|
Time |
Topic |
|
|
Monday, August
14
- Celeste Brown |
|
8:00 am |
Workshop Introduction |
|
|
8:05 am |
Introduction to IBEST
Computers
IBEST Network |
|
|
8:10
am |
Unix
-
Introduction to the UNIX operating
system
|
|
|
9:05 am |
Word-processing in UNIX
|
|
|
9:20 am |
Logging on and getting your data to the computers
-
SSH-Secure shell client on
Windows
ssh and scp on
Mac or Unix
|
|
|
9:30 am |
Running programs on Solaris,
Linux, OSX-Unix
Introduction to
programs on the IBEST system
-
EMBOSS
-
Blastall
-
Clustalx/Clustalw
-
Phylip/PAUP*
|
|
|
11:00 am |
Basic Shell
scripting |
|
|
Noon |
Lunch |
|
|
1:00 pm |
IBEST Cluster Computers: oceanus
and phlegathon
-
Sun Grid Engine
-
qsub
-
qstat
|
|
|
2:00 pm |
Web-based tools
-
Nucleic Acids
Research Database issue
-
BioToolBox
-
Biology Workbench
-
PISE
|
|
|
3:00 pm |
An introduction to Vector NTI |
|
|
|
|
Tuesday, August
15th - Matt Settles |
|
8:00 am |
Workshop Introduction |
|
|
8:05 am |
Introduction to Microarray Analysis
|
|
|
8:30 am |
An
Introduction to R and Bioconductor
-
Websites
-
Installing R and add-on packages
|
|
|
9:30 am |
Two
Channel - cDNA arrays
-
Quality Control
-
Preprocessing
-
Normalization
|
|
|
10:30 am |
Single
Channel - Affymetrix
-
Quality Control
-
Preprocessing
-
Normalization
|
|
|
11:30 am |
Differential Expression
|
|
|
Noon |
LUNCH
sponsored by Insightful
Dr. David Henderson |
|
|
1:00 pm |
DE
continued and Annotating Lists of Interesting Genes
-
Chip Annotation
-
Meta-data
|
|
|
2:00 pm |
Advanced Topics
-
Clustering and Heatmaps
-
Gene Ontology Analysis
-
Machine Learning / Classification
|
|
|
3:30 pm |
Additional Software
-
BRB array tools
-
GeneSpring GX
-
ExpressionNTI
|
|
|
|
|
|
|
Wednesday, August 16th - Celeste Brown and Matt Settles |
|
8:00 am |
Celeste Brown and Matt Settles will
be available to aid those who attended Monday and Tuesday sessions
in analysis of their own data. |
|
|
Noon |
Lunch sponsored by Affymetrix
Mark Daly |
|
