The document discusses the opportunities and challenges in next-generation sequencing (NGS) research, highlighting the need for affordable sequencing and the associated bioinformatics challenges. It emphasizes the importance of computational resources, training, and collaboration to effectively analyze the increasing data generated by NGS technologies. The document also suggests potential solutions like web-based programs and contributions to data standards.

1. Next generation sequencing research opportunities and bioinformatic challengesLex NederbragtNorwegian High-Throughput Sequencing Centre (NSC)andCentre for Ecological and Evolutionary Synthesis (CEES)

2. Found on twitter:

3. Sequencing cost

4. Doubling times http://genomebiology.com/2010/11/5/207

5. Democratizationpathogenomics.bham.ac.uk/hts

6. DemocratizationOslo: 5 instrumentsTromsø: 1 instrumentpathogenomics.bham.ac.uk/hts

7. Norwegian Sequencing CenterIlluminaHiSeqIlluminaGaIIx454 GS FLX

8. Norwegian Sequencing Centermore than 75 runs in 2010two thirds 454 GS FLXUsers from Norway and abroadall possible applications

9. Research possibilitiesAffordable sequencingAccessible sequencing

10. Research possibilitiesA genome project in Norway!wikimedia commons

11. Research possibilitiesSoon: sequencing human genomes in Norway!Apologies to www.prism-magazine.org

12. But...

13. ChallengeLow cost sequencing+Availability to every lab=Data deluge

14. Challenges"The rule of thumb in the genomics community is that every dollar spent on sequencing hardware must be matched by a comparable investment in informatics."http://www.the-scientist.com/2011/3/1/60/1/

15. Challenges http://genomebiology.com/2010/11/5/207

16. ChallengesConstant stream of new softwarehttp://seqanswers.com/forums/showthread.php?t=43

17. ChallengesConstant stream of new softwarehard to judge if programs are any goodsometimes a challenge to install a program and get it workinghttp://neidetcher.com/ubuntu_package_dependency.html

18. Dependency hellhttp://neidetcher.com/ubuntu_package_dependency.html

19. Dependency hellhttp://en.wikipedia.org/wiki/Dependency_hellhttp://neidetcher.com/ubuntu_package_dependency.html

20. ChallengesCpu power/memory needs high for some applications

21. ChallengesNew technologies coming soonNext-Next-Generation SequencingNSC expectsdelivery of thePacific Biosciences RSin December 2011http://www.pacificbiosciences.com

22. ChallengesNew instruments coming soonOxford NanoporeGridIONIon Torrent PGMIlluminaMiSeq

23. ChallengesNew technologies coming soonNew data formatsNew types of experimentsNew types of analyses

24. Lessons from the cod projectSteep learning curvewikipedia.org

25. Lessons from the cod projectLearn unixwikipedia.org

26. Lessons from the cod projectDo not underestimate the bioinformaticsBuying sufficient compute power saved us

27. Lessons from the cod project'Hiring' people for specific tasks can help

28. Lessons from the cod projectIt is possible!34 tables, 23 figures, 78 pages supplementaryhttp://www.wordle.net

29. Cod project bioinformatics plots heatmaps

30. Cod project bioinformaticscombined plots

31. Cod project bioinformaticsWe learned a lot!but...

32. Cod project bioinformaticsHow many times did we reinvent the wheel?blogs.technet.com

33. Norwegian Sequencing CenterJust a data provider?www.sequencing.uio.no

34. Norwegian Sequencing CenterUser gets stuck with analysis=No paper=Waste of resources

35. Norwegian Sequencing CenterUser:"I have the hypothesis""You gave me the data""I need help to answer my question"

36. NSC useruser comfortable with data amounts, type, software?should user learn unix?should user buy commercial programs?are these good enough?should user go into cloud computing?fsteurope.com

37. NSC bioinformaticiansshould NSC test these programs?should NSC/UiO provide computing power?does NSC have a responsibility to provideinfrastructure?applications?training?analyses?

38. NSC bioinformaticiansif we do analyses:as collaboration, i.e. coauthor?charge per hour?are Norwegian researchers used to collaborate in this way?

39. NSC bioinformaticianswhere does analysis stop?assembly?comparative genomics?annotation?

40. Example: CEESMore and more NGS projectsToo few bioinformaticians

41. SolutionsTrainingCourses

42. SolutionsFunds for bioinformaticianshttp://www.dinside.no

43. Solutionsweb-based programs

44. Galaxyusegalaxy.org

45. Hyperbrowserhyperbrowser.uio.no

46. Solutionsweb-based programsgalaxyhyperbrowser (UiO!)Can NSC contribute to the development of these?

47. SolutionsFile standardscomingSAMBAMBEDWIG...Can NSC/UiO contribute to the development of these standards?samtools.sourceforge.net

48. SolutionsFUGE bioinformatics platformbioinfo.no

49. SolutionsComputational Life Science initiative?(http://www.ifi.uio.no/research/clsi/)linkedin.comifi.uio.no

50. Thank you!lex.nederbragt@bio.uio.nowww.sequencing.uio.nowww.sequencing.uio.no