Asi k-dense-ai

Name: k-dense-ai
Author: plurigrid

K-Dense-AI Scientific Computing Bundle

install

source · Clone the upstream repo

git clone https://github.com/plurigrid/asi

Claude Code · Install into ~/.claude/skills/

T=$(mktemp -d) && git clone --depth=1 https://github.com/plurigrid/asi "$T" && mkdir -p ~/.claude/skills && cp -r "$T/skills/k-dense-ai" ~/.claude/skills/plurigrid-asi-k-dense-ai && rm -rf "$T"

manifest: skills/k-dense-ai/SKILL.md

source content

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