Introduction Sample Projects Resources Summary Future Plans

IntroductionSample ProjectsResourcesSummaryFuture Plans Bioinformatics Support

Information Session

Karsten Hokamp

TCD

3rd October, 2007

Introduction:backgroundjob description

Sample ProjectsResources SummaryFuture Plans

IntroductionBackground


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


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


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




Sample ProjectsPrediction of miRNA targets

Loscher et al., Genome Biology (accepted for publication)

experiments

miRandaSanger miRDB

4 microRNAs

predictedtargets

retina-specificgenes

ESTlibraries




Sample ProjectsCASBAH: The CAspase Substrate dataBAse

http://www.casbah.ie




Sample ProjectsCASBAH: The CAspase Substrate dataBAse

Luthi and Martin (2007) Cell Death Differ 14, 641-650




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




Sample Projectsmiscellaneous activities

microarray data analysis (ArrayPipe, BioConductor)





microarray data analysis

programming help

(Perl, C, Java)






programming help

local installation of programs

(clustalw, BLAST, hmmpfam)






programming help


advise on experimental design

(microarray experiments)






programming help


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


hardwareonline


Resourceshardware

hosted server:

genserver.tchpc.tcd.ie

2 x dual core AMD Opteron8 GB RAM1.5 TB disk space

linked via Infiniband to IITAC


hardwareonline


Resourcesonline

http://bioinf.gen.tcd.ie


hardwareonline


Resourcesbioinf.gen.tcd.ie

links to locally installed programs

PubCrawler: It goes to the library. You go to the pub


hardwareonline


Resources bioinf.gen.tcd.ie


course material:

Computer programming for Biologists

Bioinformatics from the UNIX command line


hardwareonline




course material

mailing list


hardwareonline




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

Introduction Sample Projects Resources Summary Future Plans

Documents

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