Pre-Agent Ontology Skill
Generates a structured experiment plan with compute-aware recommendations and saves it via the plan API endpoint.
Von Holst reafference and corollary discharge for behavioral verification and signal processing
Discover recent arXiv papers matching a research profile and generate Obsidian-compatible Markdown notes. Use this skill when the user wants to find new papers, refresh their literature inbox, or search arXiv based on their interests.
Gay MCP skill at invocation 23
Succulent rosette growth as propagator network — golden angle = Nash equilibrium, auxin chemotaxis = affective taxis, BCI modulation = closed-loop biofeedback
Comprehensive Artificial Life skill combining ALIFE2025 proceedings, classic texts (Axelrod, Epstein-Axtell), ALIEN simulation, Lenia, NCA, swarm intelligence, and evolutionary computation. 337 pages extracted, 80+ papers, 153 figures.
Skill for adding and validating ontology term references in the dismech knowledge base. This skill should be used when working with disorder YAML files that need ontology term annotations (HPO for phenotypes, CL for cell types, GO for biological processes, MONDO for diseases, UBERON for anatomical entities). Use this skill when adding phenotype_term, cell_types term, biological_processes term, or other ontology-bound fields to disorder files.
Mine Disease Trajectories (DT/DisTraj) outputs for comorbidity/trajectory candidates, including parsing DT JSON/TSV, extracting directed pairs, filtering by sex or significance, and mapping signals into dismech comorbidity YAML.
Skill for validating and repairing evidence references in the dismech knowledge base. Use this skill when working with evidence items in disorder YAML files, validating that snippet text matches PubMed abstracts, and repairing misquoted or fabricated evidence. Critical for ensuring scientific accuracy and preventing AI hallucinations.
Independent verification of literature review quality — citation checks, claim tracing, coverage analysis
Use when starting a new experiment — scaffolds exp/{exp_id}/ directory with README, config, run.py, analyze.py, and results structure.
Use when an experiment has completed and results need analysis, interpretation, or presentation.
Open Targets Platform for target-disease associations and genetic evidence
UniProt protein database - accessions, annotations, and programmatic access
Structured hypothesis formulation for scientific research. Use when generating testable hypotheses from observations.
PubMed biomedical literature search. Use for finding papers, clinical evidence, and research.
RCSB PDB for 3D protein structures, resolution, and experimental methods
ESM protein language models for sequence embeddings and structure prediction
AlphaFold DB for predicted protein structures and pLDDT confidence scores
Molecular biology toolkit. Use for FASTA parsing, sequence analysis, and translation.
Skill for curating cancer and neoplastic disease entries in the dismech knowledge base. Use this skill when creating or enhancing cancer entries, adding oncogene/tumor suppressor pathophysiology, curating histopathology findings, adding targeted therapy information, and linking genetic drivers to treatment responses. Covers fusion genes, two-hit hypothesis, oncogene addiction, and precision oncology concepts.
Translate programming concepts to biological parallels using real ontology terms from EBI OLS.
Comprehensive index of Artificial Life repositories across history, with special focus on 2024-2025 breakthroughs. ASAL, Flow-Lenia, CAX, ALIEN, JaxLife, and 256+ GitHub repos.
' Layer 4: Derivational Pattern Generation via Seed Chaining'
Human Connectome Project analysis bridging cortical thickness, transcription factors, and depression biomarkers. Connects zubyul's Nikolova lab neuroscience to geomstats manifold geometry, Vertex AI protein expression, and the propagator lattice.
Stigmergic agent coordination through environment modification, not messages. Vehicle semantics where carrier encodes meaning.
ALIFE 2025 Proceedings - 337 pages, 80+ papers on artificial life, evolution, emergence, cellular automata, neural networks, agent-based models. Full Mathpix extraction with equations and figures.
Comprehensive Artificial Life skill combining ALIFE2025 proceedings,