Transcript Bioinformatics Support - Trinity College, Dublin

Introduction
Sample Projects
Resources
Summary
Future Plans
Bioinformatics Support
Information Session
Karsten Hokamp
TCD
3rd October, 2007
Introduction:
background
job description
Sample Projects
Resources
Summary
Future Plans
Introduction
Background
Introduction:
background
job description
Sample Projects
Resources
Summary
Future Plans
Introduction
Background
1998: M.Sc. equiv. in
Bioinformatics
Bielefeld University
2002: Ph.D. in Genetics
2002 -2005:
Research Fellow,
SFU, B.C., Canada
2005: current position
Introduction
Introduction:
background
job description
Job Description
Biochemistry
Genetics
Microbiology
Physiology
Sample Projects
Resources
Summary
Future Plans
Data
Applications
Bioinformatics
Introduction
Sample Projects
Resources
Summary
Future Plans
Sample Projects
Sample Projects
Introduction
The extracellular Leucine-Rich Repeat superfamily
Sample Project:
ext. LRRs
miRNA targets
The CASBAH
complete
misc
Resources
Summary
Future Plans
Protein datasets
Annotation
general
IPI
MGC
human, mouse human, mouse
Pipeline
Ensembl
fly, human,
mouse, worm
Ensembl, IPI, MGC
(gene ID, location, …)
architecture
hmmpfam with Pfam,
SMART
BLAST all vs all
non-redundant
proteomes:
fly, human,
mouse, worm
signal
TribeMCL clustering
merging of isoforms
TMHMM, HMMTOP,
TMPRED, SignalP
selection for eLRR
manual curation
final list
Dolan et al, BMC Genomics. 2007 Sep 14;8(1):320
Introduction
Sample Project:
ext. LRRs
miRNA targets
The CASBAH
complete
misc
Resources
Summary
Future Plans
Sample Projects
Prediction of miRNA targets
experiments
4 microRNAs
miRanda
Sanger miRDB
predicted
targets
EST
libraries
retina-specific
genes
Loscher et al., Genome Biology (accepted for publication)
Introduction
Sample Project:
Sample Projects
CASBAH: The CAspase Substrate dataBAse
ext. LRRs
miRNA targets
The CASBAH
complete
misc
Resources
Summary
Future Plans
http://www.casbah.ie
Introduction
Sample Project:
Sample Projects
CASBAH: The CAspase Substrate dataBAse
ext. LRRs
miRNA targets
The CASBAH
complete
misc
Resources
Summary
Future Plans
Luthi and Martin (2007) Cell Death Differ 14, 641-650
Introduction
Sample Project:
ext. LRRs
miRNA targets
The CASBAH
complete
misc
Resources
Summary
Future Plans
Sample Projects
speed up programs through parallelisation
LDhat
complete
LDhat
LDhat
LDhat
LDhat
LDhat
LDhat
LDhat
LDhat
LDhat
complete
complete
complete
complete
complete
complete
complete
complete
complete
single CPU
vs
TCHPC IITAC
(up to 356 CPUs)
stopped
after
six weeks
finished within
two days
Sample Projects
Introduction
Sample Project:
ext. LRRs
miRNA targets
The CASBAH
complete
misc
Resources
Summary
Future Plans
miscellaneous activities
microarray data analysis
(ArrayPipe, BioConductor)
Sample Projects
Introduction
Sample Project:
ext. LRRs
miRNA targets
The CASBAH
complete
misc
Resources
Summary
Future Plans
miscellaneous activities
microarray data analysis
programming help
(Perl, C, Java)
Sample Projects
Introduction
Sample Project:
ext. LRRs
miRNA targets
The CASBAH
complete
misc
Resources
Summary
Future Plans
miscellaneous activities
microarray data analysis
programming help
local installation of programs
(clustalw, BLAST, hmmpfam)
Sample Projects
Introduction
Sample Project:
ext. LRRs
miRNA targets
The CASBAH
complete
misc
Resources
Summary
Future Plans
miscellaneous activities
microarray data analysis
programming help
local installation of programs
advise on experimental design
(microarray experiments)
Sample Projects
Introduction
Sample Project:
ext. LRRs
miRNA targets
The CASBAH
complete
misc
Resources
Summary
Future Plans
miscellaneous activities
microarray data analysis
programming help
local installation of programs
advise on experimental design
help with grant applications
Introduction
Sample Project:
Resources
hardware
online
Summary
Future Plans
Resources
hardware
local servers:
2 x 1 TB
backup
bioinf.gen.tcd.ie
2 x dual core G5
8 GB RAM
1 TB disk space
external HTTP
and SSH access
gen152061.gen.tcd.ie
gen152063.gen.tcd.ie
gen152064.gen.tcd.ie
shared home directories
gigabit connection
Introduction
Sample Project:
Resources
hardware
online
Summary
Future Plans
Resources
hardware
hosted server:
2 x dual core AMD Opteron
8 GB RAM
1.5 TB disk space
genserver.tchpc.tcd.ie
linked via Infiniband to IITAC
Introduction
Sample Project:
Resources
hardware
online
Summary
Future Plans
Resources
online
http://bioinf.gen.tcd.ie
Introduction
Sample Project:
Resources
hardware
online
Resources
bioinf.gen.tcd.ie
links to locally installed programs
Summary
Future Plans
PubCrawler: It goes to the library. You go to the pub
Introduction
Sample Project:
Resources
hardware
online
Summary
Future Plans
Resources
bioinf.gen.tcd.ie
links to locally installed programs
course material:
Computer programming for Biologists
Bioinformatics from the UNIX command line
Resources
Introduction
Sample Project:
Resources
hardware
online
Summary
Future Plans
bioinf.gen.tcd.ie
links to locally installed programs
course material
mailing list
Resources
Introduction
Sample Project:
Resources
hardware
online
Summary
Future Plans
bioinf.gen.tcd.ie
links to locally installed programs
course material
mailing list
contact information
Introduction
Sample Project:
Resources
Summary
Future Plans
Summary
Which program can I use to do XXX?
I’d like to learn how to program!
Where can I store my data?
What does this
parameter do?
I can only load up 20 sequences on the web!
I need help analysing my gene expression data!
I need access to I can’t get this program to run!
a powerful
UNIX computer! How can I make this run faster?
I wonder how Bioinformatics can boost this study?
Introduction
Sample Project:
Resources
Summary
Future Plans
Future Plans
tutorial: interactive web graphics
survey
backups
downstream microarray data analyses
(network visualisations, GO enrichment)
Introduction
Sample Project:
Resources
Summary
Future Plans
End