161 skills · sorted by relevance
Calculate alignment statistics including sequence identity, conservation scores, substitution matrices, and similarity metrics. Use when comparing alignment quality, measuring sequence divergence, and analyzing evolutionary patterns.
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Track finance investment signal evolution and update logic based on new finance market information. Use when monitoring finance signals and determining if they are strengthened, weakened, or falsified.
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Quantum mechanics simulations and analysis using QuTiP (Quantum Toolbox in Python). Use when working with quantum systems including: (1) quantum states (kets, bras, density matrices), (2) quantum operators and gates, (3) time evolution and dynamics (Schrödinger, master equations, Monte Carlo), (4) open quantum systems with dissipation, (5) quantum measurements and entanglement, (6) visualization (Bloch sphere, Wigner functions), (7) steady states and correlation functions, or (8) advanced methods (Floquet theory, HEOM, stochastic solvers). Handles both closed and open quantum systems across various domains including quantum optics, quantum computing, and condensed matter physics.
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Help users recruit compatible co-founders, sequence early leadership hires to fill capability gaps, and manage the evolution of the executive team as the company scales.
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Detect introgression and admixture between species or populations using Dsuite (Malinsky 2021 fast D-statistics), Patterson's D / ABBA-BABA test (Green 2010; Durand 2011), f4-ratio and f-branch statistic (Malinsky 2018), TreeMix (Pickrell & Pritchard 2012), HyDe (Blischak 2018), QuIBL (Edelman 2019), sprime (Browning 2018), Twisst (Martin 2017), PhyloNet (Than 2008) for explicit phylogenetic networks, and qpAdm / qpGraph (Patterson 2012). Distinguish introgression from incomplete lineage sorting (ILS), ancestral structure, ghost-lineage admixture, and rate variation. Use when testing inter-species gene flow, dating admixture events, identifying introgressed segments, building phylogenetic networks for reticulate evolution, or applying the ABBAclustering (Koppetsch-Malinsky-Matschiner 2024) framework for divergent-species gene flow.
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Perform multiple sequence alignment using MAFFT, MUSCLE5, ClustalOmega, or T-Coffee. Guides tool and algorithm selection based on dataset size, sequence divergence, and downstream application. Use when aligning three or more homologous sequences for phylogenetics, conservation analysis, or evolutionary studies.
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Calculate alignment statistics including sequence identity, conservation scores, substitution matrices, and similarity metrics. Use when comparing alignment quality, measuring sequence divergence, and analyzing evolutionary patterns.
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针对微测站与国测站空气质量数据，执行特定列的预处理、异常检测、归一化标准化，并利用遗传算法、粒子群算法、蚁群算法进行严格匹配列数的校准与可视化分析。
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Protein language models (ESM3, ESM C) for sequence generation, structure prediction, inverse folding, and embeddings. Design novel proteins, extract ML features, or fold sequences. Local GPU or EvolutionaryScale Forge API. Use AlphaFold for traditional folding; RDKit for small molecules.
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ETE Toolkit (ETE3): Python phylogenetic tree analysis and visualization. Parse Newick/NHX/PhyloXML, traverse/annotate nodes, render figures with TreeStyle/NodeStyle, integrate NCBI taxonomy, run PhyloTree comparative genomics. Use for species trees, gene family evolution, annotated tree figures.
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API + Python SDK for ordering cell-free protein expression and binding assays. Submit sequences for expression (10–100 µg), measure binding affinity (KD) against targets, track status, and retrieve results programmatically — no wet-lab setup. Built for ML-guided directed evolution and antibody/nanobody optimization. Requires Adaptyv account and API key.
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Use AgileRL for reinforcement learning workflows: classical RL training, evolutionary HPO, evolvable networks, multi-agent PettingZoo training, offline/bandit data, and LLM fine-tuning.
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Guide for managing consent for scientific research under GDPR Article 89 and Recital 33 broad consent provisions. Covers ethical review board coordination, purpose evolution management, appropriate safeguards including pseudonymization, and the interplay between consent and other lawful bases for research processing.
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Optimize DSPy programs with dspy.GEPA — a reflective/evolutionary optimizer to consider against task-specific baselines within an authorized evaluation budget. Use when the user says optimize, compile, GEPA, reflective optimization, or "make this program better" and a DSPy program + metric + trainset exist.
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Identify bug-introducing commits using semantic analysis that extends traditional SZZ algorithm. Distinguishes semantic changes from refactorings or code movements using control-flow and data-flow similarity analysis. Use when analyzing bug-fix commits to trace back to bug-introducing changes, investigating software evolution, conducting empirical studies on defect prediction, or reducing false positives in bug localization. Supports git repositories and provides explanations for why commits are identified as bug-introducing.
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Automatically generate regression tests for Java codebases by analyzing changes between old and new code versions. Use when users need to: (1) Generate tests after refactoring or code changes, (2) Ensure previously tested behavior still works in new versions, (3) Cover modified or newly added code paths, (4) Migrate existing tests to work with updated APIs or signatures, (5) Maintain test coverage during code evolution. Supports JUnit and TestNG frameworks with unit tests, parameterized tests, and exception testing patterns.
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Estimate divergence times using molecular clock models with BEAST2, MCMCTree, and TreePL. Use when dating speciation events, calibrating phylogenies with fossils, choosing between strict and relaxed clock models, or estimating evolutionary rates across lineages.
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Compute evolutionary distances and build phylogenetic trees using Biopython Bio.Phylo.TreeConstruction. Use when creating distance matrices from alignments, building NJ/UPGMA trees, generating bootstrap consensus, or needing quick exploratory phylogenies before running full ML analysis.
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Analyze codon usage, calculate CAI (Codon Adaptation Index), and examine synonymous codon bias using Biopython. Use when analyzing coding sequences for expression optimization or evolutionary analysis.
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Workflow for orthology, synteny, ancestral reconstruction, and evolutionary comparison across genomes.
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Migration specialist for zero-downtime schema changes, data migrations, and backward-compatible evolutionUse when "migration, schema change, database migration, zero downtime, backward compatible, rollback, blue green, data migration, migration, schema, database, zero-downtime, backward-compatible, rollback, blue-green, feature-flag, ml-memory" mentioned.
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Expert in navigating and manipulating git history. Covers finding bugs with bisect, understanding code evolution, recovering lost work, and rewriting history safely. Understands that git history is your time machine. Use when "git history, git bisect, find when bug introduced, recover deleted, rewrite history, git blame, lost commit, " mentioned.
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Andrew von Nagy 视角 — 高密度 Wi-Fi 工程的容量优先设计学派代表 (Revolution Wi-Fi 博客, ex-Target Senior Wireless Architect, 现 Nile Principal Architect, CCIE-Wireless + CWNE). 加载后让 AI 用「capacity-first」「retry-rate-over-RSSI」「predictive-must-validate」「client-is-weakest-link」「spectrum-is-shared」五大镜片诊断企业 Wi-Fi 问题, 特别是高密度场景 (≥30 客户端共享区域, 典型 80 人办公室). 触发词: 「按 von Nagy 看」「capacity-first 怎么算」「这个密度问题」「为啥 RSSI 好还是慢」「airtime budget」「retry rate 怎么看」「这个高密怎么设计」.
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Orchestrate a phased WinForms-to-Avalonia migration: behavior contracts, UI-independent application logic, platform adapters, MVVM shell, parity/cutover, evolution, and hardening. Use when the request explicitly involves moving a WinForms or .NET Framework desktop UI to Avalonia, or continuing that migration. Do not trigger for unrelated migrations, rewrites, ViewModel refactors, settings work, or command-line work without WinForms-to-Avalonia context. Load this orchestrator before one matching phase skill.
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