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Docs, README files, API references, tutorials, specs, and changelogs
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Showing 6,697–6,720 of 16,089 skills
- QutipQuantum physics simulation library for open quantum systems. Use when studying master equations, Lindblad dynamics, decoherence, quantum optics, or cavity QED. Best for physics research, open system dynamics, and educational simulations. NOT for circuit-based quantum computing—use qiskit, cirq, or pennylane for quantum algorithms and hardware execution.Votes: 0GitHub stars: 11
- PyveneProvides guidance for performing causal interventions on PyTorch models using pyvene's declarative intervention framework. Use when conducting causal tracing, activation patching, interchange intervention training, or testing causal hypotheses about model behavior.Votes: 0GitHub stars: 11
- PysamGenomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.Votes: 0GitHub stars: 11
- PydicomPython library for working with DICOM (Digital Imaging and Communications in Medicine) files. Use this skill when reading, writing, or modifying medical imaging data in DICOM format, extracting pixel data from medical images (CT, MRI, X-ray, ultrasound), anonymizing DICOM files, working with DICOM metadata and tags, converting DICOM images to other formats, handling compressed DICOM data, or processing medical imaging datasets. Applies to tasks involving medical image analysis, PACS systems, ...Votes: 0GitHub stars: 11
- Pubchem DatabaseQuery PubChem via PUG-REST API/PubChemPy (110M+ compounds). Search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics.Votes: 0GitHub stars: 11
- Provider ActionsImplement Terraform Provider actions using the Plugin Framework. Use when developing imperative operations that execute at lifecycle events (before/after create, update, destroy).Votes: 0GitHub stars: 11
- Prose SkillsA hard-edged writing style contract for timeless, forceful English prose without modern AI tics. Use when users ask for prose or rewrites that must be clean, exact, concrete, and free of AI cadence, filler, or therapeutic tone.Votes: 0GitHub stars: 11
- Polars BioHigh-performance genomic interval operations and bioinformatics file I/O on Polars DataFrames. Overlap, nearest, merge, coverage, complement, subtract for BED/VCF/BAM/GFF intervals. Streaming, cloud-native, faster bioframe alternative.Votes: 0GitHub stars: 11
- OutlinesGuarantee valid JSON/XML/code structure during generation, use Pydantic models for type-safe outputs, support local models (Transformers, vLLM), and maximize inference speed with Outlines - dottxt.ai's structured generation libraryVotes: 0GitHub stars: 11
- OutlineSearch, read, and manage Outline wiki documents. Use when: (1) searching wiki for documentation, (2) reading wiki pages or articles, (3) listing wiki collections or documents, (4) creating or updating wiki content, (5) exporting documents as markdown. Works with any Outline wiki instance (self-hosted or cloud).Votes: 0GitHub stars: 11
- Ontology MapperMap materials science terms, crystal structures, and sample descriptions to ontology classes and properties. Supports any ontology registered in ontology_registry.json. Use when translating natural-language material descriptions to ontology terms, annotating simulation inputs with ontology metadata, or mapping crystal parameters (space group, Bravais lattice, lattice constants) to standardized ontology representations.Votes: 0GitHub stars: 11
- Ontology ExplorerParse, navigate, and query materials science ontology structure (classes, properties, hierarchy). Use when exploring an ontology like CMSO, understanding class relationships, finding properties for a given class, or searching for ontology terms related to a materials science concept. Supports OWL/XML format from the OCDO ecosystem (CMSO, ASMO, CDCO, PODO, PLDO, LDO).Votes: 0GitHub stars: 11
- Omero IntegrationMicroscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, batch processing, for high-content screening and microscopy workflows.Votes: 0GitHub stars: 11
- Oc2 DiscordDiscord ops via the message tool (channel=discord).Votes: 0GitHub stars: 11
- Oc Chief EditorYou are a professional chief editor.# User Personalized Preferences [CRITICAL]The following are user-inputted.Votes: 0GitHub stars: 11
- NnsightProvides guidance for interpreting and manipulating neural network internals using nnsight with optional NDIF remote execution. Use when needing to run interpretability experiments on massive models (70B+) without local GPU resources, or when working with any PyTorch architecture.Votes: 0GitHub stars: 11
- Molecular DynamicsRun and analyze molecular dynamics simulations with OpenMM and MDAnalysis. Set up protein/small molecule systems, define force fields, run energy minimization and production MD, analyze trajectories (RMSD, RMSF, contact maps, free energy surfaces). For structural biology, drug binding, and biophysics.Votes: 0GitHub stars: 11
- Metabolomics Workbench DatabaseAccess NIH Metabolomics Workbench via REST API (4,200+ studies). Query metabolites, RefMet nomenclature, MS/NMR data, m/z searches, study metadata, for metabolomics and biomarker discovery.Votes: 0GitHub stars: 11
- MatlabMATLAB and GNU Octave numerical computing for matrix operations, data analysis, visualization, and scientific computing. Use when writing MATLAB/Octave scripts for linear algebra, signal processing, image processing, differential equations, optimization, statistics, or creating scientific visualizations. Also use when the user needs help with MATLAB syntax, functions, or wants to convert between MATLAB and Python code. Scripts can be executed with MATLAB or the open-source GNU Octave interpre...Votes: 0GitHub stars: 11
- Markdown Mermaid WritingComprehensive markdown and Mermaid diagram writing skill. Use when creating any scientific document, report, analysis, or visualization. Establishes text-based diagrams as the default documentation standard with full style guides (markdown + mermaid), 24 diagram type references, and 9 document templates.Votes: 0GitHub stars: 11
- Llama FactoryExpert guidance for fine-tuning LLMs with LLaMA-Factory - WebUI no-code, 100+ models, 2/3/4/5/6/8-bit QLoRA, multimodal supportVotes: 0GitHub stars: 11
- IssuesInteract with GitHub issues - create, list, and view issues.Votes: 0GitHub stars: 11
- Interpro DatabaseQuery InterPro for protein family, domain, and functional site annotations. Integrates Pfam, PANTHER, PRINTS, SMART, SUPERFAMILY, and 11 other member databases. Use for protein function prediction, domain architecture analysis, evolutionary classification, and GO term mapping.Votes: 0GitHub stars: 11
- Gnomad DatabaseQuery gnomAD (Genome Aggregation Database) for population allele frequencies, variant constraint scores (pLI, LOEUF), and loss-of-function intolerance. Essential for variant pathogenicity interpretation, rare disease genetics, and identifying loss-of-function intolerant genes.Votes: 0GitHub stars: 11