cience Studio

Science Studio CANARIE Review

July 7, 2009

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

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 discussion10.20: 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

Welcome to Canadian Light Source

Objectives of CLS

170.88 m circumference 2.9 GeV DBA lattice with 12-fold periodNominal Tune:

x = 10.22 y = 3.26

Eloss per turn: > 0.876 MeVBend magnet radiation:

c = 1.6 Å Ec = 7.6 keV

x = 18.1 nm•radDamping times:

x = 2.4 ms, y = 3.8 ms, E = 2.7 ms~10 mm bunch length

MAX-II

TLS-I

BESSY-IIALS

ELETTRA

PLS

SLS(240m)

ANKA

ESRFAPS

Spring-8

CLS (171m)SPEAR3 (240m)

Super-SORLSB

BOOMERANGTLS-II

SOLEIL(2006,354m)

NSLS-II

DIAMOND(2007,562m)

ESRFAPS Spring-8ELETTRA

1

10

100

0 1 2 3 4 5 6 7 8 9Energy(GeV)

Em

ittan

ce(n

m·r

ad)

KSRS (124m)

Machine Layout

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

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

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.

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

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.

Distributed Architecture

CLSI

UWO

Concordia U.

Data Storage as A Service

Data Processing as a Service

OptionsScience Studio Version 1.1

CLS

UWONanofab Lab

Science Studio Version 1

Chalk River

UBC

CLS

UWONanofab Lab

Chalk River

UBC

Object Exchange

Object Exchange(e.g. proposal)

Object Exchange

CLS-proposal-vespers

UWONanofab Lab

-proposal-electron mic.

Chalk River-proposal

-beamlineX

UBC-proposal

-beamlineY

Project Repository

- project-samples

-data

Common Service

(Processing)

Common Services

(Processing, Data Storage, Exchange Mediation)

Architecture Overview

Browser

RDBMS

Business ModelLayer

PersistenceLayer

DeviceProxies

Client ServicesLayer

Browser Browser

IOCs

LabatoryControl Module

IOCs

LaboratoryControl Module

ProcessingService

ServiceProxies

DataService

Science Studio

Beamline

Beamline

Product Mapping

Browser

RDBMS

Business ModelLayer

PersistenceLayer

DeviceProxies

Client ServicesLayer

Browser Browser

Beamline

IOCs

LabatoryControl Module

Beamline

IOCs

LaboratoryControl Module

ProcessingService

ServiceProxies

DataService

Science Studio

ExtJSFirefox | Chrome

XML / AJAXHTML

SPRING MVC

J2EE / TOMCAT SERVLETS

TBD

TBD

TBD

DERBY | SQL Server | MySQL

JDBC

JMS

SPRING IOC

IBATIS

jsecurity

Infrastructure Services

User Interface Services

Common Services

Data Forms

Experiment Control

Message Broker, Transformation & other SOA

Middleware

Business Application Services

External Services i.e. Existing Applications and

Information Assets

Common Event Infrastructure (error

handling)

Experiment Management

Services

User Services

User Training Proposal

ProcessProject & Task Mgt

Lab Scheduling

Sample Mgt

Information Services

File Transfer

Search Engine

Config Mgt

EPICS

LDAP

SHARCNET

File System

VESPERS Beamline

Analysis s/w

Information Model

Audit & Logging

Application Framework

Services MgtManage and secure services, applications and resources

Access MgtFacilitate interactions with exiting assets

DAO

Data Processing

Module

EPICS JCA

Web Services Engine

Common Directory Services

Security

Business Process Management

Workflow Engine

Scheduling

Lab Control Module

Lab Mgt

Data Mgt

Legend

Science Studio Component

Science Studio Common Infrastructure

& Frameworks

External Component

Browser Framework

UI Framework

Navigation Tree

Data Processing Module

Device Simulation

NanoFab

Parallel Processing Services

Spring MVC

Ext JS, JQuery, Custom

Custom

Ext JS & JQuery

Custom

YAWL Custom

ActiveMQ

Custom CVS, MKS

Custom

Active Directory@CLS,

Spring LDAP

iBATIS

Custom

Custom

SpringApache KiTomcat, Apache

Custom

Custom, Spring

Custom

Custom

Distributed Architecture

CLSI

UWO

Concordia U.

Data Storage as A Service

Data Processing as a Service

OptionsScience Studio Version 1.1

CLS

UWONanofab Lab

Science Studio Version 1

Chalk River

UBC

CLS

UWONanofab Lab

Chalk River

UBC

Object Exchange

Object Exchange(e.g. proposal)

Object Exchange

CLS-proposal-vespers

UWONanofab Lab

-proposal-electron mic.

Chalk River-proposal

-beamlineX

UBC-proposal

-beamlineY

Project Repository

- project-samples

-data

Common Service

(Processing)

Common Services

(Processing, Data Storage, Exchange Mediation)

Architecture Overview

Browser

RDBMS

Business ModelLayer

PersistenceLayer

DeviceProxies

Client ServicesLayer

Browser Browser

IOCs

LabatoryControl Module

IOCs

LaboratoryControl Module

ProcessingService

ServiceProxies

DataService

Science Studio

Beamline

Beamline

Product Mapping

Browser

RDBMS

Business ModelLayer

PersistenceLayer

DeviceProxies

Client ServicesLayer

Browser Browser

Beamline

IOCs

LabatoryControl Module

Beamline

IOCs

LaboratoryControl Module

ProcessingService

ServiceProxies

DataService

Science Studio

ExtJSFirefox | Chrome

XML / AJAXHTML

SPRING MVC

J2EE / TOMCAT SERVLETS

TBD

TBD

TBD

DERBY | SQL Server | MySQL

JDBC

JMS

SPRING IOC

IBATIS

jsecurity

Infrastructure Services

User Interface Services

Common Services

Data Forms

Experiment Control

Message Broker, Transformation & other SOA

Middleware

Business Application Services

External Services i.e. Existing Applications and

Information Assets

Common Event Infrastructure (error

handling)

Experiment Management

Services

User Services

User Training Proposal

ProcessProject & Task Mgt

Lab Scheduling

Sample Mgt

Information Services

File Transfer

Search Engine

Config Mgt

EPICS

LDAP

SHARCNET

File System

VESPERS Beamline

Analysis s/w

Information Model

Audit & Logging

Application Framework

Services MgtManage and secure services, applications and resources

Access MgtFacilitate interactions with exiting assets

DAO

Data Processing

Module

EPICS JCA

Web Services Engine

Common Directory Services

Security

Business Process Management

Workflow Engine

Scheduling

Lab Control Module

Lab Mgt

Data Mgt

Legend

Science Studio Component

Science Studio Common Infrastructure

& Frameworks

External Component

Browser Framework

UI Framework

Navigation Tree

Data Processing Module

Device Simulation

NanoFab

Parallel Processing Services

Spring MVC

Ext JS, JQuery, Custom

Custom

Ext JS & JQuery

Custom

YAWL Custom

ActiveMQ

Custom CVS, MKS

Custom

Active Directory@CLS,

Spring LDAP

iBATIS

Custom

Custom

SpringApache KiTomcat, Apache

Custom

Custom, Spring

Custom

Custom

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!

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.

WebApplication

BeamlineControlModule

DBSANSAN

JMS CA

VESPERS

HTTP

(a) X ray Fluorescence spectra and mapping

(b) Laue X ray Diffraction and mapping Orientation Strain

VESPERS Demo

User Services Demo

Tasks and Schedule

Duration Start_Date Finish_Date Completion as Today Deliverables Start_Date % Completion Finish_Date01 - Science Studio 761 days 05/01/2008 03/31/2011 40.54%

Phase 1 87 days 05/01/2008 08/31/2008 100.00% 87%Requirements and initial design 18 days 05/01/2008 05/26/2008 100.00% 6/1/2008 100% 8/31/2008Requirements workshop 0 days 05/26/2008 05/26/2008 100.00% 10/28/2008 100% 10/28/2008Initial product selection and prototyping 18 days 05/27/2008 06/19/2008 100.00% 6/1/2008 100% 6/28/2008Setup software infrastructure 17 days 06/20/2008 07/14/2008 100.00% 6/10/2008 100% 6/28/2008User services - proposal management 17 days 07/15/2008 08/06/2008 100.00% 9/15/2008 10% 11/28/2009Refine frameworks and start core development 17 days 08/07/2008 08/31/2008 100.00% 7/5/2008 100% 8/30/2008

Phase 2 88 days 09/01/2008 12/31/2008 100.00% 76%User Services - additional services 13 days 09/01/2008 09/17/2008 100.00% 9-Jan 50% 11/28/2009Release ScienceStudio on VESPERS 0 days 09/17/2008 09/17/2008 100.00% 5/12/2008 100% 5/12/2008Demo to CANARE and interested parties 0 days 09/17/2008 09/17/2008 100.00% 10/29/2008 100% 10/29/2008Simulated beamline 13 days 09/18/2008 10/06/2008 100.00% 9/10/2008 100% 10/27/2008Refine frameworks 13 days 10/07/2008 10/23/2008 100.00% 9/22/2008 100% 11/28/2008Define Strategy for Stream Computing Integration with ScienceStudio13 days 10/24/2008 11/11/2008 100.00% 9/10/2008 100% 26-NovImplement scheduling service 12 days 11/12/2008 11/27/2008 100.00% 5/1/2009 20% 11/1/2009Performance tuning 12 days 11/28/2008 12/15/2008 100.00% 11/15/2008 100% 12//15/2008User profile services 12 days 12/16/2008 12/31/2008 100.00% 12/4/2008 30% 11/1/2009

Task_NamePlanned Actual or Expected

Tasks and Schedules

Duration Start_Date Finish_DateCompletion as TodayDeliverables Start_Date% CompletionFinish_Date01 - Science Studio 761 days 05/01/2008 03/31/2011 40.59%

Phase 3 86 days 01/01/2009 04/30/2009 100.00% 71%Harden user services 12 days 01/01/2009 01/16/2009 100.00% 1/6/2009 90% 9/1/2009Refine frameworks and core development 12 days 01/19/2009 02/03/2009 100.00% /6/2009 100% 1/26/2009Performance tuning 12 days 02/04/2009 02/19/2009 100.00% 11-Jan 100% 4/30/2009VESPERS Remote Access – Integrate Processing of Data and Sample Management 12 days 02/20/2009 03/09/2009 100.00% 1/15/2009i/ 100% 3/15/2009VESPERS/XRF – Working with Selected Users 12 days 03/10/2009 03/25/2009 100.00% 1/20/2009 100% 3/200/2009Redeploy ScienceStudio in User Office 12 days 03/26/2009 04/10/2009 100.00% 3/26/2009 75% 9/1/2009Deploy and Configure ScienceStudio for NanoFab Facility (Servers installs at UWO) 12 days 04/15/2009 04/30/2009 100.00% 6/1/2009 10% 12/22/2009

Phase 4 87 days 05/01/2009 08/31/2009 54.81% 96%Performance Tuning Existing System 22 days 05/01/2009 06/01/2009 100.00% 5/1/2009 100% 6/15/2009VESPERS Remote Access – Integrate Processing of Data and Sample Management 22 days 06/02/2009 07/01/2009 100.00% 5/1/2009 100% 6/15/2009Release ScienceStudio 0 days 07/01/2009 07/01/2009 0.00% 1/5/1900 100% 6/15/2009Demo to CANARIE and Interested Parties 0 days 07/01/2009 07/01/2009 0.00% 7/7/2009 0% 7/7/2009Project and experiment management service 22 days 07/02/2009 07/31/2009 17.26% 11/1/2008 100% 1/5/2009Job management service 21 days 08/03/2009 08/31/2009 0.00% 11/1/2008 90% 8/30/2009

Task_NamePlanned Actual or Expected

Tasks and Schedules

Duration Start_Date Finish_DateCompletion as TodayDeliverables Start_Date% CompletionFinish_Date01 - Science Studio 761 days 05/01/2008 03/31/2011 40.59%

Phase 5 88 days 09/01/2009 12/31/2009 0.00% 25% Data processing packages services installed for VESPERS 13 days 09/01/2009 09/17/2009 0.00% 9/15/2008 90% 8/30/2009VESPERS/Laue X-Ray diffraction working 13 days 09/18/2009 10/06/2009 0.00% 6/1/2009 20% 8/30/2009Harden Scheduling Service 13 days 10/07/2009 10/23/2009 0.00% 5/1/2009 20% 11/11/2009Update Job management service 13 days 10/26/2009 11/11/2009 0.00%Implement security services 12 days 11/12/2009 11/27/2009 0.00%Harden Sample Management Services 12 days 11/30/2009 12/15/2009 0.00%Implement integration collaboration tools 12 days 12/16/2009 12/31/2009 0.00%

Phase 6 86 days 01/01/2010 04/30/2010 0.00%Harden collaboration integration 22 days 01/01/2010 02/01/2010 0.00%NanoFab facility data analysis integration 22 days 02/02/2010 03/03/2010 0.00%Opportunistic Access for VESPERS 21 days 03/04/2010 04/01/2010 0.00%Refine core services including security services 21 days 04/02/2010 04/30/2010 0.00%Demo to CANARIE and Interested Parties 0 days 04/30/2010 04/30/2010 0.00%

Task_NamePlanned Actual or Expected

Tasks and Schedule

Duration Start_Date Finish_DateCompletion as TodayDeliverablesStart_Date% CompletionFinish_Date01 - Science Studio 761 days 05/01/2008 03/31/2011 40.59%

Phase 7 87 days 05/01/2010 08/31/2010 0.00%NanoFab Facility Data Integration 22 days 05/01/2010 06/01/2010 0.00%Experiment Automation on VESPERS 22 days 06/02/2010 07/01/2010 0.00%Integrate with SHARCNET Data Storage 22 days 07/02/2010 08/02/2010 0.00%Integrate eLog-Book Capability 21 days 08/03/2010 08/31/2010 0.00%

Phase 8 88 days 09/01/2010 12/31/2010 0.00%VESPERS Running 30% Time in Automation Mode 0 days 09/01/2010 09/01/2010 0.00%Harden System Management and Administration Services 44 days 09/01/2010 11/01/2010 0.00%Update ScienceStudio based on operational feedback 44 days 11/02/2010 12/31/2010 0.00%

Phase 9 64 days 01/01/2011 03/31/2011 0.00%Conference Presentation 32 days 01/01/2011 02/15/2011 0.00%Demo to CANARIE and Interested Parties 0 days 02/15/2011 02/15/2011 0.00%Update ScienceStudio documentation and code cleanup 32 days 02/16/2011 03/31/2011 0.00%

Task_NamePlanned Actual or Expected

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)

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Positive features

Reliable sample movement

Download feature functions well

System readily recovered after a dump

Scanning service appears robust

Latency is acceptable

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

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 informationBUT... No movement of any other motors is contemplated

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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 detectorsand fixed irradiation conditions.

Where are we going with Nanafab?

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.

◊ 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.

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 ScienceStudio to enable a user to operate the Oxford Instruments software. The terminalwindow 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.

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

Software is user friendly.

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

User Services

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User Services Status Overview

User Services Draft Reqs Solid Reqs Design Code Test Production

User Training

User Survey and Feedback

Scheduling

Proposal, Task and Sample management Workflow

Reporting Search Security

User management

User Training Module Features

User Management• Registration• User and Admin Views

Intuitive Materials Categorization• Modules• Exams• Sections• Questions• Presentation

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 Creation• Flexible question format• Randomized questions• Test Expiry• Automatic Validation

e.g. empty choice selected as correct

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

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.

Calendar view

ULCP

Science Studio and ANISE

Science Studio and ANISE

ProcessingService

DataServiceData

ServiceProcessing

Service

ANISE

Business ModelLayer

PersistenceLayer

DeviceProxies

Client ServicesLayer

BrowserBrowser

LaboratoryControl Module

ServiceProxies

Science Studio

LabatoryControl Module

IOCs

Beamline

IOCs

Beamline

General, commonComponent

XRD Processing

XRF Processing

Science Studio specificComponent

Lessons Learning, etc.

Lessons Learned Questions CLS Tour