BIOL L388/Z620 DB
Tues, Thur 11:10a - 12:25p (Credits: 3.0); Biology Building (JH) 001
| DAY | DATE | LECTURE | TOPIC | LECTURER |
| Tues | Jan 14 | 0.1 | OrientationWhat is Digital Biology? Topics in bioinformatics, scope of class, and resources Motivation COVID-19 pandemic and a 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 16 | 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 nano editor HowTo vi(m) editor tutorial | Volker Brendel |
| Tues | Jan 21 | 1.2 | Customizing your Linux work space Getting code with git Working with NCBI data Homework Assignment 1 posted. Due: Jan 27, 4:00pm | Volker Brendel |
| Thur | Jan 23 | 1.3 | Command line access to NCBI data: EDirect Entrez Direct NCBI Sequence search fields MEDLINE/PubMed search fields | Volker Brendel |
| Tues | Jan 28 | 1.4 | Expanding our tool set: seqkit bedtools Practice, practice, ...: Interactive bioinformatics tutorials Wrangle FASTA/Q with SeqKit Genomic intervals with bedtools | Volker Brendel |
| Thur | Jan 30 | 1.5 | Review: Statistical evaluation of sequence features Using generic Linux commands to process sequence data (at least for previews or consistency checks ...) Homework Assignment 2 posted. Due: Feb 3, 4:00pm | Volker Brendel |
| Tues | Feb 4 | 2.1 | Module 2: Pairwise Sequence AlignmentMotivation How Do We Compare Biological Sequences? from Bioinformatics Algorithms: An Active Learning Approach | Volker Brendel |
| Thur | Feb 6 | 2.2 | PWSA: Definition and representation of "alignments" | Volker Brendel |
| Tues | Feb 11 | 2.3 | Global alignment (Needleman-Wunsch) How to calculate the number of NW alignments Homework Assignment 3 posted. Due: Feb 17, 4:00pm | Volker Brendel |
| Thur | Feb 13 | 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) Practice: EMBOSS Tutorial | Volker Brendel |
| Tues | Feb 18 | 2.5 | Sequence analysis with scores: Concepts and statistical foundations Homework Assignment 4 posted. Due: Feb 24, 4:00pm | Volker Brendel |
| Thur | Feb 20 | 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 25 | 3.1 | Module 3: Basic Concepts in Molecular PhylogeneticsMolecular Phylogeny: Models The powers and pitfalls of parsimony | Volker Brendel |
| Thur | Feb 27 | 3.2 | Lectures on molecular phylogeny (from Bioinformatics: An Active Learning Approach) | Volker Brendel |
| Tues | Mar 4 | 3.3 | Methods I: Parsimony Homework Assignment 5 posted. Due: Mar 10, 10:00pm | Volker Brendel |
| Thur | Mar 6 | 3.4 | Methods II: Distance matrix methods | Volker Brendel |
| Tues | March 11 | 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 13 | 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 18 | Spring Break | ||
| Thur | March 20 | Spring Break | ||
| Tues | March 25 | 5.1 | Module 5: Genome Assembly and AnnotationEukaryotic gene finding: Snowy Owl genome Chicken genome Ab initio prediction tools: GeneMark AUGUSTUS Spliced alignment tools: GeneSeqer GenomeThreader miniprot Homework Assignment 6 posted. Due: Mar 31, 4:00pm | Volker Brendel |
| Thur | March 27 | 5.2 | Genome Annotation: Evaluation Sensitivity, specificity, and all that sample paper How to evaluate gene structure prediction accuracy | Volker Brendel |
| Tues | April 1 | 5.3 | Genome Sequencing: Illumina sequencing nanopore sequencing Assembly basics NCBI Assembly Help | Volker Brendel |
| Thur | April 3 | 5.4 | Genome assembly: How do we assemble genomes? from Bioinformatics Algorithms: An Active Learning Approach | Volker Brendel |
| Tues | April 8 | 6.1 | Module 6: Genetic VariationHomework Assignment 7 posted. Due: Apr 14, 4:00pm | Volker Brendel |
| Thur | April 10 | 6.2 | Sequence Alignment Map format (SAM) SAM flags explained Pileup format (used by samtools) Relevant code: samtools bwa | Volker Brendel |
| Tues | April 15 | 6.3 | Relevant file format specifications: Variant Call Format (VCF) Relevant code: NCBI SRA Toolkit freebayes | Volker Brendel |
| Thur | April 17 | 6.4 | Gene Expression Analyses from Bioinformatics Algorithms: An Active Learning Approach MIT Lecture: Gene Regulatory Networks MIT Data Science: Clustering Final Project posted. Due: in finals week, TBD | Volker Brendel |
| Tues | April 22 | 7.1 | Managing workflows SingularityCE SingularityCE Releases HPC at IU Quartz at IU Using modules loops in bash | Volker Brendel |
| Thur | April 24 | 8.1 | Module 7: Protein StructurePDB: What is a protein? PDB: How enzymes work Guide to PDB PDB Molecule of the Month NCBI Protein 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 29 | 8.1 | Review: Managing workflows loops in bash | Volker Brendel |
| Thur | May 1 | 8.2 | Review | Volker Brendel |
| Thur | Nay 8 | 12:20pm | Final Project submission due | Students |