Digital Biology: A survey of topics in bioinformatics and functional genomics
BIOL-L/MLS-M 388 Spring 2023
Course description
BIOL L388 DB
Class times and locations
Tues, Thur 11:30a - 12:45p (Credits: 3.0); Swain East (SE) 010
Tentative schedule (click the icon for a 
version)
| DAY | DATE | LECTURE | TOPIC | LECTURER |
| Tues | Jan 10 | 0.1 | OrientationWhat is Digital Biology? Topics in bioinformatics, scope of class, and resources Motivation New virus outbreak: BBC Jan. 19, 2020 New virus outbreak: BBC Jan. 20, 2020 2023: XBB.1.5 NCBI SARS-CoV-2 Precedence: The Fastest Outbreak - connection to bioinformatics work Bioinformatics Databases and Computing Resources National Center for Biotechnology Information (NCBI), a great starting point for "anything" bioinformatics Mapping biological question onto computational problems: The modeling spiral Sequence gazing: the famous TATA-box AlphaFold | Volker Brendel |
| Thur | Jan 12 | 1.1 | Module 1: Bioinformatics resources and workspacesUbuntu on Windows: ... a quick way to get to a command line terminal Virtual Machines: VirtualBox Linux Basics Basic UNIX shell tutorial Command-line bootcamp The UNIX Shell The UNIX Shell: Summary of Basic Commands vi(m) editor tutorial | Volker Brendel |
| Tues | Jan 17 | 1.2 | Customizing your Linux work space Getting code with git Working with NCBI data | Volker Brendel |
| Thur | Jan 19 | 1.3 | Command line access to NCBI data: EDirect Entrez Direct NCBI Sequence search fields MEDLINE/PubMed search fields | Volker Brendel |
| Tues | Jan 24 | 1.4 | Review: Command-line bootcamp | Volker Brendel |
| Thur | Jan 26 | 1.5 | Review: Statistical evaluation of sequence features Using generic Linux commands to process sequence data (at least for previews or consistency checks ...) Home Work Assignment 1 posted. Due: Feb. 2, 6:00pm | Volker Brendel |
| Tues | Jan 31 | 2.1 | Module 2: Pairwise Sequence AlignmentMotivation How Do We Compare Biological Sequences? from Bioinformatics Algorithms: An Active Learning Approach | Volker Brendel |
| Thur | Feb 2 | 2.2 | PWSA: Definition and representation of "alignments" Home Work Assignment 1 due at 6:00pm | Volker Brendel |
| Tues | Feb 7 | 2.3 | Global alignment (Needleman-Wunsch) How to calculate the number of NW alignments | Volker Brendel |
| Thur | Feb 9 | 2.4 | Scoring alignments How to calculate the optimal alignment score (and find an optimal alignment) PWSA: allowing "double-gaps" PWSA: local alignment (Smith-Waterman) Home Work Assignment 2 posted. Due: Feb. 17, 6:59pm | Volker Brendel |
| Tues | Feb 14 | 2.5 | Sequence analysis with scores: Concepts and statistical foundations | Volker Brendel |
| Thur | Feb 16 | 2.6 | Sequence analysis with scores: Practice BLAST and Substitution scoring matrices Biological Sequence Analysis I (Lecturer: Dr. Andy Baxevanis) Slides for Sequence Analysis I presentation Handout for Sequence Analysis I presentation | Volker Brendel |
| Tues | Feb 21 | 3.1 | Module 3: Basic Concepts in Molecular PhylogeneticsMolecular Phylogeny: Models The powers and pitfalls of parsimony | Volker Brendel |
| Thur | Feb 23 | 3.2 | Lectures on molecular phylogeny (from Bioinformatics: An Active Learning Approach) | Volker Brendel |
| Tues | Feb 28 | 3.3 | Methods I: Parsimony Home Work Assignment 3 posted. Due: March 7, 11:00pm | Volker Brendel |
| Thur | March 2 | 3.4 | Methods II: Distance matrix methods | Volker Brendel |
| Tues | March 7 | 4.1 | Module 4: Hidden Markov ModelsHidden Markov Models: Concepts and Algorithms Hidden Markov Models (from Bioinformatics: An Active Learning Approach) | Volker Brendel |
| Thur | March 9 | 4.2 | Hidden Markov Models: Applications Profile Hidden Markov Models TagDust Tagdust2 on github GeneMark.hmm prokaryotic GENSCAN; paper see here Background: GeneMark article Review: Conditional Probability | Volker Brendel |
| Tues | March 14 | Spring Break | ||
| Thur | March 16 | Spring Break | ||
| Tues | March 21 | 5.1 | Module 5: Genome Assembly and AnnotationEukaryotic gene finding: GeneMark AUGUSTUS | Volker Brendel |
| Thur | March 23 | 5.2 | Genome Annotation: Evaluation Sensitivity, specificity, and all that sample paper How to evaluate gene structure prediction accuracy | Volker Brendel |
| Tues | March 28 | 5.3 | Genome Sequencing: Illumina sequencing nanopore sequencing Assembly basics NCBI Assembly Help | Volker Brendel |
| Thur | March 30 | 5.4 | Genome assembly: How do we assemble genomes? from Bioinformatics Algorithms: An Active Learning Approach | Volker Brendel |
| Tues | April 4 | 6.1 | Module 6: Genetic VariationHome Work Assignment 5 posted. Due: April 11, 7:00pm Home Work Assignment 6 posted. Due: April 14, 11:00pm | Volker Brendel |
| Thur | April 6 | 6.2 | Sequence Alignment Map format (SAM) SAM flags explained Pileup format (used by samtools) Relevant code: samtools bwa | Volker Brendel |
| Tues | April 11 | 6.3 | Relevant file format specifications: Variant Call Format (VCF) Relevant code: NCBI SRA Toolkit freebayes | Volker Brendel |
| Thur | April 13 | 6.4 | Gene Expression Analyses from Bioinformatics Algorithms: An Active Learning Approach MIT Lecture: Gene Regulatory Networks MIT Data Science: Clustering | Volker Brendel |
| Tues | April 18 | 7.1 | Module 7: Protein StructurePDB: What is a protein? PDB: How enzymes work Guide to PDB PDB Molecule of the Month NCBI Protein | Volker Brendel |
| Thur | April 20 | 7.2 | peptide bond Ramachandran plot ... very nice visualization thereof (thanks to Prof. Eric Martz) Secondary Structure 2StruCompare server Jpred - secondary structure prediction SPIDER3 HMMer PFAM foldit AlphaFold | Volker Brendel |
| Tues | April 25 | 8.1 | Review: Managing workflows loops in bash | Volker Brendel |
| Thur | April 27 | 8.2 | Review | Volker Brendel |
| Thur | May 4 | 12:20pm | Final Project submission due | Students |