IntroductionSample ProjectsResourcesSummaryFuture Plans Bioinformatics Support
Information Session
Karsten Hokamp
TCD
3rd October, 2007
Introduction:backgroundjob description
Sample ProjectsResources SummaryFuture Plans
IntroductionBackground
Introduction:backgroundjob description
Sample ProjectsResources SummaryFuture Plans
1998: M.Sc. equiv. in Bioinformatics
2002: Ph.D. in Genetics
Bielefeld University
2005: current position
2002 -2005: Research Fellow, SFU, B.C., Canada
IntroductionBackground
Introduction:backgroundjob description
Sample ProjectsResources Summary Future Plans
Data
IntroductionJob Description
Biochemistry Genetics Microbiology Physiology
Bioinformatics
Applications
IntroductionSample Projects
Resources SummaryFuture Plans
Sample Projects
IntroductionSample Project:
ext. LRRsmiRNA targetsThe CASBAHcompletemisc
Resources SummaryFuture Plans
Sample ProjectsThe extracellular Leucine-Rich Repeat superfamily
Dolan et al, BMC Genomics. 2007 Sep 14;8(1):320
BLAST all vs all
TribeMCL clustering
selection for eLRR
manual curation
merging of isoforms
final list
IPI human, mouse
MGC human, mouse
Ensembl fly, human,
mouse, worm
non-redundant proteomes:fly, human,
mouse, worm
architecture
hmmpfam with Pfam, SMART
signal
TMHMM, HMMTOP, TMPRED, SignalP
general
Ensembl, IPI, MGC (gene ID, location, …)
Protein datasets Annotation
Pipeline
IntroductionSample Project:
ext. LRRsmiRNA targetsThe CASBAHcompletemisc
Resources SummaryFuture Plans
Sample ProjectsPrediction of miRNA targets
Loscher et al., Genome Biology (accepted for publication)
experiments
miRandaSanger miRDB
4 microRNAs
predictedtargets
retina-specificgenes
ESTlibraries
IntroductionSample Project:
ext. LRRsmiRNA targetsThe CASBAHcompletemisc
Resources SummaryFuture Plans
Sample ProjectsCASBAH: The CAspase Substrate dataBAse
http://www.casbah.ie
IntroductionSample Project:
ext. LRRsmiRNA targetsThe CASBAHcompletemisc
Resources SummaryFuture Plans
Sample ProjectsCASBAH: The CAspase Substrate dataBAse
Luthi and Martin (2007) Cell Death Differ 14, 641-650
IntroductionSample Project:
ext. LRRsmiRNA targetsThe CASBAHcompletemisc
Resources SummaryFuture Plans
Sample Projectsspeed up programs through parallelisation
LDhatcomplete
stoppedafter
six weeks
finished within two days
single CPUvs
TCHPC IITAC(up to 356 CPUs)
LDhatcomplete
LDhatcomplete
LDhatcomplete
LDhatcomplete
LDhatcomplete
LDhatcomplete
LDhatcomplete
LDhatcomplete
LDhatcomplete
IntroductionSample Project:
ext. LRRsmiRNA targetsThe CASBAHcompletemisc
Resources SummaryFuture Plans
Sample Projectsmiscellaneous activities
microarray data analysis (ArrayPipe, BioConductor)
IntroductionSample Project:
ext. LRRsmiRNA targetsThe CASBAHcompletemisc
Resources SummaryFuture Plans
Sample Projectsmiscellaneous activities
microarray data analysis
programming help
(Perl, C, Java)
IntroductionSample Project:
ext. LRRsmiRNA targetsThe CASBAHcompletemisc
Resources SummaryFuture Plans
Sample Projectsmiscellaneous activities
microarray data analysis
programming help
local installation of programs
(clustalw, BLAST, hmmpfam)
IntroductionSample Project:
ext. LRRsmiRNA targetsThe CASBAHcompletemisc
Resources SummaryFuture Plans
Sample Projectsmiscellaneous activities
microarray data analysis
programming help
local installation of programs
advise on experimental design
(microarray experiments)
IntroductionSample Project:
ext. LRRsmiRNA targetsThe CASBAHcompletemisc
Resources SummaryFuture Plans
Sample Projectsmiscellaneous activities
microarray data analysis
programming help
local installation of programs
advise on experimental design
help with grant applications
IntroductionSample Project:Resources
hardwareonline
Summary Future Plans
Resourceshardware
local servers:
bioinf.gen.tcd.iegen152061.gen.tcd.iegen152063.gen.tcd.iegen152064.gen.tcd.ie
external HTTP and SSH access
2 x dual core G58 GB RAM1 TB disk space
2 x 1 TBbackup
shared home directoriesgigabit connection
IntroductionSample Project:Resources
hardwareonline
Summary Future Plans
Resourceshardware
hosted server:
genserver.tchpc.tcd.ie
2 x dual core AMD Opteron8 GB RAM1.5 TB disk space
linked via Infiniband to IITAC
IntroductionSample Project:Resources
hardwareonline
Summary Future Plans
Resourcesonline
http://bioinf.gen.tcd.ie
IntroductionSample Project:Resources
hardwareonline
Summary Future Plans
Resourcesbioinf.gen.tcd.ie
links to locally installed programs
PubCrawler: It goes to the library. You go to the pub
IntroductionSample Project:Resources
hardwareonline
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
IntroductionSample Project:Resources
hardwareonline
Summary Future Plans
Resources bioinf.gen.tcd.ie
links to locally installed programs
course material
mailing list
IntroductionSample Project:Resources
hardwareonline
Summary Future Plans
Resources bioinf.gen.tcd.ie
links to locally installed programs
course material
mailing list
contact information
IntroductionSample Project:ResourcesSummary
Future Plans
Summary
I need help analysing my gene expression data!
Where can I store my data?
I’d like to learn how to program!
Which program can I use to do XXX?
I need access toa powerful
UNIX computer! How can I make this run faster?
I can only load up 20 sequences on the web!
What does this parameter do?
I can’t get this program to run!
I wonder how Bioinformatics can boost this study?
IntroductionSample Project:ResourcesSummaryFuture Plans
Future Plans
tutorial: interactive web graphics
survey
backups
downstream microarray data analyses (network visualisations, GO enrichment)
IntroductionSample Project:ResourcesSummaryFuture Plans
End
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