K-Dense-AI Scientific Computing Bundle

k-dense-ai

- `alphafold-database` - Protein structure prediction

plurigrid/asi·0installs67starsSecurity

SKILL.md

Full skill instructions

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

Install skill

Copy and run in your terminal

npx -y skills add https://github.com/plurigrid/asi --skill k-dense-ai

View on GitHub

skills/k-dense-ai/SKILL.md

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