Course Details
| Course Code | Course Name | Credit Type |
|---|---|---|
| CUBI2547 | PROGRAMMING FOR BIOSCIENCES (BIOPYTHON) | 0+2+2 |
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| Course Code | Course Name | Credit Type |
|---|---|---|
| CUBI2547 | PROGRAMMING FOR BIOSCIENCES (BIOPYTHON) | 0+2+2 |
This course introduces students to advanced Biopython functionalities. Using falsification as a core pedagogical approach, students will critically evaluate and test various Biopython methods through hypothesis testing and iterative experimentation.
| CO / PO | PO1 Engineering Knowledge |
PO2 Problem Analysis |
PO3 Design / Development |
PO4 Investigation |
PO5 Modern Tool Usage |
PO6 Societal Impact |
PO7 Environment & Sustainability |
PO8 Ethics |
PO9 Team Work |
PO10 Communication |
PO11 Project Mgmt & Finance |
PO12 Life-long Learning |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| CO1 | 3 | 2 | – | – | 3 | 2 | – | – | – | – | – | – |
| CO2 | – | 3 | 3 | 3 | 3 | – | – | – | – | – | – | – |
| CO3 | – | – | 3 | 3 | 3 | 2 | 2 | 2 | 3 | 3 | 2 | 3 |
Click below to access the official Biopython tutorial:
| S.No. | Title | Author(s) / Link |
|---|---|---|
| 1 | Biopython Tutorial and Cookbook | Jeff Chang, Brad Chapman, Iddo Friedberg, Thomas Hamelryck, Michiel de Hoon, Peter Cock, Tiago Antao, Eric Talevich, Bartek Wilczyński |
| Session No. | Topic / Title | Activities / Tasks | Expected Outcome |
|---|---|---|---|
| MODULE 1 — Biopython Fundamentals (Sessions 1–10) | |||
| P1 | Introduction to Biopython | Install Biopython, verify environment | Understand Biopython setup |
| P2 | Working with Seq Objects | Create, slice, edit sequences | Perform basic sequence operations |
| P3 | Sequence Transformations | Case changes, length, composition | Manipulate sequence structure |
| P4 | Parsing FASTA Files | Read/write FASTA via SeqIO | Import FASTA sequences |
| P5 | Parsing GenBank Files | Extract annotations, metadata | Understand annotated data |
| P6 | Falsification Task 1 | Compare manual vs. Biopython parsing | Evaluate parsing efficiency |
| P7 | Reverse Complement & GC% Calculation | Compute complement, GC% | Perform nucleotide analysis |
| P8 | Transcription & Transliteration | DNA→RNA workflows | Model biological processes |
| P9 | Translation | Translate ORFs, validate protein outputs | Perform accurate translation |
| P10 | Mini-Project 1 | Build FASTA parsing workflow | Create automated sequence pipeline |
| MODULE 2 — Advanced Sequence Handling (Sessions 11–20) | |||
| P11 | SeqRecord Object | Create annotated records | Understand container structure |
| P12 | Annotation & Qualifiers | Add features, metadata | Build rich annotations |
| P13 | Location Objects | Start/stop, fuzzy locations | Manage feature coordinates |
| P14 | GenBank Feature Extraction | CDS, exons, UTRs | Analyze feature-rich sequences |
| P15 | Falsification Task 2 | Compare annotated vs plain sequences | Interpret annotation importance |
| P16 | Writing FASTA & GenBank | Export sequences | Create standard format files |
| P17 | Sequence Dictionaries | Build lookup maps | Efficient sequence retrieval |
| P18 | Automated Parsing Scripts | Batch parse multiple files | Create automation workflows |
| P19 | Error Handling | try/except parsing | Robust processing |
| P20 | Mini-Project 2 | Genome annotation workflow | Understand complex annotations |
| MODULE 3 — File Parsing, BLAST & Entrez (Sessions 21–30) | |||
| P21 | File Reading/Writing | SeqIO, AlignIO | Manage data formats |
| P22 | Sequence Dictionaries | Map IDs → sequences | Fast retrieval |
| P23 | NCBI Entrez Basics | esearch, efetch | Retrieve remote data |
| P24 | NCBI Metadata Access | esummary, elink | Access biological metadata |
| P25 | Fetching FASTA/GenBank | Automated downloads | Streamline data access |
| P26 | Falsification Task 3 | Speed comparison: manual vs Biopython | Understand efficiency differences |
| P27 | Running BLAST Online | qblast execution | Perform similarity search |
| P28 | Parsing BLAST Output | XML parsing | Interpret BLAST results |
| P29 | Local BLAST Setup | BLAST+ installation | High-speed alignment |
| P30 | Mini-Project 3 | BLAST automation pipeline | Integrate BLAST into workflows |
| MODULE 4 — Multiple Sequence Alignment (Sessions 31–40) | |||
| P31 | Alignment Basics | Load alignment files | Interpret alignment structure |
| P32 | Pairwise Alignment | globalxx, localxx | Perform pairwise comparisons |
| P33 | ClustalW Alignment | Execute MSA | Generate standard MSA |
| P34 | MUSCLE Alignment | Run advanced MSA | Generate high-quality alignments |
| P35 | Alignment Slicing | Column, row slicing | Analyze variability |
| P36 | Array Representation | Convert alignment to arrays | Perform numeric analysis |
| P37 | Falsification Task 4 | Compare MSA tools vs reference | Evaluate alignment accuracy |
| P38 | Writing MSA Files | Export aligned sequences | Create publication files |
| P39 | MSA Visualization | Plot alignment patterns | Visual analysis of MSA |
| P40 | Mini-Project 4 | Comparative alignment project | Interpret alignment differences |
| Session | Topic | Activities | Outcome |
|---|---|---|---|
| P41 | Introduction to AlignIO | Read alignment files; navigate objects | Understand alignment structures |
| P42 | Pairwise Alignment | Use globalxx, localxx scoring | Perform pairwise alignment |
| P43 | ClustalW Execution | Run ClustalW via Biopython | Generate MSA using ClustalW |
| P44 | MUSCLE Alignment | Perform MUSCLE-based alignment | Compare MSA tools |
| P45 | Alignment Slicing | Slice columns/rows; analyze variation | Extract region-specific insights |
| P46 | Alignment Arrays | Convert alignments to arrays | Enable numerical alignment analysis |
| P47 | Falsification: MSA Accuracy | Compare aligners with references | Evaluate tool accuracy |
| P48 | Writing MSA Files | Export aligned sequences | Save MSA in various formats |
| P49 | MSA Visualization | Plot and analyze alignments | Interpret alignment visually |
| P50 | Mini-Project | Comparative alignment study | Complete an MSA workflow |
| Session | Topic | Activities | Outcome |
|---|---|---|---|
| P51 | Introduction to NCBI Entrez | Use esearch, efetch | Retrieve biological data |
| P52 | Advanced Entrez Queries | Filters, summaries | Master NCBI API usage |
| P53 | Online BLAST (qblast) | Submit BLAST jobs | Perform similarity searches |
| P54 | Parsing BLAST XML | Extract hits, scores, e-values | Analyze BLAST results |
| P55 | Local BLAST Setup | Install BLAST+ and run locally | Perform offline BLAST searches |
| P56 | Using SearchIO | Parse BLAST, HMMER | Handle multiple search outputs |
| P57 | Falsification: BLAST Efficiency | Compare manual vs Biopython parsing | Evaluate automation benefits |
| P58 | Batch BLAST Automation | Run BLAST on multiple sequences | Build BLAST pipelines |
| P59 | BLAST Visualization | Plot BLAST metrics | Interpret BLAST results graphically |
| P60 | Mini-Project | BLAST-based annotation workflow | Complete annotated BLAST pipeline |
| Session | Topic | Activities | Outcome |
|---|---|---|---|
| P61 | Intro to Bio.Phylo | Load and inspect trees | Understand tree structures |
| P62 | Tree I/O Operations | Read/write Newick, Nexus files | Handle phylogenetic formats |
| P63 | Tree Visualization | Plot trees using Bio.Phylo | Interpret phylogenetic trees |
| P64 | Tree Comparison Methods | Topology comparison, distance metrics | Evaluate evolutionary relationships |
| P65 | Gene Diagram Visualization | Use GenomeDiagram | Draw gene structures |
| P66 | Machine Learning Basics | KNN, Regression demos | Link ML with genomics |
| P67 | Falsification Task: Phylogeny | Compare manual vs. Biopython trees | Validate tool-based phylogenies |
| P68 | Integrated Workflow I | BLAST → MSA → Tree pipeline | Understand end-to-end analysis |
| P69 | Integrated Workflow II | Build full evolutionary workflow | Execute advanced pipelines |
| P70 | Final Practical Project | Presentation of pipeline results | Demonstrate complete mastery |