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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.
Time-to-event modeling with scikit-survival: Cox PH (elastic net), Random Survival Forests, Boosting, SVMs for censored data. C-index, Brier, time-dependent AUC; Kaplan-Meier, Nelson-Aalen, competing risks. Pipeline/GridSearchCV compatible. Use statsmodels for frequentist, pymc for Bayesian, life...
An MCP server that provides on-demand skill loading for AI coding assistants.
Multi-stage research pipeline with evidence-quality ratings and citations. Classifies intent, clarifies scope, then routes to shallow (single-pass) or deep (parallel fan-out) research. Composes with Parallel AI MCP when available.
Papers and tutorials on KAN learnable activation networks
---name: aav-vector-design-agent description: AI-powered adeno-associated virus (AAV) vector design for gene therapy including capsid engineering, promoter selection, and tropism optimization. license: MIT metadata: author: AI Group version: "1.0.0" created: "2026-01-19" compatibility:
Frames Bayesian phylogenetics as approximating a posterior distribution over trees conditioned on data AND priors via an MCMC that must be proven to have converged, using MrBayes, BEAST2, RevBayes, and PhyloBayes-MPI. Covers why convergence (ESS, PSRF, ASDSF, topology vs scalar) is the load-beari...
Performs retrosynthetic planning using AiZynthFinder (MCTS, template-based), Chemformer (template-free transformer), ASKCOS, and emerging RetroSynFormer with explicit handling of route scoring, building-block availability (eMolecules, Enamine, Mcule), forward prediction validation (Molecular Tran...
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 20...
Detect, date, and contextualize whole-genome duplication (WGD / paleopolyploidy) events using wgd v2 (Chen & Zwaenepoel 2024), KsRates (Sensalari 2022 substitution-rate-corrected Ks dating), DupGen_finder (Qiao 2019), MAPS (Li 2018 phylogenomic), POInT (Conant 2008 ordered-block), SLEDGe (2024 ML...
Creative research ideation and exploration. Use for open-ended brainstorming sessions, exploring interdisciplinary connections, challenging assumptions, or identifying research gaps. Best for early-stage research planning when you do not have specific observations yet. For formulating testable hy...
Guidance for cell-free protein synthesis (CFPS) optimization. Use when: (1) Planning CFPS experiments, (2) Troubleshooting low yield or aggregation, (3) Optimizing DNA template design for CFPS, (4) Expressing difficult proteins (disulfide-rich, toxic, membrane).
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