SyMBA (http://symba.sf.net) is a data archive and integrator based on Version 1 of the Functional Genomics Experiment (FuGE, http://fuge.sf.net) Object Model (FuGE-OM), and which archives, stores, and retrieves raw high-throughput data. Until now, few published systems have successfully integrated multiple omics data types and information about experiments in a single database. SyMBA includes a database back-end, expert and standard interfaces, and a Life Science Identifier (LSID) Resolution and Assigning service to identify objects and provide programmatic access to the database. Having a central data repository prevents deletion, loss, or accidental modification of primary data, while giving convenient access to the data for publication and analysis. It also provides a central location for storage of metadata for the high-throughput data sets, and will facilitate subsequent data integration strategies. We encourage the use, installation and development of SyMBA by other groups. Please let us know if you are interested in using or evaluating SyMBA for use at your own Centre. Contact us: symba-devel at lists.sourceforge.net

1. SyMBA Overview Allyson Lister [email_address] CISBAN, Newcastle University March 2009 Allyson Lister, CC BY-SA 3.0 unless otherwise specified

3. Why use SyMBA?

4. What is SyMBA?

5. How is SyMBA used? CC-SA-2.0, Tom Murphy VII, commons.wikimedia.org

6. Background: Handling Big Data CC-SA-2.0, Tom Murphy VII, commons.wikimedia.org

8. “This transition will require...standardized methods” Nature 455, 47-50 Release of September 2 2008: http://uniprot.org

10. “ This takes a degree of intellectual and practical commitment to what can seem like tedious bookkeeping.” Nature 455, 1 Nature Biotechnology 25, 1127 - 1133

12. “ Researchers need to be obliged to document and manage their data with as much professionalism as they devote to their experiments.” ( Nature 455, 1) CC-NC-2.0

14. [researchers]... “should receive greater support in this endeavour than they are afforded at present.” Nature 455, 1

16. Defining and recording appropriate metadata to allow for later interpretation of the data

17. Definition of metadata best done at the time of data capture

19. What is SyMBA? CC-SA-2.0, Tom Murphy VII, commons.wikimedia.org

21. Syntax: the structure for that information

22. Semantics: providing agreed-upon definitions for the information PD: http://commons.wikimedia.org/wiki/Image:Duke_Ellington_-_Hurricane_Ballroom_-_trio.jpg

24. the final processed (normalised) data for the set of hybridisations in the experiment

25. the essential sample annotation

26. the experimental design

27. sufficient annotation of the array

28. the essential laboratory and data processing protocols adapted from mibbi.org (image) and text from http://www.mged.org/Workgroups/MIAME/miame.html

30. standardizes and structures experimental metadata for a range of omics experiments

31. models experimental objects such as samples, protocols, instruments, and software

32. provides extension points for the creation of individual community standards PD: http://commons.wikimedia.org/wiki/Image:Syntax_tree.svg

34. 'universal' terms, that are applicable across various biological and technological domains

35. enables computational exploitation of information PD: http://commons.wikimedia.org/wiki/Image:Enigma.jpg

36. Why Use SyMBA? CC-SA-2.0, Tom Murphy VII, commons.wikimedia.org

38. CISBAN has a way to allow researchers to provide this metadata at the same time as they archive and backup their data: SyMBA

39. The Big Data special was only 2 weeks ago, but SyMBA has been in development for > 2 years! CC BY-SA 3.0: http://commons.wikimedia.org/wiki/File:DNA_microarray.svg

41. Protected

42. Well-organized

43. Easily-accessible

44. Searchable PD: http://commons.wikimedia.org/wiki/Image:Affymetrix_GeneChip.jpg

46. Promote data sharing through the use of standards

47. Aids conformance to journal standards of data deposition and description nature.com

50. How is SyMBA Used? CC-SA-2.0, Tom Murphy VII, commons.wikimedia.org

52. When the design of the website was being developed, the users said you wanted something quick and simple to use .

54. Discover what protocols, equipment, and software are used (e.g. answers to MIBBI checklists)

55. Templates are made

56. This saves users from entering data multiple times! GNU: commons.wikimedia.org/wiki/Image:Cyberduck_document.png

57. GNU: commons.wikimedia.org/wiki/Image:Cyberduck_document.png Template Exp. 1 Exp. 2 Exp. 3 SyMBA Developer-created Templates User-created Experiments SyMBA SyMBA

59. Template Creation Wizard

60. Provide batch loading features CC BY 2.5: http://commons.wikimedia.org/wiki/Image:DeLorean_DMC-12_Head_with_doors_open.png

62. This could mean automatic upload from SyMBA to EBI

63. If other research groups store data using the FuGE format, then we could share experimental information much more easily

65. Thank You CC-SA-2.0: http://commons.wikimedia.org/wiki/Image:Thank_you_trashcan.jpg

67. Project documentation: http://symba.sf.net

68. Mailing list: [email_address]

69. Sandbox (playground) installation: http://www.cisban.ac.uk/symba-sandbox

71. CC-BY-2.5 is under the Creative Commons Attribution – 2.5 Generic license. Details here: http://creativecommons.org/licenses/by/2.5

73. I have strived to keep attribution for all images used. Please let me know if I have gotten anything wrong. Please note all other portions of this presentation are copyright by Allyson Lister and her employers under the CC BY-SA 3.0. See http://creativecommons.org/licenses/by-sa/3.0