Computational Biology

ACTIVE STREAM

Analyze genomes, simulate protein folding, and discover new drugs.

Projects

Project 1: The DNA Hard Drive

Learn to encode digital data into DNA sequences. Explore the future of biological storage.

Project 2: The Virtual Lab

Simulate essential molecular biology techniques: PCR, Gel Electrophoresis, and Restriction Digests.

2.1 PCR Simulation

2.1.1 Exponential Growth 2.1.2 Efficiency 2.1.3 Primer Binding 2.1.4 Melting Temp 2.1.5 Thermal Cycler

2.2 Restriction Enzymes

2.2.1 Recognition Sites 2.2.2 Digestion 2.2.3 Sticky Ends 2.2.4 Double Digest 2.2.5 Ligation

2.3 Gel Electrophoresis

2.3.1 Migration Rate 2.3.2 The Ladder 2.3.3 Run the Gel 2.3.4 Resolution 2.3.5 Voltage

2.4 Sequencing

2.4.1 Sanger Sequencing 2.4.2 Chromatogram 2.4.3 Reads 2.4.4 Coverage 2.4.5 Simple Assembly

2.5 Capstone: Cloning Experiment

2.5.1 Design Primers 2.5.2 Amplify 2.5.3 Digest 2.5.4 Ligate 2.5.5 Verify

Project 3: The Gene Editor

Design CRISPR-Cas9 systems. Find targets, avoid off-targets, and edit the genome.

3.1 CRISPR Basics

3.1.1 PAM Finder 3.1.2 Guide RNA 3.1.3 GC Efficiency 3.1.4 Poly-T Terminator 3.1.5 Complementarity

3.2 Off-Target Search

3.2.1 Exact Matches 3.2.2 Mismatches 3.2.3 Seed Region 3.2.4 Genome Scan 3.2.5 Scoring

3.3 DNA Repair

3.3.1 NHEJ 3.3.2 Frameshift 3.3.3 HDR 3.3.4 Knockout 3.3.5 Knock-in

3.4 Prime Editing

3.4.1 pegRNA 3.4.2 Nickase 3.4.3 RT Template 3.4.4 Flap Cleavage 3.4.5 Ligation

3.5 Capstone: Cure a Disease

3.5.1 Identify Mutation 3.5.2 Design Guide 3.5.3 Design Template 3.5.4 Simulate Edit 3.5.5 Verify Cure

Project 4: The Bio-Computer

Build biological circuits. Logic gates, toggle switches, and oscillators inside cells.

4.1 Genetic Parts

4.1.1 Promoters 4.1.2 RBS 4.1.3 CDS 4.1.4 Terminators 4.1.5 Cassette

4.2 Logic Gates

4.2.1 NOT Gate 4.2.2 AND Gate 4.2.3 OR Gate 4.2.4 NAND Gate 4.2.5 Truth Table

4.3 Genetic Memory

4.3.1 Toggle Switch 4.3.2 Hysteresis 4.3.3 Stability 4.3.4 SR Latch 4.3.5 Counter

4.4 Oscillators

4.4.1 The Repressilator 4.4.2 Simulation 4.4.3 Phase Plot 4.4.4 Period 4.4.5 Synchronization

4.5 Capstone: Edge Detector

4.5.1 Light Sensor 4.5.2 Diffusion 4.5.3 Logic Network 4.5.4 Run Plate 4.5.5 Final Image

Project 5: The Outbreak Tracer

Track a virus. Align sequences, build phylogenetic trees, and find patient zero.

5.1 Sequence Alignment

5.1.1 Hamming Distance 5.1.2 Dot Plot 5.1.3 Scoring 5.1.4 Needleman-Wunsch 5.1.5 Traceback

5.2 Distance Matrix

5.2.1 Pairwise Comparison 5.2.2 Jukes-Cantor 5.2.3 Normalization 5.2.4 Heatmap 5.2.5 Closest Pair

5.3 Tree Building

5.3.1 UPGMA Step 5.3.2 Newick Format 5.3.3 Build Tree 5.3.4 Branch Length 5.3.5 Rooting

5.4 Epidemiology

5.4.1 Patient Zero 5.4.2 R0 Calculation 5.4.3 SIR Model 5.4.4 Mutation Rate 5.4.5 Transmission Chain

5.5 Capstone: The Pandemic

5.5.1 Load Data 5.5.2 Compute Tree 5.5.3 Visualize 5.5.4 Clusters 5.5.5 Predict

Project 6: The Cell Factory

Engineer metabolism. Optimize pathways to turn cells into chemical factories.

6.1 Stoichiometry

6.1.1 Reactions 6.1.2 S-Matrix 6.1.3 Mass Balance 6.1.4 Bounds 6.1.5 Objective

6.2 Flux Balance Analysis

6.2.1 LP Problem 6.2.2 The Solver 6.2.3 Growth Rate 6.2.4 Flux Map 6.2.5 Shadow Prices

6.3 Engineering

6.3.1 Knockout 6.3.2 Overexpression 6.3.3 Production Envelope 6.3.4 Heterologous 6.3.5 Yield

6.4 Regulation

6.4.1 Feedback 6.4.2 Gene Reg 6.4.3 dFBA 6.4.4 Diauxic Shift 6.4.5 Toxicity

6.5 Capstone: Biofuel

6.5.1 Design 6.5.2 Optimize 6.5.3 Scale Up 6.5.4 Cost 6.5.5 Carbon Footprint

Project 7: The Protein Folder

Solve the folding problem. Simulate how amino acid chains fold into 3D structures.

7.1 HP Model

7.1.1 Hydrophobicity 7.1.2 Lattice 7.1.3 Energy 7.1.4 Collisions 7.1.5 Random Walk

7.2 Optimization

7.2.1 Monte Carlo 7.2.2 Metropolis 7.2.3 Annealing 7.2.4 Genetic Alg 7.2.5 Landscape

7.3 Secondary Structure

7.3.1 Alpha Helix 7.3.2 Beta Sheet 7.3.3 Ramachandran 7.3.4 Disulfides 7.3.5 Loops

7.4 Prediction

7.4.1 Homology 7.4.2 Threading 7.4.3 Rosetta Lite 7.4.4 Contact Map 7.4.5 RMSD

7.5 Capstone: AlphaFold Mini

7.5.1 Features 7.5.2 Neural Net 7.5.3 Gradient Descent 7.5.4 Refinement 7.5.5 View 3D

Project 8: The Neural Interface

Decode the brain. Analyze spike trains, sort neurons, and control a robotic arm.

8.1 Spike Processing

8.1.1 Raw Signal 8.1.2 Thresholding 8.1.3 Waveform 8.1.4 Filtering 8.1.5 SNR

8.2 Spike Sorting

8.2.1 PCA 8.2.2 Clustering 8.2.3 ISI 8.2.4 Templates 8.2.5 Overlap

8.3 Decoding

8.3.1 Raster Plot 8.3.2 PSTH 8.3.3 Tuning Curve 8.3.4 Population Vector 8.3.5 Kalman Filter

8.4 Stimulation

8.4.1 Charge Balance 8.4.2 Activation 8.4.3 Patterned Stim 8.4.4 Closed Loop 8.4.5 Plasticity

8.5 Capstone: Mind Control

8.5.1 Train 8.5.2 Control 8.5.3 Reach 8.5.4 Adaptation 8.5.5 Hand

Project 9: The Drug Hunter

Discover new medicines. Molecular docking, virtual screening, and ADMET prediction.

9.1 Molecules

9.1.1 SMILES 9.1.2 Graph 9.1.3 3D Coords 9.1.4 Fingerprints 9.1.5 Similarity

9.2 Docking

9.2.1 Pocket 9.2.2 Scoring 9.2.3 Optimization 9.2.4 Flexibility 9.2.5 Induced Fit

9.3 ADMET

9.3.1 Lipinski Rules 9.3.2 LogP 9.3.3 Toxicity 9.3.4 Metabolism 9.3.5 BBB

9.4 Library Design

9.4.1 Scaffold 9.4.2 R-Groups 9.4.3 Diversity 9.4.4 Synthesis 9.4.5 Virtual Screen

9.5 Capstone: The Cure

9.5.1 Target ID 9.5.2 Growing 9.5.3 Optimize 9.5.4 Trial 9.5.5 Approval

Project 10: The Artificial Life

Create life. Cellular automata, genetic algorithms, and evolutionary simulations.

10.1 Cellular Automata

10.1.1 Game of Life 10.1.2 Patterns 10.1.3 Entropy 10.1.4 Langton's Ant 10.1.5 Rule 30

10.2 Genetic Algorithms

10.2.1 Population 10.2.2 Fitness 10.2.3 Selection 10.2.4 Crossover 10.2.5 Evolution

10.3 Dynamics

10.3.1 Genetic Drift 10.3.2 Fixation 10.3.3 Selection Coeff 10.3.4 Muller's Ratchet 10.3.5 Speciation

10.4 Digital Organisms

10.4.1 Instruction Set 10.4.2 Virtual CPU 10.4.3 Replication 10.4.4 Competition 10.4.5 Adaptation

10.5 Capstone: The Ecosystem

10.5.1 World 10.5.2 Predator-Prey 10.5.3 Brains 10.5.4 Coevolution 10.5.5 Extinction

Total Projects

Estimated Time

40+ hrs

Difficulty Range

BeginnerIntermediateAdvanced

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