Results for “cell-biology”

Use when triaging a study before any writing — stress-tests whether it clears Cell's bar (a complete, mechanistic, hypothesis-driven story with multiple converging lines of evidence) or belongs at a sibling. Use this first to decide Cell vs Molecular Cell vs Cell Reports vs Cell Reports Medicine before investing in framing or figures.

Notebook Cell References

Use after Cell reviews arrive to triage the decision, prioritize the (often substantial) new experiments by impact × feasibility, and draft a point-by-point response that is respectful, evidence-led, and closes the "completeness" gaps reviewers demand. Do not run before the experiments and revision are actually done.

Query the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data, enabling efficient access to cell metadata, gene expression slices, summary counts, and embeddings without downloading whole datasets.

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.

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

Use to build Cell's data and code deposition plan and the Data and Code Availability statement that lives inside STAR Methods Resource Availability — approved repositories, accessions/DOIs at submission, and Cell's three-bullet availability format with Mendeley Data as Elsevier's default.

MaxFuse parameter tuning for datasets with large protein:RNA cell ratios (>100:1)

Use to finalize Cell Press display items — column-width sizing, minimum fonts, RGB, show-the-data with defined error bars/n/replicate type, scale bars, colorblind-safe palettes, multi-panel discipline, stand-alone legends, and image integrity.

Botany Based Prediction Skill

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

Botany Testing Advanced Skill

Extract battery features for degradation analysis and health monitoring in MATLAB. Covers cycling test features, differential curves (IC/DV/DT), and measurement statistics. Use when working with battery cycling data, SOH estimation, RUL prediction, or any battery test data analysis in MATLAB. Triggers on battery* functions such as batteryTestDataParser, batteryTestFeatureExtractor, batteryMeasurementFeatures, batteryDifferentialCurves.

Botany Design Advanced Skill

Botany Based Simulation Skill

Botany Testing Expert Skill

Applied Botany Analysis Skill

Applied Botany Synthesis Skill

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 Modeling Expert Skill

Applies medicinal-chemistry filters with the medchem library — drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, and molecular complexity metrics for compound prioritization and library cleanup. Use when filtering or triaging a compound library, flagging PAINS or reactive groups, or assessing drug-likeness of candidate molecules. Part of the AlterLab Academic Skills suite.

Botany Based Debugging Skill

Applied Botany Testing Skill

Botany Based Derivation Skill

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

Modelagem metabólica baseada em restrições (COBRA). FBA, FVA, knockouts de genes, amostragem de fluxo, modelos SBML, para análise de biologia de sistemas e engenharia metabólica.

Normalize long-form CODEX cycle folders to short form before notebooks run. Trigger: cyc001_reg001_*, hard-coded cyc paths breaking, staged CODEX raw data failing in Notebooks 1/2.

Applied Botany Modeling Skill