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Introduction Sample Projects Resources Summary Future Plans

Introduction Sample Projects Resources Summary Future Plans. Bioinformatics Support Information Session. Karsten Hokamp TCD 3rd October, 2007. Introduction Background. Introduction: background job description Sample Projects Resources Summary Future Plans. Bielefeld University.

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Introduction Sample Projects Resources Summary Future Plans

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

  2. IntroductionBackground • Introduction: • background • job description • Sample Projects • Resources • Summary • Future Plans

  3. Bielefeld University IntroductionBackground • Introduction: • background • job description • Sample Projects • Resources • Summary • Future Plans 1998: M.Sc. equiv. in Bioinformatics 2002: Ph.D. in Genetics 2002 -2005: Research Fellow, SFU, B.C., Canada 2005: current position

  4. Bioinformatics IntroductionJob Description • Introduction: • background • job description • Sample Projects • Resources • Summary • Future Plans Biochemistry Genetics Microbiology Physiology Data Applications

  5. Sample Projects Introduction Sample Projects Resources Summary Future Plans

  6. general Ensembl, IPI, MGC (gene ID, location, …) TMHMM, HMMTOP, TMPRED, SignalP hmmpfam with Pfam, SMART architecture signal Sample ProjectsThe extracellular Leucine-Rich Repeat superfamily • Introduction • Sample Project: • ext. LRRs • miRNA targets • The CASBAH • complete • misc • Resources • Summary • Future Plans Protein datasets Annotation IPI human, mouse MGC human, mouse Pipeline Ensembl fly, human, mouse, worm BLAST all vs all non-redundant proteomes:fly, human, mouse, worm TribeMCL clustering merging of isoforms selection for eLRR manual curation final list Dolan et al, BMC Genomics. 2007 Sep 14;8(1):320

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

  8. Sample ProjectsCASBAH: The CAspase Substrate dataBAse • Introduction • Sample Project: • ext. LRRs • miRNA targets • The CASBAH • complete • misc • Resources • Summary • Future Plans http://www.casbah.ie

  9. Sample ProjectsCASBAH: The CAspase Substrate dataBAse • Introduction • Sample Project: • ext. LRRs • miRNA targets • The CASBAH • complete • misc • Resources • Summary • Future Plans Luthi and Martin (2007) Cell Death Differ 14, 641-650

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

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

  12. Sample Projectsmiscellaneous activities • Introduction • Sample Project: • ext. LRRs • miRNA targets • The CASBAH • complete • misc • Resources • Summary • Future Plans microarray data analysis programming help (Perl, C, Java)

  13. Sample Projectsmiscellaneous activities • Introduction • Sample Project: • ext. LRRs • miRNA targets • The CASBAH • complete • misc • Resources • Summary • Future Plans microarray data analysis programming help local installation of programs (clustalw, BLAST, hmmpfam)

  14. Sample Projectsmiscellaneous activities • Introduction • Sample Project: • ext. LRRs • miRNA targets • The CASBAH • complete • misc • Resources • Summary • Future Plans microarray data analysis programming help local installation of programs advise on experimental design (microarray experiments)

  15. Sample Projectsmiscellaneous activities • Introduction • Sample Project: • ext. LRRs • miRNA targets • The CASBAH • complete • misc • Resources • Summary • Future Plans microarray data analysis programming help local installation of programs advise on experimental design help with grant applications

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

  17. Resourceshardware • Introduction • Sample Project: • Resources • hardware • online • Summary • Future Plans 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

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

  19. Resourcesbioinf.gen.tcd.ie • Introduction • Sample Project: • Resources • hardware • online • Summary • Future Plans links to locally installed programs PubCrawler: It goes to the library. You go to the pub

  20. Resourcesbioinf.gen.tcd.ie • Introduction • Sample Project: • Resources • hardware • online • Summary • Future Plans links to locally installed programs course material: Computer programming for Biologists Bioinformatics from the UNIX command line

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

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

  23. Summary Introduction Sample Project: Resources Summary Future Plans Which program can I use to do XXX? I’d like to learn how to program! What does this parameter do? Where can I store my data? 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?

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

  25. End Introduction Sample Project: Resources Summary Future Plans

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