This document discusses provenance and collaboration in science. It presents use cases in astronomy, biology, and other disciplines to illustrate challenges around data packaging, preservation, retrieval and reuse of scientific workflows. These include dealing with large datasets, versioning data from external sources, and understanding and reusing other researchers' workflows. The role of research objects and linked data for supporting provenance, identity, context and the lifecycle of scientific work is also examined.

1. Provenance in the Dynamic, Collaborative New Science Dr Jun Zhao Department of Zoology University of Oxford [email_address]

5. Technological infrastructure for the preservation and efficient retrieval and reuse of scientific workflows in a range of disciplines

6. Packaging, preserving and publishing

7. Dealing with big amounts of tabular data

8. A lot of small scripts to avoid creating blackbox process

9. Local resource sharing, public access only after publication

10. Data must be frequently updated from external data repositories

11. Data updates must be tested before being executed

12. Data must be locally stored with versioning

13. “ ... we don't like to spread [the tasks] and lose controls who is doing what ...” Astronomy Use Case: A Repeater's Story

14. Research Objects Aggregation – Pointers or literals of internal and external content;

15. Identity –Equivalence, equality;

16. Metadata – A reusable object;

17. Lifecycle – Stages of development. Impacts on available functionality ;

18. Versioning – Recording changes;

19. Security – Access, authentication, ownership, trust;

20. Graceful Degradation of Understanding – Opaque RO domain content.

21. Mixed stewardship

22. Provenance Of compound objects

23. Of evolutions

24. Of dynamic objects and static objects ROs are Content Aware Objects that bundle things together http:/www.wf4ever-project.org

25. Biology Use Case: A Reuser's Story Takes a set of genes from gene experiment results performed by others, as read in a scientific paper

26. Perform 'dry' analysis to understand which genes and which biological processes were disturbed by which chemical compounds basic affymetrix data processing

27. statistical analysis to identify genes that are significantly differentially expressed under different conditions (with/without the compounds)

28. find those pathways that are most prominent among the filtered genes

29. Biology Use Case: A Reuser's Story Search for existing experiments from myExperiment (http://myexperiment.org)

30. Challenge: Understand the workflow Perform test runs with test data and his own data

31. Read others' logs

32. Read annotations to workflows Reuse scripts from colleagues and perform tests that his colleagues are familiar with

33. How Can It be Supported? A reference to the source of the data and the people to acknowledge for it.

34. The initial hypothesis

35. The conceptual workflow or a summary of the experiment plan

36. References to workflows that were tested , with comments on their application for the user's use case

37. The workflow of the user's, possibly with a backlog of previous versions that the user wishes to keep for reference (with notes and comments)

38. The runs of the user's own workflow, results and the recorded steps that lead to the results, in some cases with comments for later reference (e.g. 'here I used parameter A, next time I may try B')

39. The final hypothesis, with comments.

40. A reference to the results of the workflow

41. Design logs that record the user's considerations while making the workflow

42. Run logs that record the user's considerations while running and interpreting the workflow

43. Where is Linked Data?

44. The Role of Linked Data in Wf4Ever Collaborative science

45. Dynamic science

46. Open science

47. Provenance Challenge Identity

48. Context

49. Storage

50. Retrieval

51. Take home Provenance should be user-driven

52. Linked Data should be a means to an end

53. http://www.wf4ever-project.org

54. Acknowledgement Marco Roos of Leiden Unveristy (NL) and Jose Enrique Ruiz of Instituto de Astrofísica de Andalucía (Spain)

55. Carole Goble of University of Manchester (UK) and Jose Manuel Gomez of iSOCO (Spain)

56. Hui Hua and Jenny Molly of University of Oxford (UK)