Spring 2013, BIOS493

Class titlePractical Bioinformatics for Biologists
Class timeTu/Th 9:30am-10:45am
InstructorDr. Yanbin Yin
Office hoursTu/Th 2-4pm, (yyin@niu.edu, MO325A or MO429)


This course is designed for teaching biologists who are interested or have the need in using bioinformatics in their research. It features practical use of bioinformatics techniques to solve real sequence analysis problems. It covers:
How to fetch DNA or protein sequences, e.g. 200 proteins or 1000 bacterial genomes at a time, from NCBI?
How to install Ubuntu Linux on a laptop/desktop?
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?
Given a list of protein IDs, say of a gene family, how to extract their sequences from a large protein database, say a file with all proteins of a genome?
and many more ...


WeekDateTopicMaterial Download/Reading
Week 115-JanCourse overview slides
Origin of Bioinformatics
The roots of Bioinformatics
Computational Biologists: The Next Pharma Scientists?
Bioinformatics: alive and kicking
17-JanBasic 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 222-JanNCBI resources I: databases and Entrez slides
NCBI mcbios workshop
NCBI web resource tutorials
NCBI discovery workshops
NCBI Help Manual
example gene list
24-JanNCBI resources II: web-baesd BLAST slides
NCBI discovery workshops
NCBI tutorial on Youtube
example mRNA file
example protein file
Week 329-JanNCBI resources III: GEO, SRA and ftp resources slides
GEO Handout
GEO NAR paper
31-JanEBI resources I: UniProt and GO slides
EBI online training courses
example id file
example protein file
Week 45-FebEBI resources II: Ensembl and InterPro, scop, superfamily slides
InterPro training
Ensembl tutorials
Ensembl introduction
7-FebEBI 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 512-FebJGI 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
14-FebPopular bioinformatics tools in Galaxy I slides
Galaxy 101
Galaxy GB paper
Galaxy CPMB 2010 paper
Galaxy CPB 2012 paper
Week 619-FebPopular bioinformatics tools in Galaxy II slides
delimited data
grouping data
interval data
21-FebPopular bioinformatics tools in Galaxy III slides
fastq 1
fastq 2
NGS using Galaxy @ UCR
How newbler works
454 read assembly
Week 726-FebPhylogeny and visualization: Clustalx and MEGA slides
hands-on material
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
28-FebPhylogeny and visualization: MEGA and iTOL slides
example color definition file
example domain definition file
newick format
Week 85-MarInstall Linux and Introduction to project 1 slides
Project 1
youtube install ubuntu
7-MarLinux command line basics I slides
Unix chapter
SIB Unix course
EMBL Unix guide
quick guide
quick guide
cheat sheet
cheat sheet
Week 912-MarSpring recess, no class
14-MarSpring recess, no class
Week 1019-MarLinux command line basics II slides
command line examples 1
command line examples 2
Project 1 description
21-MarPractice useful Linux commands slides
Useful Shell commands
sed example
awk example
Shell one liner example
Week 1126-MarInstall bioinformatics softwares on Ubuntu Linux as root slides
Shell loop example
28-MarInstall bioinformatics tools using the hard way slides
environment variable
environment variable
Week 122-AprRun BLAST, HMMER, EMBOSS using command line slides
HMMER user guide
emboss command line training
BLAST command line user manual
FASTA guide
4-AprPerl basics and Introduction to project 2 slides
Project 2 description
Unix and Perl Primer for Biologists
Introduction to Programming: Perl for Biologists
Google "Perl Programming for Biologists pdf"
Google "beginning perl for bioinformatics pdf"
Week 139-AprPerl basics: variables and loops slides
Perl functions
Perl special variables
11-AprPerl example script:
retrieving fasta sequences from a large database file
Week 1416-AprPerl basics: subroutines, modules slides
Bioperl course at Pasteur
Bioperl HOWTO:Beginners
Bioperl HOWTO
Google "Perl Programming for Biologists pdf" and read Chapter 5 and 8
Google "Mastering perl for bioinformatics pdf" and read Chapter 1
18-AprBioperl basics slides
Week 1523-AprBioperl example scripts slides
25-AprBioperl example scripts slides
Week 1630-AprStudent presentation of projects 1 Group 1 Group 2
2-MayStudent presentation of projects 2 Group 1 Group 2
Week 177-MayClass ends

Last update: 05/10/2013 by Yanbin Yin