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Research

Scientific computing and academic tools.

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computational-chemistry
45

spec-driven-task-decomposer

Use this skill when approved requirements and design need to be decomposed into tasks.md for Phase 3 of a Spec-Driven change. It creates atomic, traceable implementation and testing tasks, validates the plan, and should not be used to design architecture or write implementation code.

lindoelio
lindoelio
research
open
lab-tools
45

manten

Manten testing library patterns - standalone imports via AsyncLocalStorage, async tests, describe groups, hooks, snapshots, timeouts, retries, and concurrency. Use when writing tests with manten, running node test files, or setting up a no-config test suite.

privatenumber
privatenumber
research
open
lab-tools
45

continuous-compliance

Guides continuous privacy compliance monitoring implementation including automated control testing, evidence collection automation, real-time compliance dashboards, alert-based remediation workflows, regulatory change integration, and deviation management. Covers GRC platform configuration, control framework mapping, and compliance-as-code approaches. Keywords: continuous compliance, automated monitoring, evidence collection, dashboard, regulatory change, compliance-as-code.

mukul975
mukul975
research
open
lab-tools
45

review

Validate experiment metrics and findings — run metrics-first to check computations are meaningful, then findings to check conclusions are valid

victoriacity
victoriacity
research
open
lab-tools
45

synthesize

Use when multiple experiments or analyses have accumulated and their findings need to be interpreted together

victoriacity
victoriacity
research
open
lab-tools
45

audit-sampling-methods

Guides privacy audit sampling methodology including statistical and non-statistical sampling, sample size determination, stratification techniques, attribute sampling for compliance testing, confidence level selection, tolerable deviation rates, and extrapolation of results to the population. Keywords: audit sampling, statistical sampling, attribute testing, sample size, confidence level, stratified sampling, privacy audit.

mukul975
mukul975
research
open
lab-tools
45

diagnose

Use when experimental results are unexpected, confusing, or need interpretation

victoriacity
victoriacity
research
open
lab-tools
45

design

Use when designing a new experiment or research protocol and need to ensure methodological rigor

victoriacity
victoriacity
research
open
academic
44

ln-001-standards-researcher

Research standards/patterns via MCP Ref. Generates Standards Research for Story Technical Notes subsection. Reusable worker.

levnikolaevich
levnikolaevich
research
open
scientific-computing
44

ln-002-best-practices-researcher

Research best practices via MCP Ref/Context7 and create documentation (guide/manual/ADR). Single research, multiple output types.

levnikolaevich
levnikolaevich
research
open
academic
44

research

블로그 콘텐츠를 위한 심층 웹 리서치 프로토콜. 웹 검색, 미디어 수집, 출처 검증, 인용 관리를 포함한다. 콘텐츠 작성 전 리서치가 필요하거나 출처 기반 콘텐츠를 생성할 때 사용한다.

modu-ai
modu-ai
research
open
computational-chemistry
44

cleanup-quarantine-manager

Classify cleanup candidates and apply conservative quarantine moves with reversible manifests.

livepeer
livepeer
research
open
lab-tools
44

competitive-analysis

Investigar cómo resuelven el mismo problema otras herramientas. Activar cuando el usuario quiera hacer un analisis competitivo, saber que hace la competencia, evaluar alternativas existentes o realizar benchmarking de mercado.

686f6c61
686f6c61
research
open
lab-tools
44

exploratory-testing

Usar para testing exploratorio con sesiones documentadas. También: probar sin script, buscar bugs, testing manual, edge cases, sesión de testing.

686f6c61
686f6c61
research
open
scientific-computing
43

lobster-bioinformatics

Run bioinformatics analyses using Lobster AI - single-cell RNA-seq, bulk RNA-seq, literature mining, dataset discovery, quality control, and visualization. Use when analyzing genomics data, searching for papers/datasets, or working with H5AD, CSV, GEO/SRA accessions, or biological data. Requires lobster-ai package installed.

the-omics-os
the-omics-os
research
open
computational-chemistry
43

qutip

Quantum 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.

Zaoqu-Liu
Zaoqu-Liu
research
open
computational-chemistry
43

molecular-dynamics

Autonomous molecular dynamics simulation pipeline inspired by DynaMate (2026). Designs, executes, and analyzes complete MD workflows for protein and protein-ligand systems. Covers structure retrieval, system preparation, minimization, equilibration, production, and trajectory analysis (RMSD, RMSF, hydrogen bonds, binding free energy). Uses OpenMM as the primary engine with AmberTools for preparation. Self-correcting — detects and fixes common simulation failures. Use when users ask for MD simulations, protein stability analysis, binding free energy calculations, or "跑个分子动力学模拟". Requires OpenMM and optionally AmberTools.

Zaoqu-Liu
Zaoqu-Liu
research
open
computational-chemistry
43

qiskit

IBM quantum computing framework. Use when targeting IBM Quantum hardware, working with Qiskit Runtime for production workloads, or needing IBM optimization tools. Best for IBM hardware execution, quantum error mitigation, and enterprise quantum computing. For Google hardware use cirq; for gradient-based quantum ML use pennylane; for open quantum system simulations use qutip.

Zaoqu-Liu
Zaoqu-Liu
research
open
computational-chemistry
43

cirq

Google quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits, or running quantum characterization experiments. Best for Google hardware, noise modeling, and low-level circuit design. For IBM hardware use qiskit; for quantum ML with autodiff use pennylane; for physics simulations use qutip.

Zaoqu-Liu
Zaoqu-Liu
research
open
computational-chemistry
43

pxdesign

De novo protein binder design using PXDesign. Use this skill when designing non-antibody protein binders against a target structure. Covers YAML config creation, CLI invocation, output parsing, and result interpretation. For antibody/nanobody binders, use proteus-ab instead. For structure prediction only, use proteus-fold. For scoring and screening, use proteus-scoring and proteus-screening.

001TMF
001TMF
research
open
computational-chemistry
43

boltzgen

Antibody and nanobody binder design using Proteus-AB (BoltzGen diffusion + Protenix refolding). Covers entity YAML specification, CLI invocation, protocol selection (nanobody-anything / antibody-anything), MSA modes, and output parsing. Use this skill whenever the user needs to design an antibody or nanobody binder against a protein target.

001TMF
001TMF
research
open
computational-chemistry
43

pxdesign

De novo protein binder design using PXDesign. Use this skill when designing non-antibody protein binders against a target structure. Covers YAML config creation, CLI invocation, output parsing, and result interpretation. For antibody/nanobody binders, use boltzgen instead. For structure prediction only, use proteus-fold. For scoring and screening, use by-scoring and by-screening.

001TMF
001TMF
research
open
computational-chemistry
43

by-research

Deep academic research for antibody design campaigns — target analysis, literature review, prior art search, epitope identification. Uses an 8-phase pipeline with quality gates and persistent memory. Use this skill whenever researching a protein target, starting a new design campaign, investigating prior art, analyzing epitopes, reviewing literature for design strategy, or when the user mentions target research, literature search, or prior art in the context of protein/antibody design.

001TMF
001TMF
research
open
computational-chemistry
43

proteus-research

Deep academic research for antibody design campaigns — target analysis, literature review, prior art search, epitope identification. Uses an 8-phase pipeline with quality gates and persistent memory. Use this skill whenever researching a protein target, starting a new design campaign, investigating prior art, analyzing epitopes, reviewing literature for design strategy, or when the user mentions target research, literature search, or prior art in the context of protein/antibody design.

001TMF
001TMF
research
open
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