biology-ecology

Biology and Ecology

Overview

This skill covers experimental biology and ecology workflows: from designing valid experiments with appropriate controls and replicates, to analyzing assay data, microscopy images, ecological surveys, and survival data. For genomics and sequencing data, also see the bioinformatics-analysis skill.

When to Use This Skill

• Analyzing in vitro or in vivo experimental data (cell lines, animal studies)
• Processing ecology survey data (species counts, diversity indices)
• Fitting dose-response curves (IC50, EC50)
• Analyzing flow cytometry, ELISA, or imaging data
• Survival analysis (Kaplan-Meier, Cox regression)
• Choosing the right statistical test for biological data

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1. Experimental Design for Biology

Controls

Control type	Purpose	Example
Negative control	Establish background / baseline	Vehicle (DMSO, PBS), untreated cells
Positive control	Confirm assay works	Known active compound, reference drug
Vehicle control	Separate drug effect from solvent effect	DMSO at matched concentration
Isotype control (flow)	Estimate non-specific antibody binding	Matched isotype antibody

Rule: Always include both negative AND positive controls in every experiment run.

Replicates

• Biological replicates: independent samples (different cell passages, different animals, different patients) → what you use for statistics
• Technical replicates: same sample measured multiple times → estimate measurement variability only, do NOT treat as independent samples

Minimum n: Aim for n ≥ 3 biological replicates per condition. For animal studies, use power analysis (see experiment-design skill) targeting power ≥ 0.80.

Randomization and Blinding

import random

# Randomize treatment assignment
wells = list(range(96))
random.seed(42)
random.shuffle(wells)
treatment_wells = wells[:24]  # randomly assigned
control_wells = wells[24:48]

# Document blinding: encode sample IDs before measurement
sample_map = {f"Sample_{i}": f"Unknown_{i:03d}" for i in range(1, 25)}
# Decode only after all measurements are complete