Fall 2015, BIOS441/641

Class title	Practical Bioinformatics for Biologists
Class time	Tu/Th 11:00am-12:15am
Classroom	MO444
Instructor	Dr. Yanbin Yin
Office hours	Tu/Th 2-4pm, (yyin@niu.edu, MO325A or MO429)
Syllabus	download

Introduction

This course is offered to biology students at both graduate and undergraduate levels. It will focus on how to use existing bioinformatics tools. The department offers another two bioinformatics courses: (i) BIOS443/643 covering the theoretical basis of bioinformatics algorithms/tools and (ii) BIOS646 covering computer programing for bioinformatics.

Our course BIOS441/641 features practical hands-on skills in using various bioinformatics softwares, including web-based tools (using web browser), stand-alone tools with GUI (need no programming) and without GUI (use Linux terminal function and need bash programming). It emphasizes applications of computational tools to solve real biology problems (a lot of examples will be used in class). Students will work on two course projects and homework will be assigned every two or three lectures. Students may expect to learn to address the following questions:

- How to fetch DNA or protein sequences, e.g. 200 proteins or 1000 bacterial genomes at a time, from NCBI?
- What is Unix and Linux and how to install Linux on a laptop/desktop?
- What is a Linux server and how to access a remote Linux machine from Windows?
- How to work with Linux terminals?
- How to install bioinformatics softwares using terminals?
- How to run bioinfo tools e.g. BLAST in the Linux terminal?
- How to do basic sequence analysis using bioinfo tools such as EMBOSS commands?
- How to annotate a newly sequenced genomes?
- How to analyze transcriptome data?
and many more ...

Schedule

Week	Date	Topic	Material Download/Reading
Week 1	8/25	Course overview slides	Origin of Bioinformatics The roots of Bioinformatics Computational Biologists: The Next Pharma Scientists? An Explosion Of Bioinformatics Careers Bioinformatics: alive and kicking
Week 1	8/27	Basic molecular biology and overview of major bioinformatics web resources slides	EBI 2Can Nucleic Acids Research Annual Database Issue Nucleic Acids Research Annual WebServer Issue OBRC: Online Bioinformatics Resources Collection Oxford LibGuides Bioinformatics Databases & Web Resources UHK Bioinformatics Resources on the Web CCHMC Bioinformatics Resources bioinformaticsweb
Week 2	9/1	NCBI resources I: databases and Entrez slides NCBI resources II: web-based BLAST slides NCBI resources III: GEO, SRA and ftp resources slides	NCBI mcbios workshop NCBI web resource tutorials NCBI discovery workshops NCBI Help Manual NCBI tutorial on Youtube example mRNA file example protein file example gene list GEO Handout GEO NAR paper plant species list
Week 2	9/3
Week 3	9/8
Week 3	9/10
Week 4	9/15	EBI resources I: UniProt and GO slides EBI resources II: InterPro, scop, superfamily slides EBI resources III: tools at EBI, ExPASy and DTU slides	EBI online training courses example id file example protein file slides InterPro training Ensembl tutorials Ensembl introduction ExPASy NAR paper FASTA guide example protein file example nucleotide file example alignment file example boxshade file
Week 4	9/17
Week 5	9/22
Week 5	9/24
Week 6	9/29	Phylogeny and visualization: MEGA and iTOL slides	Molecular evolution and phylogenetic analysis Phylogeny for the faint of heart: a tutorial A step by step guide to phylogeny reconstruction Multiple sequence alignment accuracy and phylogenetic inference example color definition file example domain definition file newick format
Week 6	10/1
Week 7	10/6
Week 7	10/8
Week 8	10/13	Go over project 1	Project 1
Week 8	10/15	Go over project 1	Project 1
Week 9	10/20	Linux introduction slides Command line basics I: files and folders slides	youtube install ubuntu Unix chapter basics SIB Unix course EMBL Unix guide quick guide
Week 9	10/22
Week 10	10/27	Linux command line basics II: downloading and controlling files slides	command line examples 1 command line examples 2 Useful Shell commands sed example awk example Shell one liner example
Week 10	10/29
Week 11	11/3	Linux command line basics III: piping commands for text processing slides
Week 11	11/5
Week 12	11/10	Linux command line basics IV: install and run bioinformatics softwares on Linux slides	environment variable environment variable BLAST command line user manual emboss command line training
Week 12	11/12
Week 13	11/17	Go over project 2	Project 2 Study guide for the final exam
Week 13	11/19	Go over project 2	Project 2 Study guide for the final exam
Week 14	11/24	Holiday week (Happy Thanksgiving!)
Week 14	11/26	Holiday week (Happy Thanksgiving!)
Week 15	12/1	Catch up time: finish projects	Project 2 Study guide for the final exam Unix one-liners for project 2 Venn diagram
Week 15	12/3	Catch up time: finish projects
Week 16	12/8	Final Exam (11-12:30)

Last update: 8/15/2015 by Yanbin Yin