List of MicroSims for Bioinformatics

Interactive Micro Simulations to help students learn bioinformatics fundamentals through exploration and experimentation.

• AlphaFold Prediction Pipeline

  

  Interactive visualization of the AlphaFold protein structure prediction pipeline, from sequence input through multiple sequence alignment to 3D structure output.

• BFS vs DFS Traversal Comparison

  

  Side-by-side comparison of breadth-first and depth-first graph traversal algorithms, showing visit order and frontier expansion on the same graph.

• Biological Database Ecosystem

  

  Interactive vis-network diagram of the major biological databases and their interconnections, from sequence repositories to structure and pathway databases.

• Anatomy of a Biomedical Knowledge Graph

  

  Interactive vis-network showing the core entity types and relationships in a biomedical knowledge graph, including genes, diseases, drugs, and pathways.

• Bipartite Metabolic Graph Structure

  

  Interactive vis-network showing the bipartite structure of metabolic networks with separate node types for metabolites and reactions.

• Bipartite Metabolic Sub-network

  

  Interactive p5.js visualization of a metabolic sub-network as a bipartite graph, showing metabolite and enzyme node partitions with reaction edges.

• Central Dogma and Its Exceptions

  

  Interactive diagram of the central dogma (DNA → RNA → Protein) with clickable arrows revealing standard pathways and exceptions including reverse transcription, RNA replication, prions, and functional ncRNAs.

• Central Dogma Information Flow

  

  Step-through visualization of genetic information flow from DNA through transcription and mRNA processing to translation and protein folding, with bioinformatics data formats at each stage.

• Codon Table Explorer

  

  Translate mRNA sequences into amino acid chains using the standard genetic code. Supports custom input, random sequence generation, and reading frame visualization.

• Co-Expression Network and Module Detection

  

  Interactive visualization of gene co-expression networks with correlation-based edge weights and community detection to identify co-regulated gene modules.

• Contact Map and Residue Interaction Network

  

  Dual-view visualization showing a protein contact map alongside its residue interaction network, linking 2D distance matrices to 3D structural contacts.

• De Bruijn Graph Construction

  

  Step-by-step construction of a de Bruijn graph from sequencing reads, demonstrating how k-mer overlap graphs enable genome assembly.

• Disease Module in the Human Interactome

  

  Interactive vis-network showing how disease-associated genes cluster into modules within the human protein-protein interaction network.

• Drug-Drug Interaction Network

  

  Interactive vis-network visualization of drug-drug interactions showing pharmacological relationships and potential adverse interaction pathways.

• Drug-Target-Disease Knowledge Graph

  

  Interactive vis-network showing the tripartite relationships between drugs, their protein targets, and associated diseases for drug repurposing exploration.

• Dynamic Programming Matrix Visualization

  

  Interactive visualization of the Needleman-Wunsch dynamic programming matrix for global sequence alignment, with traceback path highlighting.

• FASTQ Quality Control Pipeline

  

  Interactive pipeline visualization showing the steps of FASTQ quality control from raw reads through adapter trimming, quality filtering, and summary statistics.

• Flux Balance Analysis Formulation

  

  Interactive visualization of flux balance analysis showing the stoichiometric matrix, flux constraints, and linear programming optimization of metabolic networks.

• The Four Omics Layers

  

  Interactive vis-network diagram of the four major omics layers (genomics, transcriptomics, proteomics, metabolomics) and the data flow between them.

• Gene Tree vs Species Tree Discordance

  

  Side-by-side comparison of gene trees and species trees showing how incomplete lineage sorting and horizontal gene transfer cause topological discordance.

• Genome Assembly Pipeline Overview

  

  Interactive pipeline visualization of the genome assembly process from raw reads through error correction, contig assembly, scaffolding, and quality assessment.

• Graph-Based Discovery Pipeline

  

  Interactive vis-network showing the stages of graph-based biological discovery from data integration through knowledge graph construction to hypothesis generation.

• Graph Data Model Design Process

  

  Interactive vis-network visualization of the iterative process for designing graph data models for biological knowledge representation.

• Graphlet Orbits and Network Comparison

  

  Interactive visualization of graphlet subgraph patterns and orbit positions used for network motif analysis and biological network comparison.

• Integrated Knowledge Graph Pipeline

  

  Interactive vis-network showing the end-to-end pipeline for building an integrated biomedical knowledge graph from heterogeneous data sources.

• Knowledge Graph Construction Pipeline

  

  Interactive vis-network visualization of the knowledge graph construction process from entity extraction through relation mapping to graph population.

• Learning Graph Viewer

  

  Interactive vis-network visualization of all course concepts and their dependencies. Search, filter, and explore the bioinformatics learning graph.

• Louvain vs. Leiden Community Detection

  

  Side-by-side comparison of the Louvain and Leiden community detection algorithms on the same network, highlighting resolution and quality differences.

• Metabolic Network Overview

  

  Interactive vis-network overview of a metabolic network showing metabolites, enzymes, and reaction pathways with pathway highlighting.

• Metabolomics to Network Mapping Pipeline

  

  Interactive pipeline showing how metabolomics data is processed and mapped onto metabolic network models for pathway analysis.

• Molecular Docking and Protein-Ligand Graph

  

  Interactive visualization of molecular docking showing protein-ligand binding interactions as a graph with binding affinity scores and interaction types.

• Module Detection in PPI Networks

  

  Interactive visualization of protein complex and functional module detection within protein-protein interaction networks using clustering algorithms.

• Mutation Types Explorer

  

  Apply SNPs, insertions, deletions, and frameshifts to a DNA sequence and immediately see the downstream effect on mRNA codons and protein sequence with automatic mutation classification.

• Network Model Comparison

  

  Compare Erdos-Renyi, Barabasi-Albert, and Watts-Strogatz network models side by side with adjustable parameters and degree distribution charts.

• Node2Vec Biased Random Walk

  

  Interactive visualization of the node2vec biased random walk algorithm showing how return parameter p and in-out parameter q control walk behavior for graph embedding.

• Patient Similarity Network Construction

  

  Interactive visualization of how patient similarity networks are constructed from clinical features and used for disease subtype identification.

• Phylogenetic Network with Reticulation Events

  

  Interactive vis-network showing phylogenetic networks with reticulation events such as hybridization, horizontal gene transfer, and recombination.

• Rooted and Unrooted Phylogenetic Trees

  

  Side-by-side comparison of rooted and unrooted phylogenetic tree representations showing how the presence of an outgroup changes tree interpretation.

• PPI Knowledge Graph Schema

  

  Interactive vis-network showing the schema design for a protein-protein interaction knowledge graph with entity types, relationships, and properties.

• PPI Network Topology Explorer

  

  Interactive exploration of PPI network topology metrics including degree distribution, betweenness centrality, clustering coefficient, and hub identification.

• Profile HMM Architecture

  

  Interactive vis-network diagram of a profile Hidden Markov Model showing match, insert, and delete states with transition probabilities for sequence family modeling.

• Prokaryotic vs Eukaryotic Cell

  

  Dual-panel interactive diagram comparing prokaryotic and eukaryotic cell structures with explore mode, quiz mode, and labeled callouts highlighting shared and unique features.

• Protein Interaction Network Overview

  

  Interactive overview of a protein-protein interaction network with node coloring by functional category and edge types representing different interaction evidence.

• Protein Structure Hierarchy

  

  Interactive visualization of the four levels of protein structure showing primary sequence, secondary elements, tertiary folding, and quaternary assembly.

• Protein Structure Levels

  

  Click-to-expand display of the four levels of protein structure (primary, secondary, tertiary, quaternary) with stabilizing forces and bioinformatics data format connections.

• RNA-Seq Pipeline Overview

  

  Interactive pipeline visualization of the RNA-Seq analysis workflow from raw reads through alignment, quantification, normalization, and differential expression analysis.

• Sequence Similarity Network

  

  Interactive vis-network showing how pairwise sequence similarity scores define edges in a network used for protein family clustering and functional annotation transfer.

• Cell Signaling Cascade Overview

  

  Interactive vis-network visualization of a cell signaling cascade from receptor activation through kinase cascades to transcription factor activation and gene expression.

• Single-Cell Clustering and Trajectory

  

  Interactive visualization of single-cell RNA-seq data showing dimensionality reduction, cell type clustering, and pseudotime trajectory inference.

• Text Mining Pipeline for Knowledge Graph Population

  

  Interactive vis-network showing the NLP pipeline for extracting biological entities and relationships from literature to populate knowledge graphs.

• The Transcriptome Landscape

  

  Interactive visualization of the transcriptome landscape showing gene expression levels across conditions with differential expression highlighting.

• Variation Graph for a Genomic Region

  

  Interactive visualization of a variation graph showing how SNPs, insertions, and deletions create alternate paths through a reference genomic sequence.

• Volcano Plot for Differential Expression

  

  Interactive volcano plot showing fold change vs. statistical significance for differential gene expression, with adjustable thresholds for identifying up- and down-regulated genes.