Science Studio and ANISE (Jan 2010 update)

1. Science Studio and ANISE(Jan 2010 update) Elder Matias Canadian Light Source

2. Overview • Beamline Control Traditional Technology • Beamline Control – ScienceStudio • Nan-Fabrication – ScienceStudio • User Office • Grid Computing • User Configurable Light Paths

3. Where is Saskatoon?

4. Scientific American May 2008 Science 2.0 – The Risk and Reward of Web-Based Research --------------------------------- “Our real mission isn’t to publish journals but to facilitate scientific communication” Timo Hannay – Head of Web Publishing at Nature Publishing Group

5. What Is the Web 2.0? • In plain English …. • Automating tedious tasks using web technology • Tools to help people and software collaborate

6. Project Team Members Jinhui Qin YuzhenXie Mike Bauer Stewart McIntyre Marina Suominen Fuller Dionisio Medrano Dylan Maxwell Dong Liu Elder Matias Chris Armstrong Khalid Subratee Ludeng (Eric) Zhao Yuhong Yan

7. Goals of the Two Projects • Science Studio • User Office Automation • Integrated Experiment Management • Remote Access to VESPERS (XRD and XRF) • Access Scanning Electron Microscope (UWO) • Grid Computing (Cell Processor) • ANISE • Integrated Stream Computing to providing near real-time data processing

8. Beamline ControlTraditional Technology

9. EPICS Channel Access Protocol CA CA Detectors Cameras etc. IOC Operator Workstation User Applications CA Touch Panels Modbus TCP/IP CA IOC Telemecanique Momentum PLC CA State Machine Engine CA GPIB IOC CA IOC CA RS-232 VME CA IOC Single Board Computer

10. Beamline Controls Interfaces • EPICS Tools • Configuration Tool • User GUI & ROOT

11. Beamline Visualization - Raster scan with fluorescence spectroscopy of a pine needle contaminated with arsenic. The technique allows multiple elements to be detected simultaneously at each point of the raster. These images show distributions of arsenic, iron, and manganese, respectively, near the tip. The highest intensity displays in red, lowest in blue. - Custom on-line plotting application scripted in CERN Root, with data stream from the CLS data acquisition application. (G. Wright, R. Igarashi, K. Chang-Yong, N. Chen) As Map Fe Map

12. Traditional Beamline Visualization Cross section views of the beam spot intensity distribution for varying degrees of monochromator detuning (50-80%). (Only one image shown). (G. Wright, R. Igarashi, K. Chang-Yong, N. Chen)

13. Beamline ControlScienceStudio Technology

14. Requirements • New User Office Functionality • Proposal submission • Peer review • User Feedback Tracking • Experiment Management • User Training/ Safety Testing • Remote Beamline Access • Integration with grid data-storage • Grid computing

15. Science Studio and ANISE

16. System Architecture Web Application Beamline Control Module VESPERS HTTP JMS CA SAN DB • VESPERS Beamline • EPICS control system • Beamline Control Module (BCM) • Web Application • Database • File Storage • Web Interface

17. VESPERS Beamline Web Application Beamline Control Module VESPERS HTTP JMS CA SAN DB • VESPERS — Very Sensitive Elemental and Structural Probe Employing Radiation from a Synchrotron • A bending magnet beamline on sector 6 at the Canadian Light Source synchrotron in Saskatoon, Saskatchewan. • A hard x-ray microprobe with an energy range of 6 to 30keV. • Techniques: X-Ray Fluorescence (XRF) & X-Ray Diffraction (XRD)

18. EPICS Low-level Control System Web Application Beamline Control Module VESPERS HTTP JMS CA SAN DB • EPICS — Experimental Physics and Industrial Control System • The standard control system at the CLS. • EPICS consists of a network of Input-Output Controls (IOCs) which are connected to directly to devices. • An IOC provides many Process Variables (PVs) which relate to either an input or output from a device and have a unique name. • Channel Access (CA) is used to read or write to any PV without knowing which IOC provides the PV. • More than 50,000 PVs in the CLS control system.

19. Beamline Control Module (BCM) Web Application Beamline Control Module VESPERS HTTP JMS CA SAN DB • The BCM provides a high-level interface to the low-level control system (EPICS). • Logical and physical separation of business logic and control logic. • Virtual device abstraction that provides independence from low-level control system. • Virtual devices can be logically organized into a device hierarchy. • Basic devices can be combined to build more functional devices. • Communication with external applications using two message queues (ActiveMQ).

20. Web Application Web Application Beamline Control Module VESPERS HTTP JMS CA SAN DB • A J2EE Servlet application that provides a web-based interface Science Studio. • Tools: Spring (MVC), iBATIS (ORM), JSecurity (Apache Ki), Apache Tomcat • Divided into two parts: the Core application and the VESPERS beamline application. • Core application is responsible for providing access to the business objects. • VESPERS application is responsible for remote control of the VESPERS beamline.

21. Database Web Application Beamline Control Module VESPERS HTTP JMS CA SAN DB • Metadata associated with the operation of a remote controlled beamline and the organization of experimental data collected on that beamline. • A project is the top level organizational unit and is associated with a project team. • A session defines a period of time allocated to a project team to conduct experiments. • An experiment relates a sample and the technique being applied to that sample. • A scan records the location of the acquired experimental data.

22. Experimental Data Storage Web Application Beamline Control Module VESPERS HTTP JMS CA SAN DB • Experimental data is stored at the CLS. • Common directory structure shared with other beamlines. • A large data storage facility is now operational at the University of Saskatchewan as part of WestGrid.

23. VESPERS Web Interface Web Application Beamline Control Module VESPERS HTTP JMS CA SAN DB • Rich web interface to Science Studio and the VESPERS beamline. • Designed to be used over commodity broadband internet. • Developed for the Firefox web browser without any additional plugins or extensions. • Known to work with other browsers, but requires the Canvas HTML tag. • AJAX is used for the VESPERS interface to provide device values in pseudo real time. • ExtJS, a JavaScript framework, provides many advanced GUI elements.

25. Beamline Setup

26. Experiment Setup

27. XRF (X-Ray Fluorescence)

28. Beamline Hutch Cameras

29. Experimental Data Viewer

31. ScienceStudio

32. Scanning

33. XRD Screen

34. (a) X ray Fluorescence spectra and mapping Orientation Strain (b) Laue X ray Diffraction and mapping

35. XRF Image XRD: orientation XRD:strain Optical image VM strain

36. University of Western OntarioNan-Fabrication FacilityUsing ScienceStudio

37. Nanofabrication Facility The Western Nanofabrication Facility is an open user facility at the University of Western Ontario for the fabrication of micro and nano structures. LEO 1540XB Scanning Electron Microscope (SEM) with an integrated Oxford x-ray system. • Oxford x-ray system is controlled by INCA. • INCA provides limited control of the SEM, and spectral analysis and quantification.

38. Nanofab Integration Design

39. NanofabImplementation

40. Initial Test: INCA Remotely

41. User Office

43. User Office Modules • User Profile/Authentication • User Profile Deployed • User Roles Deployed • Authentication (LDAP/AD) Deployed • Information Model • Beamlines Done • End-stations Done • Techniques Done • Notification Module Deployed

44. User Office Modules • Proposal Submission In Progress • User Feedback Survey Prototype • Scheduling Module Prototype • Workflow Engine Evaluation • Sample Management Requirements • Publication Tracking Requirements

45. User Office - Training Module • First User Office Module Deployed • User Profile • 1,400 + user records/accounts created • Training Module • 53 Training Modules Setup and past user records manually transferred

46. Calendar view in JQuery

47. User Office Workflow Example Prototype Implementation 1. CLS issues a call for proposals and gives deadline2. Beamline users submit proposals3. User Office administrator ends registration or extends deadline4. User Office administrator assigns proposals to user office reviewers5. Reviewers look at proposals and rank them6. User Office looks at ranking and chooses the proposals to accept7. Accepted proposals contact persons are notified8. Beamline User completes training (web service)9. After training is completed (simulated by a delay) the CLS is notified

48. User Login

49. Admin – Add Proposal

50. Admin - Setup for Cycle