Biology & Bioinformatics Examples
Natural language prompts for biological modeling and data analysis.
Systems Biology
Model a gene regulatory network with feedback loops
Simulate the cell cycle with checkpoints
Model metabolic flux through glycolysis
Simulate the lac operon switching behavior
Model calcium signaling in a cell
Analyze the stability of a genetic toggle switch
Simulate circadian rhythm oscillations
Model signal transduction cascades
Analyze the robustness of a biological network
Simulate cell fate decisions in development
Population Dynamics
Model predator-prey dynamics with carrying capacity
Simulate the spread of an invasive species
Model competition between two species
Analyze metapopulation dynamics with migration
Simulate age-structured population growth
Model disease spread with vaccination
Analyze evolutionary game theory dynamics
Simulate genetic drift in a small population
Model fishery dynamics with harvesting
Analyze the Allee effect on population persistence
Evolutionary Biology
Simulate natural selection on a quantitative trait
Model the evolution of antibiotic resistance
Simulate speciation with geographic isolation
Model coevolution between host and parasite
Analyze phylogenetic trees using molecular clocks
Simulate neutral evolution and genetic drift
Model the evolution of cooperation using game theory
Analyze selective sweeps in genomic data
Simulate adaptive radiation on an island
Model the evolution of sexual reproduction
Molecular Biology
Simulate DNA replication with error rates
Model protein folding energy landscape
Analyze codon usage bias in a genome
Simulate mRNA translation with ribosome dynamics
Model gene expression noise
Analyze protein-protein interaction networks
Simulate CRISPR-Cas9 editing efficiency
Model epigenetic inheritance patterns
Analyze alternative splicing patterns
Simulate viral replication dynamics
Bioinformatics
Align two DNA sequences using Smith-Waterman
Build a phylogenetic tree from multiple sequences
Predict protein secondary structure
Cluster gene expression data
Identify differentially expressed genes
Analyze SNP associations with phenotype
Predict transcription factor binding sites
Build a hidden Markov model for gene finding
Analyze RNA-seq read counts
Predict protein function from sequence
Neuroscience
Simulate a network of integrate-and-fire neurons
Model synaptic plasticity with STDP
Analyze spike train correlations
Simulate the visual cortex orientation selectivity
Model working memory in a recurrent network
Analyze EEG power spectra and coherence
Simulate dopamine signaling and reward
Model decision making with drift-diffusion
Analyze fMRI connectivity patterns
Simulate epileptic seizure dynamics
Ecology
Model ecosystem dynamics with multiple trophic levels
Simulate forest fire spread
Analyze species-area relationships
Model nutrient cycling in an ecosystem
Simulate climate effects on species distribution
Analyze food web stability
Model the carbon cycle
Simulate coral reef dynamics
Analyze biodiversity indices
Model pollination network dynamics
Physiology
Model cardiac electrophysiology
Simulate kidney filtration and reabsorption
Model lung gas exchange
Simulate muscle contraction dynamics
Model hormone feedback loops
Analyze heart rate variability
Simulate the baroreceptor reflex
Model thermoregulation
Analyze respiratory mechanics
Simulate the pupillary light reflex
Epidemiology
Model COVID-19 spread with interventions
Simulate endemic disease equilibrium
Analyze contact tracing effectiveness
Model vaccine distribution strategies
Simulate superspreading events
Analyze the basic reproduction number R0
Model hospital capacity during outbreak
Simulate quarantine effectiveness
Analyze age-structured disease dynamics
Model vector-borne disease transmission
Biomechanics
Analyze gait kinematics and kinetics
Model muscle force generation
Simulate bone remodeling under load
Analyze joint reaction forces
Model blood flow through heart valves
Simulate cell migration mechanics
Analyze sports biomechanics
Model wound healing mechanics
Simulate cartilage loading
Analyze swimming or flying locomotion
Structural Biology
Predict protein structure from sequence
Analyze protein dynamics with normal modes
Model ligand binding affinity
Simulate membrane protein insertion
Analyze allosteric communication pathways
Model protein aggregation
Simulate DNA-protein interactions
Analyze cryo-EM density maps
Model enzyme catalytic mechanisms
Simulate molecular crowding effects
Synthetic Biology
Design a genetic oscillator circuit
Model a biosensor response curve
Optimize codon usage for expression
Design a genetic logic gate
Model metabolic pathway optimization
Simulate cell-free expression systems
Design a kill switch for biocontainment
Model directed evolution outcomes
Simulate a synthetic minimal cell
Design orthogonal genetic systems