Fall 2016, BIOS441/641

Class titlePractical Bioinformatics for Biologists
Class timeTu/Th 11:00am-12:15am
ClassroomMO444
InstructorDr. Yanbin Yin
Office hoursTu/Th/Fri 2-4pm, (yyin@niu.edu, MO325A or MO429)
Syllabusdownload

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

WeekTopicMaterial Download/Reading
Week 1Course overview slides
Origin of Bioinformatics
The roots of Bioinformatics
Computational Biologists: The Next Pharma Scientists?
An Explosion Of Bioinformatics Careers
Bioinformatics: alive and kicking
Basic molecular biology and overview of major bioinformatics web resources slides
EBI training
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 2-3NCBI resources I: databases and Entrez slides
NCBI resources II: web-based BLAST slides
NCBI resources III: GEO, SRA and ftp resources slides
Genomics 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 4-5EBI 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 6-7Phylogeny 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 newick file
example color definition file
example branch definition file
newick format
Week 8Go over project 1 Project 1
Week 9Linux 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 10Linux 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 11Linux command line basics III: piping commands for text processing slides
Week 12Linux 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 13Go over project 2 Project 2
Week 14Holiday week (Happy Thanksgiving!)
Week 15Catch up time: finish projects Project 2
Study guide for the final exam
Unix one-liners for project 2
Venn diagram
Week 16Final Exam on December 6th (11-12:30)

Last update: 8/20/2016 by Yanbin Yin