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.

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.

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.

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.

Botany Synthesis Expert Skill

Applied Botany Analysis Skill

Botany Design Advanced Skill

Botany Based Synthesis Skill

Applied Botany Synthesis Skill

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.

Diagnoses a reported bug, error, test failure, or unexpected behavior through a 4-phase root-cause analysis before any code changes.

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

Botany Based Design Skill

Botany Based Debugging Skill

Advanced Ecology Testing Skill

CAPA system management for medical device QMS. Covers root cause analysis, corrective action planning, effectiveness verification, and CAPA metrics. Use for CAPA investigations, 5-Why analysis, fishbone diagrams, root cause determination, corrective action tracking, effectiveness verification, or CAPA program optimization.

Applied Botany Testing Skill

Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.

Applied Botany Modeling Skill

Applied Virology Design Skill

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