🧬 Bioinformatics

DNA Sequencing: Alignment & Assembly (2D)New📱Interactive 2D DNA sequencing simulator: watch short reads align to a reference genome, spot… Biomarker Panel Search Space (2D)New📱Benchmarks four real live-timed algorithms (O(n), O(n log n), O(n squared), O(n times 2^n))… ICU Organ-Failure Severity Score Lab — 3DNewA real-time 3D companion to the SOFA severity score calculator: the same six published… qPCR Amplification Curve & Ct Value SimulatorNew📱2D companion to the 3D qPCR simulator: the same efficiency-limited logistic amplification… Cell-Free ATP Regeneration Kinetics (2D)New📱Interactive 2D kinetic model of the energy-regeneration system inside a cell-free protein… Metabolic Control Analysis 2D: Rate-Limiting Enzyme ExplorerNew📱Tune the Vmax of four enzymes in a five-step Michaelis-Menten pathway and watch the exact… ChIP-seq / ATAC-seq Peak Caller (2D)New📱Interactive 2D top-down genomic-track simulator for ChIP-seq/ATAC-seq peak calling: the same… Neighbor-Joining Phylogenetic Tree Builder (2D)New📱A 2D radial phylogenetic tree builder: watch the real neighbor-joining algorithm compute the… Transcription Factor Binding Site Scanner (2D Track View)New📱Scan a synthetic DNA sequence on a zoomable, pannable 2D genome-browser track: slide a PWM… Pseudotime Radial Lineage TreeNew📱Generate a branching single-cell population in a synthetic 2D expression plane, build its… ATAC-seq Tagmentation: Chromatin Track & Gel Ladder (2D)New📱Pan and zoom a 2D beads-on-a-string chromatin track while Tn5 transposase rains onto it, and… BLAST Seed-and-Extend Dot-Plot (2D)New📱Interactive 2D dot-plot of the BLAST seed-and-extend heuristic: pan and zoom an exact-match… Gene Network Inference Lab (2D)New📱Reconstruct a hidden gene regulatory network from noisy simulated expression data across… Six-Frame ORF Browser: Codon-Bias Gene Prediction (2D)New📱2D genome-browser gene finder: scroll and zoom a six-frame translation track of a random DNA… AI Protein Fitness Landscape Explorer (2D)New📱Interactive 2D top-down protein-engineering simulator where candidate sequences climb a… DNA Data Storage 2D: Redundancy & Majority-Vote DecodingNew📱Encode a byte payload into synthetic DNA bases, synthesize R redundant molecule copies with… Spatial Spot Deconvolution: Unmixing Tissue NichesNew📱Each spatial transcriptomics spot pools mRNA from several neighbouring cells at once; this… Coevolution Contact Map: How AI Reads Structure from SequenceNew📱Generate a synthetic multiple sequence alignment, rank residue pairs by mutual information,… Droplet Microfluidics: Poisson Arrival Timeline (2D)New📱Watch a genuine exponential-interarrival Poisson process drive a scrolling cell-arrival… Spectral Unmixing: Emission Curves & Recovery MapNew📱A 2D counterpart to the 3D spectral-unmixing simulator: real Gaussian fluorophore emission… Single-Cell Pseudotime Trajectory ExplorerNew📱Generate a branching single-cell differentiation trajectory in 3D expression space, watch a… BLAST Seed-and-Extend AlignerNew📱Interactive 3D dot-plot of the BLAST seed-and-extend heuristic: exact k-mer seeds anchor… Coevolution Contact Map: How AI Reads Structure from SequenceNew📱Generate a synthetic multiple sequence alignment, rank residue pairs by mutual information,… Gene Network Inference LabNew📱Reconstruct a hidden gene regulatory network from noisy simulated expression data: compare… AI Protein Fitness Landscape ExplorerNew📱Interactive 3D protein-engineering simulator where candidate sequences climb a stability /… Droplet Microfluidics: Single-Cell Encapsulation & Poisson LoadingNew📱Watch a flow-focusing microfluidic junction encapsulate individual cells and barcoded beads… ATAC-seq Tagmentation: Mapping Open ChromatinNew📱Watch Tn5 transposase tagment accessible chromatin in 3D while nucleosome-packed DNA blocks… ChIP-seq / ATAC-seq Peak CallerNew📱Sample a genomic read-pileup track from a Poisson process, tune binding-site enrichment and… Spectral Unmixing: Multiplexed Fluorescence Panel SolverNew📱Fluorophore emission spectra bleed across detector channels and autofluorescence adds… Spatial Spot Deconvolution: Unmixing Tissue NichesNew📱Each spatial transcriptomics spot pools mRNA from several neighbouring cells at once; this… DNA Data Storage: Redundancy & Majority-Vote DecodingNew📱Encode a byte payload into synthetic DNA bases, synthesize redundant molecule copies with a… Metabolic Control Analysis: Flux Control CoefficientsNew📱Tune the Vmax of five enzymes in a linear metabolic pathway and watch flux control… Cell-Free ATP Regeneration KineticsNew📱Model the energy-regeneration system inside a cell-free protein synthesis reactor: a… Transcription Factor Binding Site ScannerNew📱Scan a 3D DNA double helix with a position-weight-matrix (PWM) motif model, computing real… Six-Frame ORF Finder: Codon-Bias Gene PredictionNew📱Scan a real 3D DNA double helix across all six reading frames for ATG-to-stop open reading… qPCR Amplification Curve & Ct Value SimulatorNew📱An interactive 3D real-time PCR simulator: DNA copies double each cycle inside a reaction… Neighbor-Joining Phylogenetic Tree BuilderNew📱Watch the real neighbor-joining algorithm build an evolutionary tree step by step from a… Bioinformatics: Sequence Alignment DP-Matrix ExplorerNew📱Watch the Needleman-Wunsch dynamic-programming matrix build itself into a 3D score landscape… Biomarker Panel Search SpaceNew📱Live-timed computational-complexity lab for systems biology: benchmark real O(n) mean, O(n… Biomarker Panel Search SpaceNewLive-timed computational-complexity lab for systems biology: benchmark real O(n) mean, O(n… De Bruijn Genome AssemblyNew📱Break overlapping DNA reads into k-mers, watch a de Bruijn graph build node by node and edge… Guide-RNA Off-Target Risk ScannerNew📱Design a CRISPR guide RNA and run a genome-wide sequence-alignment search live: compare a… Genome Sequencing — Shotgun Assembly SimulatorNew📱Interactive shotgun DNA sequencing simulator: shatter a genome into overlapping reads, tune… Metagenomics Pipeline SimulatorNew📱Interactive shotgun-metagenomics pipeline: sample a mixed community of environmental DNA… Sequence Alignment Visualizer: Needleman-Wunsch Dynamic ProgrammingNew📱Watch the Needleman-Wunsch dynamic-programming matrix for global DNA sequence alignment fill… Sequence Alignment: DNA Matching in 3DNew📱Explore how bioinformatics algorithms align DNA sequences: watch a live 3D… Sequence Alignment Explorer: Needleman-Wunsch in 3DNew📱Watch two DNA sequences get globally aligned in real time: explore the 3D… Genome Read-Alignment ExplorerNew📱Watch a sliding-window sequence-alignment algorithm scan a 3D genome for the best match to a… Bioinformatics Pipeline: Read QC, Alignment & Variant CallingNew📱Watch simulated DNA reads flow through a bioinformatics pipeline in 3D: quality filtering,… Bioinformatics Pipelines: Sequencing and AnalysisNew📱Watch a 3D sequencing pipeline turn raw reads into an aligned genome pileup: tune read… Mass Spec Protein IdentifierNew📱Run a 3D mass spectrometry proteomics workflow — digest a protein, tune length, missed… Single-Cell Sequencing ExplorerNew📱Run a 3D single-cell RNA-seq pipeline — encapsulate cells in droplets, tune loading… Single-Cell Multi-omics Integration ExplorerNew📱Integrating scRNA-seq, ATAC-seq, and spatial assays: data models, alignment, denoising,… Genomics Pipeline Flow SimulatorNew📱Raw sequencing reads flow through a pipeline graph — QC, alignment, variant calling,… Spatial Proteomics Tissue MapNew📱A grid of tissue coordinates lights up with protein expression intensity as an… Spatial Multi-Omics MapNew📱A tissue-coordinate grid captures transcriptomic and proteomic signal jointly at single-cell… Metabolic Flux Network SimulatorNew📱Metabolite nodes exchange flux along a reaction network toward a biomass objective: tune… Biofoundry Design-Build-Test-Learn SimulatorNew📱An automated biofoundry cycles constructs through Design-Build-Test-Learn stage nodes: tune… Cell-Free Biomanufacturing SimulatorNew📱Ribosomes and enzyme cascades in a cell-free extract bind mRNA template sites and translate… Genomic Cohorts: Understanding Population-Level GeneticsNew📱Explore a 3D Manhattan-plot landscape where pillar height encodes statistical significance… Cell Atlas Overview: Building Reference Maps of Human CellsNew📱Interactive 3D point-cloud of single-cell atlas construction: adjust cluster count, batch… Computational Biology та обчислювальна біологіяNew📱Computational Biology: genomics, proteomics, drug discovery — visualized here as a… Bioinformatics Pipeline SimulationNew📱This simulation models a bioinformatics pipeline used to analyze biological data, from… Bioinformatics SimulatorNew📱This simulation allows users to explore the core principles of bioinformatics by analyzing… Computational BiologyNew📱This simulation demonstrates the use of computational methods in biological research. It… BraTS Brain Tumor Segmentation — Dice Score ExplorerNew📱Adjust a simulated AI tumor-segmentation region against a fixed ground-truth brain tumor… CheXpert Uncertainty LabNew📱Set simulated confidence scores across five chest X-ray findings and switch between… ICU Organ-Failure Severity Score CalculatorNew📱Score six organ systems on the standard published SOFA scale and see the live 0-24 total… Skin Lesion ABCDE Risk-ScoreNew📱Adjust Asymmetry, Border, Color, Diameter and Evolution sliders to see a procedurally-drawn… Lung Nodule Lung-RADS Risk ClassifierNew📱Simulate how a CT-detected lung nodule is triaged using the real published Lung-RADS… ECG Waveform Feature ClassifierNew📱Adjust heart rate, QRS duration, PR interval and ST elevation to watch a stylized ECG… Histopathology Metastasis Detection & pN Staging SimulatorNew📱Simulate how whole-slide-image AI trained on datasets like CAMELYON flags tumor-positive… Molecular Docking: Ligand Binding SearchNew📱Interactive 3D lab where a small ligand molecule tumbles through many trial poses inside a… De Novo Protein DesignNew📱Interactive 3D simulator where a residue chain begins as scrambled noise and a… DNA SequencingNew📱Smith-Waterman sequence alignment, SNP detection and bioinformatics algorithms for DNA…