Week | Date | Topic | Material Download/Reading |
Week 1 | 15-Jan | Course overview |
slides
Origin of Bioinformatics
The roots of Bioinformatics
Computational Biologists: The Next Pharma Scientists?
Bioinformatics: alive and kicking |
| 17-Jan | 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 | 22-Jan | NCBI resources I: databases and Entrez |
slides
NCBI mcbios workshop
NCBI web resource tutorials
NCBI discovery workshops
NCBI Help Manual
example gene list |
| 24-Jan | NCBI resources II: web-baesd BLAST |
slides
NCBI discovery workshops
NCBI tutorial on Youtube
example mRNA file
example protein file
|
Week 3 | 29-Jan | NCBI resources III: GEO, SRA and ftp resources |
slides
GEO Handout
GEO NAR paper
|
| 31-Jan | EBI resources I: UniProt and GO |
slides
EBI online training courses
example id file
example protein file
|
Week 4 | 5-Feb | EBI resources II: Ensembl and InterPro, scop, superfamily |
slides
InterPro training
Ensembl tutorials
Ensembl introduction
|
| 7-Feb | 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 | 12-Feb | 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 |
| 14-Feb | Popular bioinformatics tools in Galaxy I |
slides
Galaxy 101
Galaxy GB paper
Galaxy CPMB 2010 paper
Galaxy CPB 2012 paper
|
Week 6 | 19-Feb | Popular bioinformatics tools in Galaxy II |
slides
delimited data
grouping data
interval data
|
| 21-Feb | Popular bioinformatics tools in Galaxy III |
slides
EMBOSS
fastq 1
fastq 2
NGS using Galaxy @ UCR
How newbler works
454 read assembly |
Week 7 | 26-Feb | Phylogeny 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-Feb | Phylogeny and visualization: MEGA and iTOL |
slides
example color definition file
example domain definition file
newick format
|
Week 8 | 5-Mar | Install Linux and Introduction to project 1 |
slides
Project 1
youtube install ubuntu
|
| 7-Mar | Linux command line basics I |
slides
Unix chapter
basics
SIB Unix course
EMBL Unix guide
quick guide
quick guide
cheat sheet
cheat sheet
|
Week 9 | 12-Mar | Spring recess, no class | |
| 14-Mar | Spring recess, no class | |
Week 10 | 19-Mar | Linux command line basics II |
slides
command line examples 1
command line examples 2
Project 1 description
|
| 21-Mar | Practice useful Linux commands |
slides
Useful Shell commands
sed example
awk example
Shell one liner example
|
Week 11 | 26-Mar | Install bioinformatics softwares on Ubuntu Linux as root |
slides
Shell loop example
|
| 28-Mar | Install bioinformatics tools using the hard way |
slides
environment variable
environment variable
|
Week 12 | 2-Apr | Run BLAST, HMMER, EMBOSS using command line |
slides
HMMER user guide
emboss command line training
BLAST command line user manual
FASTA guide
|
| 4-Apr | Perl 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 13 | 9-Apr | Perl basics: variables and loops |
slides
Perl functions
Perl special variables
|
| 11-Apr | Perl example script: retrieving fasta sequences from a large database file |
slides
|
Week 14 | 16-Apr | Perl 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-Apr | Bioperl basics |
slides
|
Week 15 | 23-Apr | Bioperl example scripts |
slides
|
| 25-Apr | Bioperl example scripts |
slides
|
Week 16 | 30-Apr | Student presentation of projects 1 |
Group 1
Group 2
|
| 2-May | Student presentation of projects 2 |
Group 1
Group 2
|
Week 17 | 7-May | Class ends | |