Computational Biology &
Biostatistics Practice Engine
Interactive analytical suite featuring live sequence manipulation, multi-factor ANOVA statistical validation, dynamic programming pairwise alignments, and macromolecular 3D visualization.
Live Biopython Sequence Studio
Directly compute Central Dogma operations, melting temperatures ($T_m$), and physicochemical properties in your browser.
Dynamic Programming Pairwise Aligner
Interactive implementation of Needleman-Wunsch (Global) and Smith-Waterman (Local) dynamic alignments.
Biostatistics ANOVA Laboratory
Simulate pharmacokinetic drug actions, evaluate variance partitioning, and run Tukey's HSD post-hoc contrasts.
| Contrast | Mean Diff | q-statistic | Status |
|---|
One-Way ANOVA Source of Variation Table
| Source of Variation | Sum of Squares ($SS$) | Degrees of Freedom ($df$) | Mean Square ($MS$) | $F$-Statistic | $p$-value |
|---|
3D Biomolecular Structure Viewer
Direct WebGL rendering of protein structures from RCSB and local crystallographic datasets (`structural_biology/1fat.cif`).
Practice Notebooks & Portfolio Catalog
Explore 18+ hands-on notebooks spanning sequence algorithms, statistical ANOVA modeling, and structural bioinformatics.
Obsidian + LLM Knowledge Wiki
An interlinked knowledge network connecting fundamental biological concepts, API entities, and synthesis documents.
One-Way ANOVA
Decomposes experimental variance into treatment vs residual error. Validates single-factor drug dose assays with F-ratio hypothesis tests.
Two-Way ANOVA & Interaction
Quantifies synergistic and antagonistic multi-variable dependencies (e.g., drug concentration × cell line mutation status).
Tukey's HSD Post-Hoc
Controls Family-Wise Error Rate (FWER) across all pairwise mean contrasts following ANOVA omnibus significance.
Central Dogma Sequence Operations
Algorithmic translation, transcription, open reading frame (ORF) discovery, and codon dictionary lookups in Bio.Seq.
Pairwise Sequence Alignment
Dynamic programming matrix scoring (Needleman-Wunsch global and Smith-Waterman local) via modern PairwiseAligner.
Protein-Ligand Profiling
3D macromolecular coordinate parsing, crystallographic CIF atom extraction, and spatial distance contact metrics.
Bio.Seq
Fundamental biological sequence representation supporting IUPAC alphabets, translation tables, and reverse complementation.
Bio.SeqIO
Stream-oriented multi-format parser for FASTA, FASTQ, GenBank (.gbk), EMBL, and SwissProt formats.
Bio.Align.PairwiseAligner
Modern high-performance replacement for legacy pairwise2, offering affine gap penalties and configurable substitution matrices.
Bio.PDB & MMCIFParser
Crystallographic coordinate parsing, atom-residue-chain-model hierarchies, and spatial vector mathematics.
statsmodels & pingouin
Rigorous statistical testing frameworks for ordinary least squares (OLS) variance partitioning and post-hoc diagnostics.
Bio.Blast & NCBI Entrez
Programmatic interface to NCBI BLAST web servers and E-utilities for automated database queries.
Biopython Modern API Migration
Comprehensive transition guide from legacy Biopython modules (Bio.pairwise2, Bio.Alphabet) to modern Python 3.12+ conventions.
Computational Biochemistry & Stats Pipeline
End-to-end operational blueprint integrating wet-lab biochemical assay results with automated ANOVA validation routines.
Obsidian-LLM Wiki Integration
The human-agent-Obsidian triad schema for continuous, linted, self-documenting research knowledge graphs.
Educational Slide Decks & Documentation
Download and review the lecture presentations covering Biopython Seq & Align modules (presentations/BioPython_DOC1.pptx, BioPython_DOC2.pptx) and technical manual.