1. Introduction Sample Projects Resources Summary Future Plans Bioinformatics Support Information Session Karsten Hokamp TCD 3rd October, 2007

2. Introduction:  background  job description Sample Projects Resources Summary Future Plans Introduction Background

3. Introduction:  background  job description Sample Projects Resources Summary Future 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 Introduction Background

4. Introduction:  background  job description Sample Projects Resources Summary Future Plans Data Introduction Job Description BiochemistryGeneticsMicrobiologyPhysiology Bioinformatics Applications

5. Introduction Sample Projects Resources Summary Future Plans Sample Projects

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

7. Introduction Sample Project:  ext. LRRs  miRNA targets  The CASBAH  complete  misc Resources Summary Future Plans Sample Projects Prediction of miRNA targets Loscher et al., Genome Biology (accepted for publication) experiments miRanda Sanger miRDB 4 microRNAs predicted targets retina-specific genes EST libraries

8. 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

9. 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

10. Introduction Sample Project:  ext. LRRs  miRNA targets  The CASBAH  complete  misc Resources Summary Future Plans Sample Projects speed up programs through parallelisation LDhat complete stopped after six weeks finished within two days single CPU vs TCHPC IITAC (up to 356 CPUs) LDhat complete LDhat complete LDhat complete LDhat complete LDhat complete LDhat complete LDhat complete LDhat complete LDhat complete

11. Introduction Sample Project:  ext. LRRs  miRNA targets  The CASBAH  complete  misc Resources Summary Future Plans Sample Projects miscellaneous activities microarray data analysis (ArrayPipe, BioConductor)

12. 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)

13. 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)

14. 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)

15. 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

16. Introduction Sample Project: Resources  hardware  online Summary Future Plans Resources hardware local servers: bioinf.gen.tcd.ie gen152061.gen.tcd.ie gen152063.gen.tcd.ie gen152064.gen.tcd.ie external HTTP and SSH access 2 x dual core G5 8 GB RAM 1 TB disk space 2 x 1 TB backup shared home directories gigabit connection

17. 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

18. Introduction Sample Project: Resources  hardware  online Summary Future Plans Resources online http://bioinf.gen.tcd.ie

19. 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

20. 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

21. Introduction Sample Project: Resources  hardware  online Summary Future Plans Resources bioinf.gen.tcd.ie links to locally installed programs course material mailing list

22. Introduction Sample Project: Resources  hardware  online Summary Future Plans Resources bioinf.gen.tcd.ie links to locally installed programs course material mailing list contact information

23. Introduction Sample Project: Resources Summary 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 to a 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?

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

25. Introduction Sample Project: Resources Summary Future Plans End