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:  background  job description Sample Projects Resources Summary Future Plans Biochemistry

Introduction Job Description

Genetics Microbiology Physiology

Data Applications

Bioinformatics

Introduction Sample Projects Resources Summary Future Plans

Sample Projects

Introduction Sample Project:  ext. LRRs  miRNA targets  The CASBAH  complete  misc Resources Summary Future Plans

Sample Projects

The extracellular Leucine-Rich Repeat superfamily Protein datasets

IPI

human, mouse

MGC

human, mouse

Ensembl

fly, human, mouse, worm Pipeline BLAST all vs all Annotation general Ensembl, IPI, MGC (gene ID, location, …)

non-redundant proteomes:

fly, human, mouse, worm TribeMCL clustering architecture hmmpfam with Pfam, SMART signal TMHMM, HMMTOP, TMPRED, SignalP merging of isoforms 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 EST libraries predicted targets retina-specific genes Loscher et al.,

Genome Biology

(accepted for publication)

Introduction Sample Project:  ext. LRRs  miRNA targets  The CASBAH  complete  misc Resources Summary Future Plans

Sample Projects

CASBAH: The CAspase Substrate dataBAse http://www.casbah.ie

Introduction Sample Project:  ext. LRRs  miRNA targets  The CASBAH  complete  misc Resources Summary Future Plans

Sample Projects

CASBAH: The CAspase Substrate dataBAse 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 LDhat complete

Sample Projects

speed up programs through parallelisation single CPU vs TCHPC IITAC (up to 356 CPUs) stopped after six weeks finished within two days

Introduction Sample Project:  ext. LRRs  miRNA targets  The CASBAH  complete  misc Resources Summary Future Plans

Sample Projects miscellaneous activities

microarray data analysis

(ArrayPipe, BioConductor)

Introduction Sample Project:  ext. LRRs  miRNA targets  The CASBAH  complete  misc Resources Summary Future Plans

Sample Projects miscellaneous activities

microarray data analysis

programming help

(Perl, C, Java)

Introduction Sample Project:  ext. LRRs  miRNA targets  The CASBAH  complete  misc Resources Summary Future Plans

Sample Projects miscellaneous activities

microarray data analysis programming help

local installation of programs

(clustalw, BLAST, hmmpfam)

Introduction Sample Project:  ext. LRRs  miRNA targets  The CASBAH  complete  misc Resources Summary Future Plans

Sample Projects miscellaneous activities

microarray data analysis programming help local installation of programs

advise on experimental design

(microarray experiments)

Introduction Sample Project:  ext. LRRs  miRNA targets  The CASBAH  complete  misc Resources Summary Future Plans

Sample Projects 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: genserver.tchpc.tcd.ie

2 x dual core AMD Opteron 8 GB RAM 1.5 TB disk space 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 Summary Future Plans

Resources

bioinf.gen.tcd.ie

links to locally installed programs

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

Introduction Sample Project: Resources  hardware  online Summary Future Plans

Resources

bioinf.gen.tcd.ie

links to locally installed programs course material

mailing list

Introduction Sample Project: Resources  hardware  online Summary Future Plans

Resources

bioinf.gen.tcd.ie

links to locally installed programs course material mailing list

contact info rmation

Summary

Introduction Sample Project: Resources Summary Future Plans 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 a powerful UNIX computer!

I can’t get this program to run!

How can I make this run faster?

I wonder how Bioinformatics can boost this study?

Future Plans

Introduction Sample Project: Resources Summary Future Plans  tutorial: interactive web graphics  survey  backups  downstream microarray data analyses (network visualisations, GO enrichment)

Introduction Sample Project: Resources Summary Future Plans

End