1. Science Studio CANARIE Review July 7, 2009

2. Team: People and Orgs Dionisio Medrano Dylan Maxwell *Elder Matias *Lavina Carter Dong Liu Chris Armstrong John Haley Mike Bauer Stewart McIntyre *Todd Simpson Marina Suominen Fuller Jinhui Qin Nathaniel Sherry *Yuhong Yan Ludeng (Eric) Zhao *Dan Ni *Owen Jian *Zahid Anwar *Glenn Wright *Ru Iragashi *Daron Chabot *Gillian Black

3. Today’s agenda 8.30: Welcome and Introduction to CLS (Elder Matias) 8.35: Scientific Goals for Science Studio and review of its components (Stewart McIntyre) 8.45: Review of Architecture of Science Studio (Chris Armstrong) 9.00: Demonstration of VESPERS XRF remote operation (Dylan Maxwell) 9.30: Demonstration of User Services software (Diony Medrano) 9.45: Review of Task Schedule and update on immediate plans (Stewart McIntyre) 10.00: Coffee and further discussion 10.20: VESPERS remote software: accomplishments future additions (Stewart McIntyre, Chris Armstrong and Elder Matias) 10.40: Development of XRD analysis software for Science Studio (Michael Bauer) 11.00: Development of XRF analysis software for Science Studio (Stewart McIntyre) 11.15: Planning for Nanofab lab software development (Stewart McIntyre) 11.30: Development of User Office Software (Elder Matias) 11.40: Potential use of UCLP (Michael Bauer) 11.50: Comparisons with ANISE, discussion on IP issues (Chris Armstrong) 12.00: Lessons Learned (Group) 12.30: Lunch (provided in room or nearby) 1.00: Wrap up questions from CANARIE visitors 1.30: Tour of CLS for CANARIE visitors 2.30: Depart for airport

4. Welcome to Canadian Light Source

5. Objectives of CLS 170.88 m circumference 2.9 GeV DBA lattice with 12-fold period Nominal Tune: x = 10.22 y = 3.26 E loss per turn: > 0.876 MeV Bend magnet radiation: c = 1.6 Å E c = 7.6 keV  x = 18.1 nmrad Damping times:  x = 2.4 ms,  y = 3.8 ms,  E = 2.7 ms ~10 mm bunch length

6. Machine Layout

7. Current Plans at CLS  Phase 1 (operation): Total of 7 scientific and 2 diagnostics beamlines.  Phase 2 (commissioning): Total of 7 additional beamlines and building expansion for medical imaging.  Phase 3 (pre-design): Total of 7 additional beamlines and building expansion.  Current Controls software: EPICS  Future: EPICS and Science Studio

8. Goals  Science Studio serves three purposes: Management of all aspects of a scientific experiment including data storage, collaboration with others, processing of data; Control of, or interaction with, remote experiments on the CLSI VESPERS Beamline and UWO Nanofabrication Laboratory and User Services (sample management, scheduling, peer review, user training) 8

9. Science Studio Goals  Allow collaborators to watch and comment on the experiments being undertaken and (in some cases) to take control.  Provide a bank of data analysis services that are compatible with the data produced.  Provide an enhanced single platform user access to the most useful beamline functions and keep keeps intricate records of the scientific steps taken and provides the user with easily downloadable results whether he/she is in Saskatoon or Samarkand. Science Studio@VESPERS: provide access for XRD and XRF Science Studio@Nanofab: provide access for high resolution microscopic measurements  Provide some common user services.

10. User Services  Intended to provide a “one stop, one site” service to remote and traditional users of VESPERS (and other lines)  Provides training/testing, “End of Run” report, user scheduling, sample handling and peer review.  Will be accessed through Science Studio site for VESPERS users. 10

11. 11 Next Steps Heavy emphasis on development of SS/XRD image analysis and transfer until September, because of its sucessful inauguration on VESPERS VESPERS SS/XRF VESPERS is being tested by user groups. Development of user service software at CLS and Concordia is mid-way in its pathway Nanofab lab SS developments to be accelerated by September Limited VESPERS SS/ XRF-XRD service to be available to internet users worldwide by November 2009 Planning for SS interaction with the ANISE project is underway.

12. Distributed Architecture

13. Options

14. Architecture Overview

15. Product Mapping

16. Spring MVC Ext JS, JQuery, Custom Custom Ext JS & JQuery Custom YAWLCustom ActiveMQ CustomCVS, MKS Custom Active Directory@CLS, Spring LDAP iBATIS Custom Spring Apache Ki Tomcat, Apache Custom Custom, Spring Custom

17. Distributed Architecture

18. Options

19. Architecture Overview

20. Product Mapping

21. Spring MVC Ext JS, JQuery, Custom Custom Ext JS & JQuery Custom YAWLCustom ActiveMQ CustomCVS, MKS Custom Active Directory@CLS, Spring LDAP iBATIS Custom Spring Apache Ki Tomcat, Apache Custom Custom, Spring Custom

22. VESPERS Techniques 1. Phase composition, orientation and distortion using Laue Diffraction (‘pink’ beam). 2. Elemental composition using X-Ray Fluorescence. 3. Chemical information using XAS (’sharp’ beam)  …all in a volume of 2 microns diameter  and 10-50 microns deep!

23. VESPERS Beamline  VESPERS — Very Sensitive Elemental and Structural Probe Employing Radiation from a Synchrotron  A new bending magnet beamline at the Canadian Light Source.  Techniques: X-Ray Fluorescence (XRF) & X-Ray Diffraction (XRD)  XRF has widespread use; XRD has great potential and enormous computing needs. Web Application Beamline Control Module DB SAN JMSCA VESPERS HTTP

24. (a) X ray Fluorescence spectra and mapping (b) Laue X ray Diffraction and mapping OrientationStrain

25. VESPERS Demo

26. User Services Demo

27. Tasks and Schedule

28. Tasks and Schedules

30. Tasks and Schedule

31. 31 Milestones for Science studio@VESPERS Nov/Dec 2008-migration of RBA to SS; incorporation of GlenRu scanning engine; live test without scanning. Jan/Feb 2009- Scanning and downloading demonstrated Mar/April 2009-Definition of capabilities for SS1.0 June 2009-First stress test-multi scans and multi users(nsm) July 2009- Second stress test (mf and tk)

32. 32 Positive features  Reliable sample movement  Download feature functions well  System readily recovered after a dump  Scanning service appears robust  Latency is acceptable

33. Negative Features  Messaging issues (under control)  2D scan issues  Ambiguous accumulation instructions  Lack of communication on testing issues  Readouts of all ion chamber currents seem spotty  Spotty dead time readout?  Stage movements are confusing (2 sets of controls) 33

34. New Slate of Objectives for Science Studio@VESPERS2.0  Stage coordinates displayed (leftover from 1.0?)  Operation of CCD (with corrected Synaps)  Operation of CCD and XRF simultaneously  Machine and beamline status information  Peer to peer data sharing  Macro camera enabled (discuss camera calibration)  Control of sample illumination  Filter change  Active version of Peakaboo for XRF data collection  Better user instructions  Creation of Experiment Accounts at CLS  Display additional beamline status information BUT...  No movement of any other motors is contemplated 34

35. Traditional EPICS Controls: are they history? Not likely, I think that motor scanning is still too specific to each application and idiosyncratic Better to concentrate on applications involving detectors and fixed irradiation conditions.

36. Where are we going with Nanafab?

37. Device: Zeiss 1540XB FIB/SEM Technique: Scanning Electron Microscopy (SEM) combined with Energy Dispersive X-ray (EDX) Analysis A highly focussed electron (primary) beam is scanned across a sample surface at an energy between 0.5-30 keV. Low energy secondary electrons are generated as a result. An image of the sample surface is constructed by measuring secondary electron intensity as a function of the primary electron beam position on the sample. Back scattered electrons and x-rays are also emitted from the bombardment of the sample surface by primary electrons. The intensity of the backscattered electrons is related to the atomic number of the element present and provides element contrast. X-rays emitted are characteristic of elements present in the sample. Quantitative elemental information can be obtained. Elemental maps can be generated.

38. ◊ The Scanning Electron Microscope is controlled by a computer system. ◊ The system is also fitted with an Oxford Instruments x-ray system allowing for elemental mapping and analysis of the sample. ◊ The x-ray system is controlled by a separate computer. This system is connected to the microscope and detector, and takes control of the microscope and detector in order to collect the emitted x-rays during elemental mapping and analysis of the sample.

39. Incorporation into Science Studio ◊ The Oxford Instruments x-ray system is proprietary. Incorporating the microscope/x-ray system into Science Studio would be done by means of ‘wrapping’, i.e., creating an interface between Science Studio and the system. A basic screen capture interface (terminal window) can be included in Science Studio to enable a user to operate the Oxford Instruments software. The terminal window can be provided within the main SS window. Sample Analysis Data ► Scanning electron micrographs (secondary electron images) ► Backscattered electron images ► EDX spectra and elemental maps Resulting data from sample analyses are incorporated into a Word document report. Data can also be exported in other formats. Data will be accessible for download from Science Studio.

40. Data is organized under the context of project, similar to our scheme in Science Studio

41. Software is user friendly.

42. System has its own analysis software with automatic identification of element peaks during acquisition.

43. User Services

44. 44 User Services Status Overview User ServicesDraft ReqsSolid ReqsDesignCodeTestProduction User Training   User Survey and Feedback   Scheduling   Proposal, Task and Sample management Workflow   Reporting  Search  Security   User management  

45. User Training Module  Goal: To automate the user training process at CLS which is prerequisite to gaining unescorted access, and performing different roles at the facility  Side effects: improved quality of training immediate feedback on exams reduced manual grading and entry of training records one database with improved reporting capabilities. increased overall efficiency and reduction in duplication and data entry error.

46. User Training Module Features User Management Registration User and Admin Views User Management Registration User and Admin Views Intuitive Materials Categorization Modules Exams Sections Questions Presentation Intuitive Materials Categorization Modules Exams Sections Questions Presentation Reports Search results Validate training Export to Excel Trace generated tests Statistics and charts Reports Search results Validate training Export to Excel Trace generated tests Statistics and charts Test Taking Timed Examination Support for disconnections Time stamps Multiple attempts e.g. successful, firstUnsuccessful, lastUnsuccessful, alternative Test Taking Timed Examination Support for disconnections Time stamps Multiple attempts e.g. successful, firstUnsuccessful, lastUnsuccessful, alternative Test Creation Flexible question format Randomized questions Test Expiry Automatic Validation e.g. empty choice selected as correct Test Creation Flexible question format Randomized questions Test Expiry Automatic Validation e.g. empty choice selected as correct

47. User Survey and Feedback Module  Goal: To automate the user feedback and survey process at CLS to facilitate scientists  Enables User Office experiment monitoring service and accurate metrics on whether: Check in procedures are efficient and user-friendly End station equipment is ready & in good working order Shifts are being utilized Beam is being delivered without interruption Identify unforseen problems

48. Scheduling Module  Goal: To automate the review process and the method by which beam time is allocated and scheduled to users depending on the access mechanism chosen by the user and the stage of operation (construction, commissioning or operation) of the beamline.  Side effects: Facilitate the management of cycles, runs and modes of operation Use automatic scheduling to handle more scheduling conditions and constraints than human beings are able to handle manually and identify optimal solutions.

49. Calendar view

50. ULCP

51. Science Studio and ANISE

53. Lessons Learning, etc.  Lessons Learned  Questions  CLS Tour