Fall 2014, BIOS441

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


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 ...


WeekDateTopicMaterial Download/Reading
Week 18/26Course overview slides
Origin of Bioinformatics
The roots of Bioinformatics
Computational Biologists: The Next Pharma Scientists?
An Explosion Of Bioinformatics Careers
Bioinformatics: alive and kicking
8/28Basic 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
Week 29/2NCBI 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
9/4NCBI resources II: web-based BLAST slides
NCBI discovery workshops
NCBI tutorial on Youtube
example mRNA file
example protein file
Week 39/9NCBI resources III: GEO and expression data analysis slides
GEO Handout
GEO NAR paper
9/11EBI resources I: UniProt and GO slides
EBI online training courses
example id file
example protein file
Week 49/16EBI resources II: Ensembl and InterPro, scop, superfamily slides
InterPro training
Ensembl tutorials
Ensembl introduction
9/18EBI 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 59/23JGI 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
9/25Popular bioinformatics tools in Galaxy I slides
Galaxy 101
Galaxy GB paper
Galaxy CPMB 2010 paper
Galaxy CPB 2012 paper
Week 69/30Popular bioinformatics tools in Galaxy II slides
delimited data
grouping data
interval data
10/2Popular bioinformatics tools in Galaxy III slides
fastq 1
fastq 2
NGS using Galaxy @ UCR
How newbler works
454 read assembly
Week 710/7Phylogeny 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
10/9Phylogeny and visualization: iTOL slides
example color definition file
example domain definition file
newick format
Week 810/14Go over project 1 Project 1
10/16Go over project 1 Project 1
Week 910/21Linux introduction and command line basics I: files and folders slides
youtube install ubuntu
Unix chapter
10/23Linux command line basics I: files and folders slides
SIB Unix course
EMBL Unix guide
quick guide
quick guide
cheat sheet
cheat sheet
Week 1010/28Linux command line basics II: downloading and controlling files slides
command line examples 1
command line examples 2
10/30Linux command line basics II: downloading and controlling files slides
Useful Shell commands
sed example
awk example
Shell one liner example
Week 1111/4Linux command line basics III: piping commands for text processing slides
11/6Linux command line basics III: piping commands for text processing slides
Week 1211/11Install bioinformatics softwares on Linux slides
environment variable
environment variable
11/13Run bioinformatics softwares on Linux slides
BLAST command line user manual
emboss command line training
Week 1311/18Go over project 2 Project 2
11/20Go over project 2 Project 2
Study guide for the final exam
Week 1411/25Holiday week
11/27Holiday week
Week 1512/2Catch up time: finish projects Project 2
Study guide for the final exam
Unix one-liners for project 2
Venn diagram
12/4Catch up time: finish projects Project 2
Study guide for the final exam
Week 1612/9Final Exam

Last update: 12/01/2014 by Yanbin Yin