Fundamental Models and Algorithms in Bioinformatics
INFO I519 (= I617) Fall 2019
Course description
INFO I519 FMAB
Class times and locations
Mon, Wed 2:30p - 3:45p; Informatics West (I) 232
Computer Laboratory, Fri 9:30a-10:45a, Geological Sciences (GY) 226
Tentative schedule (click the icon for a 
version)
| DAY | DATE | LECTURE | TOPIC | LECTURER | Mon | Aug 26 | 0.1 | Orientation Topics in bioinformatics, scope of class, and resources Mapping biological question onto computational problems: The modeling spiral Catch-up for non-life scientists: An introduction to DNA (Khan Academy) National Center for Biotechnology Information (NCBI), a great starting point for "anything" bioinformatics | Volker Brendel |
| Wed | Aug 28 | 0.2 | Computer Laboratory: Basic bioinformatics toolkit acquisition (Part I) Setting up Linux virtual machines VirtualBox Linux Mint How to Install Linux Mint 19.1 on VirtualBox (step by step) | Murat Öztürk & Volker Brendel |
| Fri | Aug 30 | Computer Laboratory: Basic bioinformatics toolkit acquisition (Part II) Basic UNIX shell tutorial Command-line bootcamp vi(m) editor tutorial Python tutorial Style matters ... Learning Scientific Programming with Python - an intriguing resource Special Opportunity: We have several seats reserved for you in the Supercomputing for Everyone Series: HPC Onboarding for Biologists @IUB workshop - highlighting IU's unique resources for bioinformatics! Please register and attend if you can fit this into your schedule. | Murat Öztürk | |
| Mon | Sept 2 | No class (Labor Day) | ||
| Wed | Sept 4 | 1.1 | Simple sequence models | Volker Brendel |
| Fri | Sept 6 | Computer Laboratory: Linux Basics | Murat Öztürk | |
| Mon | Sept 9 | 1.2 | Advanced sequence models and applications | Volker Brendel |
| Wed | Sept 11 | 0.1 - 1.2 | Quiz I | |
| Fri | Sept 13 | Computer Laboratory: | Murat Öztürk | |
| Mon | Sept 16 | 2.1 | Pairwise sequence alignment: Representation | Volker Brendel |
| Wed | Sept 18 | 2.2 | Pairwise sequence alignment: Basic algorithms | Volker Brendel |
| Fri | Sept 20 | Computer Laboratory: | Murat Öztürk | |
| Mon | Sept 23 | 2.3 | Pairwise sequence alignment: Applications How Do We Compare Biological Sequences? (from Bioinformatics: An Active Learning Approach) | Volker Brendel |
| Wed | Sept 25 | 2.4 | Multiple sequence alignment | Volker Brendel |
| Fri | Sept 27 | Computer Laboratory: | Murat Öztürk | |
| Mon | Sept 30 | 2.1 - 2.4 | Quiz II | |
| Wed | Oct 2 | 3.1 | Applications of Markov Models: Pattern probabilities | Volker Brendel |
| Fri | Oct 4 | Computer Laboratory: | Murat Öztürk | |
| Mon | Oct 7 | 4.1 | Sequence analysis with scores: Concepts and Applications | Volker Brendel |
| Wed | Oct 9 | 4.2 | Sequence analysis with scores: Substitution scoring matrices Biological Sequence Analysis I (Lecturer: Dr. Andy Baxevanis) NCBI BLAST slides for Sequence Analysis I presentation handout for Sequence Analysis I presentation NCBI BLAST download site | Volker Brendel |
| Fri | Oct 5 | Computer Laboratory: | Murat Öztürk | |
| Mon | Oct 12 | 4.3 | BLAST: Fine points of database searching Webinar: A Practical Guide to NCBI BLAST NCBI Minute: Improved Standalone BLAST Databases and Programs BLAST statistics | Volker Brendel |
| Wed | Oct 16 | 3.1 | Hidden Markov Models: Concepts and Algorithms Hidden Markov Models (from Bioinformatics: An Active Learning Approach) | Volker Brendel |
| Fri | Oct 18 | Fall Break: no class | ||
| Mon | Oct 21 | 3.2 | Hidden Markov Models: Applications Application examples GENSCAN Profile Hidden Markov Models TagDust | Volker Brendel |
| Wed | Oct 23 | 3.1 - 4.3 | Quiz III | |
| Fri | Oct 25 | Computer Laboratory: | Murat Öztürk | |
| Mon | Oct 28 | 5.1 | Practical bioinformatics: BLAST output, now what? MuSeqBox Sequence motifs: models Biological Sequence Analysis II (Lecturer: Dr. Andy Baxevanis) Pfam | Volker Brendel |
| Wed | Oct 30 | 5.2 | Sequence motifs: algorithms InterPro The MEME Suite HOMER | Volker Brendel |
| Fri | Nov 1 | Computer Laboratory: | Murat Öztürk | |
| Mon | Nov 4 | 6.1 | Molecular Phylogeny: concepts The powers and pitfalls of parsimony | Volker Brendel |
| Wed | Nov 6 | 6.2 | Molecular Phylogeny: algorithms a recent paper ... A list of Web-servers for molecular phylogeny analyses phylogeny.fr | Volker Brendel |
| Fri | Nov 8 | Computer Laboratory: Molecular Phylogeny, applications | Murat Öztürk | |
| Mon | Nov 11 | 6.3 | Molecular Phylogeny: details Lectures on molecular phylogeny (from Bioinformatics: An Active Learning Approach) | Volker Brendel |
| Wed | Nov 13 | 7.1 | Protein bioinformatics: structure prediction Nobel Price lecture 2013: Michael Levitt RCSB PDB PDB-101 - a number of wonderful tutorials! SWISS-MODEL - what to do if my protein is not in PDB!? (start here) | Volker Brendel |
| Fri | Nov 15 | Computer Laboratory: | Murat Öztürk | |
| Mon | Nov 18 | 7.2 | Protein bioinformatics: structure analysis Genetic variation NCBI dbSNP How To NCBI dbVar How To 1000 Genomes Project Nature 491:56 Example: rs1131769 Recent paper of interest | Volker Brendel |
| Wed | Nov 20 | 5.1 - 7.2 | Quiz IV | |
| Fri | Nov 22 | Computer Laboratory: | Murat Öztürk | |
| 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 | Genome assembly I: algorithms Bioinformatics Algorithms: An Active Learning Approach (Chapter 3); see Bioinformatics Algorithms | Volker Brendel |
| Wed | Dec 4 | 8.2 | Genome assembly II: practice Overview of sequencing technologies Illumina | Murat Öztürk |
| Fri | Dec 6 | Computer Laboratory: wgsim - read generator SoapDeNovo2 - assembler | Murat Öztürk | |
| Mon | Dec 9 | 9.1 | Review I: Sequence Alignment Bioinformatics Algorithms presentation | Volker Brendel |
| Wed | Dec 11 | Review | Volker Brendel | |
| Fri | Dec 13 | Computer Laboratory: | Murat Öztürk | |
| Mon | Dec 16 | 12:30-2:30pm | Final Exam | Students |