Digital Biology: A survey of topics in bioinformatics and functional genomics
BIOL-L/MLS-M 388 Spring 2022
Course description
BIOL L388 DB
Class times and locations
Tues, Thur 11:30a - 12:45p (Credits: 3.0); Biology Building (JH) A106
Tentative schedule (click the icon for a 
version)
| DAY | DATE | LECTURE | TOPIC | LECTURER |
| Tues | Jan 11 | 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 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 13 | 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 18 | 1.2 | Customizing your Linux work space Getting code with wget | Volker Brendel |
| Thur | Jan 20 | 1.3 | Basic Linux system maintenance Working with NCBI data | Volker Brendel |
| Tues | Jan 25 | 1.4 | Getting code with git | Volker Brendel |
| Thur | Jan 27 | 1.5 | Command line access to NCBI data: EDirect | Volker Brendel |
| Tues | Feb 1 | 2.1 | Module 2: Pairwise Sequence AlignmentMotivation How Do We Compare Biological Sequences? from Bioinformatics Algorithms: An Active Learning Approach | Volker Brendel |
| Thur | Feb 3 | 2.2 | PWSA: Definition and representation of "alignments" | Volker Brendel |
| Tues | Feb 8 | 2.3 | Global alignment (Needleman-Wunsch) How to calculate the number of NW alignments | Volker Brendel |
| Thur | Feb 13 | 2.4 | Scoring alignments How to calculate the optimal alignment score (and find an optimal alignment) | Volker Brendel |
| Tues | Feb 15 | 2.5 | Computers within computers: VMs and Singularity/Apptainer containers PWSA: NW algorithm with no end-gap penalties PWSA: allowing "double-gaps" PWSA: local alignment (Smith-Waterman) Home Work Assignment 1 posted. Due: Feb. 22 | Volker Brendel |
| Thur | Feb 17 | 2.6 | Sequence analysis with scores: Concepts and statistical foundations 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 22 | 3.1 | Module 3: Basic Concepts in Molecular PhylogeneticsMolecular Phylogeny: Models The powers and pitfalls of parsimony | Volker Brendel |
| Thur | Feb 24 | 3.2 | Lectures on molecular phylogeny (from Bioinformatics: An Active Learning Approach) | Volker Brendel |
| Tues | March 1 | 3.3 | Volker Brendel | |
| Thur | March 3 | 3.4 | | Volker Brendel |
| Tues | March 8 | 4.1 | Module 4: Hidden Markov ModelsHidden Markov Models: Concepts and Algorithms Hidden Markov Models (from Bioinformatics: An Active Learning Approach) Home Work Assignment 2 posted. Due: March 11 | Volker Brendel |
| Thur | March 10 | 4.2 | Hidden Markov Models: Algorithms Review: Conditional Probability GeneMark.hmm prokaryotic GeneMark article | Volker Brendel |
| Tues | March 15 | Spring Break | ||
| Thur | March 17 | Spring Break | ||
| Tues | March 22 | 5.1 | Module 5: Genome Assembly and AnnotationHome Work Assignment 3 posted. Due: March 29 | Volker Brendel |
| Thur | March 24 | 5.2 | Genome Annotation: Evaluation Sensitivity, specificity, and all that sample paper How to evaluate gene structure prediction accuracy | Volker Brendel |
| Tues | March 29 | 5.3 | Eukaryotic gene finding: GeneMark AUGUSTUS GENSCAN; paper see here Genome AssemblyIllumina sequencing nanopore sequencing Assembly basics NCBI Assembly Help How do we assemble genomes? from Bioinformatics Algorithms: An Active Learning Approach | Volker Brendel |
| Thur | March 31 | 5.4 | Home Work Assignment 4 posted. Due: April 5 | Volker Brendel |
| Tues | April 5 | 6.1 | Module 6: Genetic Variation | Volker Brendel |
| Thur | April 7 | 6.2 | Home Work Assignment 5 posted. Due: April 12 | Volker Brendel |
| Tues | April 12 | 7.1 | Relevant file format specifications: Variant Call Format (VCF) Sequence Alignment Map format (SAM) SAM flags explained Pileup format (used by samtools) Relevant code: NCBI SRA Toolkit samtools bwa freebayes | Volker Brendel |
| Thur | April 14 | 7.2 | Gene Expression Analyses from Bioinformatics Algorithms: An Active Learning Approach MIT Lecture: Gene Regulatory Networks MIT Data Science: Clustering | Volker Brendel |
| Tues | April 19 | 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 21 | 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 Home Work Assignment 6 posted. Due: April 27 | Volker Brendel |
| Tues | April 26 | 8.1 | Review | Volker Brendel |
| Thur | April 28 | 8.2 | Review | Volker Brendel |
| Thur | May 5 | 12:40pm - 2:40pm | Final Examination | Students |