cience Studio

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.

 

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.

3

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)

4

5

Team: People and Orgs

Remote Control

User Services

System Deployment

Integration

System Architecture

System Requirements

Testing

Data Analysis/Grid Computing

User Office Software

Scientific Workflow Engines

6

Team: People and Orgs

Dionisio Medrano

Dylan Maxwell

Daron Chabot

Elder Matias

Chris Armstrong

John Haley

Mike Bauer

Stewart McIntyre

Marina Suominen Fuller

Jinhui Qin

Nathaniel Sherry

Yuhong Yan

Zahid Anwar

Ludeng (Eric) Zhao

Dan Ni

Yaofeng Xu

System Architecture

WebApplication

BeamlineControlModule

DBSANSAN

JMS CA

VESPERS

HTTP

1. VESPERS Beamline2. EPICS control system3. Beamline Control Module (BCM)4. Web Application5. Database6. File Storage7. Web Interface

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)

WebApplication

BeamlineControlModule

DBSANSAN

JMS CA

VESPERS

HTTP

VESPERS Endstation

CCD Detector (XRD)

Microscope

MCA Detector (XRF)Sample

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.

WebApplication

BeamlineControlModule

DBSANSAN

JMS CA

VESPERS

HTTP

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).

WebApplication

BeamlineControlModule

DBSANSAN

JMS CA

VESPERS

HTTP

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.

WebApplication

BeamlineControlModule

DBSANSAN

JMS CA

VESPERS

HTTP

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.

WebApplication

BeamlineControlModule

DBSANSAN

JMS CA

VESPERS

HTTP

Database Schema

person

project_person

project_role

project

session

laboratory

sample experiment scan

techniqueinstrument

Instrument_technque

facility

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.

WebApplication

BeamlineControlModule

DBSANSAN

JMS CA

VESPERS

HTTP

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.

WebApplication

BeamlineControlModule

DBSANSAN

JMS CA

VESPERS

HTTP

Beamline Setup

Experiment Setup

XRF (X-Ray Fluorescence)

Beamline Hutch Cameras

Experimental Data Viewer

X-Ray Fluorescence (XRF): Reveals Elemental Composition Characteristic Element Lines Selected and Mapped Over a 2D Scan Area

S: Kα Cr: Kα & Cr: Kβ Fe: Kα & Fe: Kβ Ni: Kα & Ni: Kβ

2D Maps Generated for Selected Elemental Lines

X-Ray Diffraction (XRD): Reveals Structural Information Peak Fitting and Indexing of Image Set to Create a Grain Orientation Map

Peak Search

Old IDL Programme – Matched Peak

Old IDL Programme – Matched Peak

New C Programme – Matched Peak

New C Programme – Expected 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.

Grain Orientations

Indexing Process

User Office Workflow

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

Mar6-month cycle

CLS call for proposals

Proposal submissionTo CLS

CLS gathers proposals

CLS reviews proposals

CLS grants scientistBeamline time

cientist packs sample

I wonder if CLS

received my sample

yet?

Scientist must complete Online SS training

CLS health & safetyinspection

Many other tasks• Perform Experiment• Return Sample• Take Survey• …

User office Workflow Status Workflow Management Engine

Beamline User

User Office

Task :Training

Completed

Notify

Approved Notify

PersistentStore

Record Progress

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.

Screenshot: User Training Test Creation

Screenshot: User Survey Taking Page

Screenshot: User Survey Edit Page

Screenshot: Workflow Sample Management

Screenshot: Workflow Call for Proposals

User Office Workflow Example

Prototype Implementation1. 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

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.

Scheduling Module Features

Users Submit proposals

Integer Programming and

Heuristic Algorithm

Schedule

INPUT:

SEARCH ANDCONSTRAINTSATISFIABILITY:

OUTPUT:

Beamlines 2

Experiments 3

Release Times [1,1,2]

Deadlines [8,15,5]

Weights [4,5,1]

Processing Times [10,4,3]

Eligibility [[0,1,0],[1,0,1]]

CONSTRAINTS1. One beamline per experiment2. Start time after release time3. Only eligible beamlines can be selected..7. No overlap of experiment per beamline

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