Results for “systems-biology”

Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.

Use when studying cell biology.

Analyzes biochemical processes, including enzyme kinetics, metabolic pathways, and biomolecule characterization, with practical techniques and examples.

Explains cell structure, organelles, signaling pathways, and cell cycle regulation for biology study and research.

Applies physical principles to model biological systems, including protein folding, membrane transport, molecular forces, and neural signaling.

Teleological physiology analysis framework for understanding biological systems through multi-constraint optimization. Use when analyzing physiological mechanisms, explaining apparent biological "inefficiencies", preparing for medical examinations (CICM/ANZCA Primary), understanding why biological systems are designed the way they are, or when seeking deeper mechanistic understanding beyond descriptive knowledge. Triggers on questions like "why is X designed this way", "what purpose does Y serve", "how is Z optimized", analysis of physiological trade-offs, or exploration of evolutionary/design constraints.

Explains cellular structures, membrane transport, energetics, signaling, and division, connecting molecular events to organismal function.

Analyze complex systems through stocks, flows, and feedback loops to find high-leverage interventions. For organizational, environmental, social, and technical systems exhibiting circular causality. NOT for linear problems or simple cause-effect chains.

Use when studying biomechanics.

Diverga Memory System v7.0 - Context-persistent research support with checkpoint auto-trigger and cross-session continuity. Triggers: memory, remember, context, recall, checkpoint, decision, persist, 기억, 맥락, 세션, 체크포인트

Designs chaos experiments, creates failure injection frameworks, and facilitates game day exercises for distributed systems — producing runbooks, experiment manifests, rollback procedures, and post-mortem templates.

Battery Management System reference — cell balancing, SOC estimation, thermal management, and protection circuits. Use when designing BMS for lithium-ion packs, evaluating battery safety, or understanding cell monitoring.

Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.

Botany Synthesis Expert Skill

Applied Botany Analysis Skill

Analyzes raw genomic data (FASTQ/VCF) to generate non-medical wellness, longevity, and pharmacogenomic optimization protocols while keeping DNA processing local and private.

Processes and analyzes multiple physiological signals (ECG, respiration, EDA, EMG, PPG, EOG) together using NeuroKit2, including cross-signal features like RSA and event-related analysis.

Research the open web for enhancement opportunities (Layer 3 — Opus subagent with WebSearch + WebFetch). Topic-driven. Returns structured findings with hype tags + source URLs. Does NOT auto-implement.

Research-backed evolution advice for your knowledge system. Analyzes health reports, friction patterns, and derivation history to propose specific changes with research justification. Never auto-implements — proposals require your approval.

Builds and governs design systems with a three-layer token architecture, component specs, and design-to-code handoff, including slide generation.

Botany Design Advanced Skill

Botany Based Synthesis Skill

Applied Botany Synthesis Skill

Design reliable, scalable, and maintainable data systems by applying principles from storage engines, replication, partitioning, transactions, and consistency models.

Designs persistent memory architectures for AI agents, covering cross-session knowledge retention, entity tracking, temporal validity, graph/vector retrieval, and memory consolidation.

Esta habilidade deve ser usada ao trabalhar com LaminDB, um framework de dados de código aberto para biologia que torna dados consultáveis, rastreáveis, reproduzíveis e FAIR. Use ao gerenciar datasets biológicos (scRNA-seq, espacial, citometria de fluxo, etc.), rastrear workflows computacionais, curar e validar dados com ontologias biológicas, construir data lakehouses, ou garantir linhagem de dados e reprodutibilidade em pesquisa biológica. Aborda gerenciamento de dados, anotação, ontologias (genes, tipos de célula, doenças, tecidos), validação de esquema, integrações com orquestradores de workflow (Nextflow, Snakemake) e plataformas MLOps (W&B, MLflow), e estratégias de deployment.

Botany Based Prediction Skill

Analyze biological sequences, alignments, phylogenetic trees, and diversity metrics (alpha/beta, UniFrac) with ordination (PCoA) and PERMANOVA for microbiome and community ecology data.

Enforces a disciplined, evidence-based debugging protocol. Use when the user reports a bug, an unexpected behavior, a broken test, or asks "why is X not working?". Prevents premature fixes and treats symptoms. Blocks code changes until a root cause is confirmed.

Manage, annotate, and trace biological data with LaminDB, an open-source FAIR data framework that makes datasets queryable, versioned, and reproducible. Use when registering or querying biological datasets (scRNA-seq, spatial, flow cytometry), validating and curating data against ontologies (genes, cell types, diseases, tissues), tracking data lineage and computational workflows, building data lakehouses, or wiring integrations with Nextflow, Snakemake, W&B, or MLflow. Part of the AlterLab Academic Skills suite.

Design scalable distributed systems using structured approaches for load balancing, caching, database scaling, and message queues.

Coordinates a goal lifecycle: define, decompose, activate, track, and execute goals using a set of system skills that write markdown files.