Fall 2014, BIOS441

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	8/26	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
	8/28	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	9/2	NCBI resources I: databases and Entrez	slides NCBI mcbios workshop NCBI web resource tutorials NCBI discovery workshops NCBI Help Manual example gene list plant species list
	9/4	NCBI resources II: web-based BLAST	slides NCBI discovery workshops NCBI tutorial on Youtube example mRNA file example protein file
Week 3	9/9	NCBI resources III: GEO and expression data analysis	slides GEO Handout GEO NAR paper
	9/11	EBI resources I: UniProt and GO	slides EBI online training courses example id file example protein file
Week 4	9/16	EBI resources II: Ensembl and InterPro, scop, superfamily	slides InterPro training Ensembl tutorials Ensembl introduction
	9/18	EBI resources III: tools at EBI, ExPASy and DTU	slides ExPASy NAR paper FASTA guide example protein file example nucleotide file example alignment file example boxshade file
Week 5	9/23	~~JGI resources: genomes, metagenomes, GOLD~~	slides JGI Strategic vision GOLD database paper JGI's genome portal and fungal genome database paper plant genome database (phytozome) paper fungal genome database paper IMG/M metagenome info table
	9/25	~~Popular bioinformatics tools in Galaxy I~~	slides Galaxy 101 Galaxy GB paper Galaxy CPMB 2010 paper Galaxy CPB 2012 paper
Week 6	9/30	~~Popular bioinformatics tools in Galaxy II~~	slides delimited data grouping data interval data
	10/2	~~Popular bioinformatics tools in Galaxy III~~	slides EMBOSS fastq 1 fastq 2 NGS using Galaxy @ UCR How newbler works 454 read assembly
Week 7	10/7	Phylogeny and visualization: MEGA	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
	10/9	Phylogeny and visualization: iTOL	slides example color definition file example domain definition file newick format
Week 8	10/14	Go over project 1	Project 1
	10/16	Go over project 1	Project 1
Week 9	10/21	Linux introduction and command line basics I: files and folders	slides youtube install ubuntu Unix chapter
	10/23	Linux command line basics I: files and folders	slides basics SIB Unix course EMBL Unix guide quick guide quick guide cheat sheet cheat sheet
Week 10	10/28	Linux command line basics II: downloading and controlling files	slides command line examples 1 command line examples 2
	10/30	Linux command line basics II: downloading and controlling files	slides Useful Shell commands sed example awk example Shell one liner example
Week 11	11/4	Linux command line basics III: piping commands for text processing	slides
	11/6	Linux command line basics III: piping commands for text processing	slides
Week 12	11/11	Install bioinformatics softwares on Linux	slides environment variable environment variable
	11/13	Run bioinformatics softwares on Linux	slides BLAST command line user manual emboss command line training
Week 13	11/18	Go over project 2	Project 2
	11/20	Go over project 2	Project 2 Study guide for the final exam
Week 14	11/25	Holiday week
	11/27	Holiday week
Week 15	12/2	Catch up time: finish projects	Project 2 Study guide for the final exam Unix one-liners for project 2 Venn diagram
	12/4	Catch up time: finish projects	Project 2 Study guide for the final exam
Week 16	12/9	Final Exam

Last update: 12/01/2014 by Yanbin Yin