bioinformatics
332
nw-investigation-techniques
Evidence collection methods, problem categorization, analysis techniques, and solution design patterns
nWave-ai
research
sorting
stars
current ordering strategy
query
all entries
refine the visible subset
computational-chemistry
332
nw-agent-testing
5-layer testing approach for agent validation including adversarial testing, security validation, and prompt injection resistance
nWave-ai
research
lab-tools
332
nw-shared-artifact-tracking
Shared artifact registry, common artifact patterns, and integration validation. Load when tracking data that flows across journey steps or validating horizontal coherence.
nWave-ai
research
lab-tools
332
nw-diverger-review-criteria
Review criteria for the nw-diverger-reviewer — validates JTBD rigor, research quality, option diversity, taste application correctness, and recommendation coherence in DIVERGE wave artifacts
nWave-ai
research
scientific-computing
332
nw-progressive-refactoring
Progressive L1-L6 refactoring hierarchy, 22 code smell taxonomy, atomic transformations, test code smells, and Fowler refactoring catalog
nWave-ai
research
academic
330
exa-research
Use when researching products, finding academic papers, discovering competitors, reading webpage content, or getting cited answers grounded in real web sources. Use over generic search when semantic relevance matters.
BlockRunAI
research
academic
328
explore
Explore literature by fetching papers from OpenAlex with multi-dimensional filters (ISSN, concept, author, institution, keyword, etc.), building local embeddings, running BERTopic clustering, and multi-mode search (semantic/keyword/unified). Data is isolated in data/explore/<name>/. Use when the user wants to survey a journal, explore a research field, analyze an author's output, or do landscape analysis.
ZimoLiao
research
academic
328
citation-check
Verify citations in AI-generated or human-written text against the local knowledge base. Catches hallucinated references, wrong metadata, and missing papers. Use when the user wants to check if citations are real and accurate.
ZimoLiao
research
academic
328
scientific-runtime
Use when serving scientific CLI tasks through ScholarAIO, especially when the agent should prefer scholaraio toolref, handle partial coverage safely, and avoid turning user work into documentation maintenance.
ZimoLiao
research
academic
328
search
Search academic papers in the local ScholarAIO knowledge base. Supports unified search (keyword + semantic fusion), keyword-only (FTS5), semantic-only (FAISS), author search, and federated search across main library, explore databases, and arXiv. Use when the user wants to find papers, look up literature, search by author, explore research topics, or search across multiple sources. For citation rankings and citation count updates, see the /citations skill.
ZimoLiao
research
academic
328
literature-review
Write a literature review based on papers in a workspace. Covers topic organization, narrative structure, gap identification, and BibTeX export. Use when the user wants to draft a literature review, survey a research area, or summarize the state of the art.
ZimoLiao
research
academic
328
paper-writing
Assist with writing sections of a research paper (Introduction, Related Work, Method, Results, Discussion, Conclusion). Leverages workspace papers for citations and evidence. Use when the user wants help drafting or revising specific paper sections.
ZimoLiao
research
academic
328
research-gap
Identify research gaps and open questions from the literature in a workspace. Combines topic clustering, citation analysis, and cross-paper comparison. Use when the user wants to find unexplored areas, formulate research questions, or assess where the field is heading.
ZimoLiao
research
bioinformatics
328
bioinformatics
Use when working on bioinformatics toolchains such as alignment, variant calling, phylogenetics, or protein-structure analysis, especially when the agent must route across BLAST, minimap2, samtools, bcftools, MAFFT, IQ-TREE, or ESMFold.
ZimoLiao
research
computational-chemistry
328
quantum-espresso
Use when working on first-principles materials calculations with Quantum ESPRESSO, especially SCF, band structures, DOS, phonons, electron-phonon coupling, Fermi surfaces, or charge-density analysis.
ZimoLiao
research
computational-chemistry
328
vcad-assembly
Build multi-part assemblies with joints and run physics simulations. Use when the user asks about robot arms, mechanisms, hinges, joints, physics simulation, reinforcement learning environments, or assembly of multiple parts.
ecto
research
lab-tools
328
scientific-tool-onboarding
Use when adding or upgrading ScholarAIO support for a new scientific computing tool, especially when the work needs official docs ingestion, toolref integration, lightweight skill design, and end-to-end CLI verification
ZimoLiao
research
scientific-computing
328
pymol-visualization
Generate publication-quality molecular visualization images using PyMOL. Use this skill whenever the user mentions PyMOL, molecular visualization, protein rendering, structure figures, PDB visualization, ray tracing molecules, or wants to create images of proteins, ligands, binding sites, protein-protein interactions, or any biomolecular structure. Also trigger when the user wants to: make a figure of a crystal structure for a paper or presentation; render a protein surface; show binding pockets; visualize protein-ligand interactions; create Goodsell-style illustrations; produce cartoon representations with highlighted residues; compare multiple structures side by side; or generate any molecular graphics output — even if they don't mention "PyMOL" by name. Trigger for any request involving PDB files, molecular surfaces, cartoon ribbons, stick models, electron density, or structural biology figures.
ChatMol
research