Fundamental Models and Algorithms in Bioinformatics
INFO I519 (= I617) Fall 2024
Course description
INFO I519 FMAB
Class times and locations
Mon, Wed 3:00p - 4:15p (Credits: 3.0); Lindley Hall (LH) 023
Computer Laboratory, Fri 9:45a - 11:00a; Lindley Hall (LH) 101
Tentative schedule
HTML version of this schedule
| DAY | DATE | LECTURE | TOPIC | LECTURER | Mon | Aug 26 | 1.1 | Motivation and Orientation: Topics in bioinformatics, prerequisites, scope of class, and resources National Center for Biotechnology Information (NCBI), a great starting point for "anything" bioinformatics Prerequisites - a few resources for review: Molecuar Biology: ... basic concepts Genomics: NHGRI Tutorial Statistics: Event probabilities Union of events Bayes Theorem Probability distributions Expected value Conditional Probability Data structures, algorithms, and programming: Python for Everybody, QTPP class Sequence Gazing: Case study: The "TATA-box" motif. Mapping biological question onto computational problems: The Modeling Spiral Aim high: AlphaFold Module 1: Bioinformatics workspacesUbuntu on Windows: ... a quick way to get to a command line terminal Virtual Machines: VirtualBox VMware Research Desktop (RED) at IU: RED Overview access via ThinLinc Client access via browser | Volker Brendel |
| Wed | Aug 28 | 1.2 | Basic bioinformatics toolkit acquisition (Part I) Getting code: git GitHub Brendel Group on GitHub GitHub HowTo git: working with branches CodeFMAB Entrez Direct Insider's Guide: NCBI E-Utilities ... slides EDirect Sample Code Explained NCBI Sequence search fields MEDLINE/PubMed search fields | Volker Brendel |
| Fri | Aug 30 | L1.1 | Computer Laboratory: Linux Basics Basic UNIX shell tutorial The UNIX Shell The UNIX Shell: Summary of Basic Commands vi editor tutorial vim editor tutorial | AI |
| Mon | Sept 2 | Labor Day | no class | |
| Wed | Sept 4 | 1.3 | Basic bioinformatics toolkit acquisition (Part II) Apptainer Apptainer User Guide Applications: Tools and Workflows SeqKit SeqKit Tutorial Homework I posted | Volker Brendel |
| Fri | Sept 6 | L1.2 | Practice session: Simple bioinformatics workflows on the command line. | AI |
| Mon | Sept 9 | 2.1 | Module 2: Sequence Models and SpacesSimple Sequence Models Homework I due 7pm | Volker Brendel |
| Wed | Sept 11 | 2.2 | Markov Models for Sequences | Volker Brendel |
| Fri | Sept 13 | L2.1 | Computer Laboratory: Python Basics Python for Everybody PY4E Lessons Python Scripting for Computational Molecular Science J. Sundnes: Introduction to Scientific Programming with Python Style matters ... | AI |
| Mon | Sept 16 | 2.3 | Applications of Markov Models I. Sequence classification: GENMARK Sensitity, specificity, and all that | Volker Brendel |
| Wed | Sept 18 | 2.4 | Applications of Markov Models II. Waiting time and pattern probability calculations Homework II posted | Volker Brendel |
| Fri | Sept 20 | L2.1 | Computer Laboratory: Simple coding, complex insights. Coding random sequence generation and pattern probability calculations | AI |
| Mon | Sept 23 | 3.1 | Module 3: Pairwise Sequence AlignmentModels for Pairwise Sequence Alignment Representations of alignments NW alignments Number of alignments (nNW algorithm) | Volker Brendel |
| Wed | Sept 25 | 3.2 | PWSA: gNW algorithm. Homework II due 9:30pm | Volker Brendel |
| Fri | Sept 27 | L3.1 | Computer Laboratory: Coding the nNW and gNW algorithms | AI |
| Mon | Sept 30 | 3.3 | Algorithms for Pairwise Sequence Alignment: gSW, lSW, and other algorithms How Do We Compare Biological Sequences? (from Bioinformatics: An Active Learning Approach) | Volker Brendel |
| Wed | Oct 2 | 3.4 | PWSA: Review and extensions. Homework III posted | Volker Brendel |
| Fri | Oct 4 | L3.2 | Computer Laboratory: Coding PWSA algorithms. | AI |
| Mon | Oct 7 | 4.1 | Module 4: Sequence Analysis with ScoresSequence Analysis with Scores: Theory | Volker Brendel |
| Wed | Oct 9 | 4.2 | Notes4.2 Homework III due 9pm, Oct. 10 | Volker Brendel |
| Fri | Oct 11 | Fall Break: no class | ||
| Mon | Oct 14 | 4.3 | Sequence Analysis with Scores: Applications | Volker Brendel |
| Wed | Oct 16 | 4.4 | Brief review and outlook Homework IV posted | Volker Brendel |
| Fri | Oct 18 | L4.2 | Computer Lab | AI |
| Mon | Oct 21 | 5.1 | Module 5: Hidden Markov ModelsHidden Markov Models: Motivation Rabiner's Tutorial Homework IV due 7pm | Volker Brendel |
| Wed | Oct 23 | 5.2 | Hidden Markov Models: Algorithms Hidden Markov Models (from Bioinformatics: An Active Learning Approach) Homework Va posted | Volker Brendel |
| Fri | Oct 25 | L5.1 | Computer Laboratory: Coding and applications of HMM algorithms | AI |
| Mon | Oct 28 | 5.3 | Hidden Markov Models: Applications Application examples GENSCAN Profile Hidden Markov Models TagDust Tagdust2 on github Sequence motifs: models Biological Sequence Analysis II (Lecturer: Dr. Andy Baxevanis) InterPro Homework Va due 2:30pm | |
| Wed | Oct 30 | 5.4 | Gene Finding: GeneMark.hmm prokaryotic GeneMark.hmm paper GeneMark training Sequence motifs: algorithms HMMER The MEME Suite HOMER Homework Vb to be posted | Volker Brendel |
| Fri | Nov 1 | L5.2 | Computer Laboratory: Implementation of HMM algorithms | AI |
| Mon | Nov 4 | 6.1 | Module 6: Basic Concepts of Molecular PhylogeneticsThe Molecular Clock Linus Pauling Molecular Phylogeny: Models The powers and pitfalls of parsimony | Volker Brendel |
| Wed | Nov 6 | 6.2 | Parsimony and Distance Matrix Methods Lectures on molecular phylogeny (from Bioinformatics: An Active Learning Approach) Homework Vb due 6pm | Volker Brendel |
| Fri | Nov 8 | L6.1 | Computer Laboratory: Molecular Phylogeny, applications | AI |
| Mon | Nov 11 | 6.3 | Molecular Phylogeny: Applications MEGA | Volker Brendel |
| Wed | Nov 13 | 6.4 | Molecular Phylogeny: Design of a workflow for a sample research project Homework VI posted | Volker Brendel |
| Fri | Nov 15 | L6.2 | Molecular Phylogeny, practice | AI |
| Mon | Nov 18 | 7.1 | Module 7: Genome Assembly and AnnotationDNA Sequencing Sanger sequencing Illumina sequencing nanopore sequencing Genome Resources The Genomic Landscape circa 2016 (Lecturer: Dr. Andy Green) Assembly basics NCBI Assembly Help NCBI Genome Genome Assembly Introduction to genome sequencing How do we assemble genomes? from Bioinformatics Algorithms: An Active Learning Approach | Volker Brendel |
| Wed | Nov 20 | 7.2 | Homework VI due Thur, Nov 21, 11:30am | Volker Brendel |
| Fri | Nov 22 | L7.1 | Computer Laboratory: Exploration of genome sequencing by simulation and genome assembly wgsim - read generator SoapDeNovo2 - assembler Hoemwork VII posted | AI |
| Mon | Nov 25 | THANKSGIVING BREAK | n/a | |
| Wed | Nov 27 | THANKSGIVING BREAK | n/a | |
| Fri | Nov 29 | THANKSGIVING BREAK | n/a | |
| Mon | Dec 2 | 8.1 | Module 8: Genetic VariationGenetic variation Interpreting an individual genome NCBI dbSNP How To NCBI dbVar How To 1000 Genomes Project Nature 491:56 Example: rs1113769 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 |
| Wed | Dec 4 | 9.1 | Module 9: Protein Structurepeptide bond Ramachandran plot ... very nice visualization thereof (thanks to Prof. Eric Martz) PDB: What is a protein? PDB: How enzymes work HIV I HIV II Guide to PDB PDB Molecule of the Month NCBI Protein Secondary Structure Jpred - secondary structure prediction SPIDER3 foldit AlphaFold Homework VII due 6pm | Volker Brendel |
| Fri | Dec 6 | L7.2 | Lab7.2 | AI |
| Mon | Dec 9 | Review Sessions | Volker Brendel | |
| Wed | Dec 11 | Volker Brendel | ||
| Fri | Dec 13 | Office hour | AI | |
| Mon | Dec 16 | 3:00-5:00pm | Final Examination | Students |