Chemistry & Drug Discovery

• rdkit - Cheminformatics
• deepchem - Deep learning for chemistry
• catalyst-chemical - Reaction modeling

Molecular Simulation

• enzyme-autodiff - Automatic differentiation for enzymes

Lab & Workflow

• benchling-integration - Lab notebook
• bioservices - Web service APIs
• adaptyv - Adaptive experiments
• biomni - Multi-omics

Physics & Quantum

• astropy - Astronomy
• cirq - Quantum circuits

ML for Science

• scikit-bio - Biological data science
• scikit-learn - Machine learning
• scikit-survival - Survival analysis
• arboreto - Gene regulatory networks
• aeon - Time series for science

Categorical

• phylogenetic-operad-acset - Tree structures as operads

Mutual Awareness Protocol

{:bundle "k-dense-ai"
 :trit :plus
 :aware-of ["trailofbits-security"]
 :interface
 {:analyze (fn [molecule] "Use rdkit/deepchem")
  :validate (fn [result] "Delegate to trailofbits for security review")
  :synthesize (fn [target] "Generate candidates")}
 :handoff-to "trailofbits-security"
 :handoff-trigger [:untrusted-input :external-api :file-parsing]}

Usage

# Load bundle
skill k-dense-ai

# Cross-bundle workflow
skill k-dense-ai -> trailofbits-security  # Validate drug candidate data pipeline