Science Studio: Remote Access to Scientific Experiments using a Comprehensive Management Tool

1. Science Studio: Remote Access to Scientific Experiments using a Comprehensive Management Tool

2. User Access to Synchrotrons • Who is the community that will use your platform? • Synchrotrons are electron storage rings that emit high intensity photons that are used for experiments by a large scientific community (tens of thousands worldwide). • Access is normally granted for single periods of 1-3 days in a half-year cycle. • What couldn’t your community do without the platform? • Physical distances and episodic access prevent rapid scientific progress and limit scientific collaboration. • Why was that a problem or limitation? • Governments worldwide have invested >$2B in these facilities, yet the scientific outcomes could be optimised.

3. User Access to Synchrotrons • What middleware was needed to resolve the limitations? • Workflow management Engine for the User Office • Web Portal for remote data access (during and post experiment) • Enterprise Service Bus and SOA to integrate internal and external data analysis services • How do your plans meet the needs • Users will have frequent remote access to the VESPERS beamline at the Canadian Light Source under conditions where many collaborators can participate in the experiment.

4. 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)

5. Team: People and Orgs System Requirements Testing Data Analysis/Grid Computing Remote Control User Services System Deployment Integration User Office Software Scientific Workflow Engines System Architecture

6. Team: People and Orgs Mike Bauer Stewart McIntyre Marina Suominen Fuller Jinhui Qin Nathaniel Sherry Dionisio Medrano Dylan Maxwell Daron Chabot Elder Matias Yuhong Yan Zahid Anwar Ludeng (Eric) Zhao Dan Ni YaofengXu Chris Armstrong John Haley

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

8. Web Application Beamline Control Module VESPERS HTTP JMS CA SAN DB VESPERS Beamline • 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)

9. VESPERS Endstation CCD Detector (XRD) Microscope Sample MCA Detector (XRF)

10. Web Application Beamline Control Module VESPERS HTTP JMS CA SAN DB EPICS Low-level Control System • 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.

11. Web Application Beamline Control Module VESPERS HTTP JMS CA SAN DB Beamline Control Module (BCM) • 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).

12. Web Application Beamline Control Module VESPERS HTTP JMS CA SAN DB Web Application • 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.

13. Web Application Beamline Control Module VESPERS HTTP JMS CA SAN DB Database • 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.

14. person facility laboratory instrument technique project_person project Instrument_technque project_role sample session experiment scan Database Schema

15. Web Application Beamline Control Module VESPERS HTTP JMS CA SAN DB Experimental Data Storage • 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.

16. Web Application Beamline Control Module VESPERS HTTP JMS CA SAN DB VESPERS Web Interface • 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.

17. Beamline Setup

18. Experiment Setup

19. XRF (X-Ray Fluorescence)

20. Beamline Hutch Cameras

21. Experimental Data Viewer

22. S: Kα Cr: Kα & Cr: Kβ Fe: Kα & Fe: Kβ Ni: Kα & Ni: Kβ X-Ray Fluorescence (XRF): Reveals Elemental Composition Characteristic Element Lines Selected and Mapped Over a 2D Scan Area 2D Maps Generated for Selected Elemental Lines

23. Peak Search X-Ray Diffraction (XRD): Reveals Structural Information Peak Fitting and Indexing of Image Set to Create a Grain Orientation Map Indexing Process Grain Orientations New C Programme – Matched Peak New C Programme – Expected Peak Old IDL Programme – Matched Peak Old IDL Programme – Matched Peak The XRD Indexing programme examines the locations of peaks in an image in order to determine the kind of lattice structure the samples constituent atoms are arranged in. Shown here are the results of an older indexing programme written in IDL, and the new indexing programme, written in C. The new indexing programme is proving to be more versatile, and more reliable than the old programme, often indexing sets of data that the old programme failed with.

24. User Office Workflow CLS health & safety inspection 6-month cycle Mar cientistpacks sample Many other tasks • Perform Experiment • Return Sample • Take Survey • … CLS call for proposals CLS grants scientist Beamline time CLS gathers proposals I wonder if CLS received my sample yet? Scientist must complete Online SS training CLS reviews proposals Proposal submission To CLS Goal: Many tasks in proposal & sample management at CLS To develop a workflow management system that • manages ordering of tasks e.g. (training beforeshipping) • Tracks manual as well as SS task progression

25. User office Workflow Status Workflow Management Engine Beamline User User Office Features Open source Petri-nets based Direct support for workflow control flow patterns Ability to interact with web services declared in WSDL Relies on XML standards e.g. XPath and XQuery for data & doesn’t use proprietary languages Architecture System Core: YAWL engine. Engine instantiates specifications designed using YAWL designer. managed by the YAWL repository Environment composed of YAWL services inspired by “web services” paradigm, end-users, applications, and organizations are all services in YAWL. Task :Training Completed Notify Record Progress Approved Notify

26. Screenshot: User Training Test Creation

27. Screenshot: User Survey Taking Page

28. Screenshot: User Survey Edit Page

29. Screenshot: Workflow Sample Management

30. Screenshot: Workflow Call for Proposals

31. 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

32. 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.

33. Scheduling Module Features Users Submit proposals INPUT: CONSTRAINTS 1. One beamlineper experiment 2. Start time after release time 3. Only eligible beamlines can be selected . . 7. No overlap of experiment perbeamline SEARCH AND CONSTRAINT SATISFIABILITY: Integer Programming and Heuristic Algorithm Schedule OUTPUT:

34. Comparison to Current State of the ArtUser Access to Synchrotrons • Synchrotrons access is normally granted for single periods of 1-3 days in a half-year cycle. But… • Episodic access requires careful pooling of samples • Little or no time for analysis of data during the experimental access. • “Reprise” experiments difficult to schedule • Travel is expensive and inconvenient • User control and records of experiments at the site is sometimes limited. The network would encourage common data formats and protocols leading to closer collaboration

35. Next Steps • Access to VESPERS /XRF2.0 available to UWO users by Fall 2009. • User training module in use at CLS by July 2009 • VESPERS/Diffraction 1.0 available by UWO Feb 2010 • All user scheduling in place by April 2010 • VESPERS available to internet users end of 2010