James Myers Computer and Information Sciences Environmental Molecular Sciences Laboratory Pacific Northwest National Laboratory Environmental Molecular

James MyersComputer and Information Sciences

Environmental Molecular Sciences Laboratory

Pacific Northwest National Laboratory


Environmental Molecular Sciences LaboratoryWilliam R.Wiley

Collaborative Research Facilities in the Environmental Molecular

Sciences Laboratory


Environmental Molecular Sciences LaboratoryWilliam R. Wiley

Outline

• EMSL

• Supporting remote collaborators

• EMSL Virtual Facilities

• Other DOE2000 Collaboratories

• Developing Collaboratories

• Understanding Scientific Collaboratories– The changing roles of researchers and research organizations

• Summary



Mission. . . provide the fundamental scientific basis needed to solve the nation’s environmental problems.. . . advance molecular science in support of the long-term missions of the U.S. Department of Energy.

National Scientific User Facility. . . make unique research resources available to DOE scientists and researchers from academia and industry.. . . provide opportunities needed to educate and recruit young scientists to meet the demanding environmental challenges of the future.

DOE2000 Participant. . . working with partners in government, academia, and industry to develop and deploy

collaborative technologies.



Advanced Research Capabilities for Environmental Molecular Science

Molecular LevelSurface

Chemistry

Cluster Structure

and DynamicsFacility

Real TimeDynamics

Facility

High PerformanceComputing

Facility

Visualization and

GraphicsLaboratory

Large MoleculeMass

Spectrometry

UltrahighField NMR

Chambers For Controlled

Simulation OfEnvironmental

Reactions

Sensor, DesignFabrication and

Testing

MaterialsSynthesis

AdvancedProcessing

InterphaseChemistry



• A Collaboratory is a “... ‘center without walls,’ in which the nation’s researchers can perform their research without regard to geographical location– interacting with colleagues, – accessing instrumentation, – sharing data and computational resources, [and] – accessing information in digital libraries.”

Bill Wulf (1989)

• ... going beyond text exchange and conference/presentation metaphors; bringing scientific resources into an environment to allow in-depth, collaborative work.

The Collaboratory Concept



DOEDOE 20002000

• R&D

– Inter-operability Framework*

– Collaboration Management*

– Electronic Notebooks*

– Security Architecture

– Floor Management

– Quality of Service

– Shared VR

• PiloPilotsts

– Diesel Collaboratory

– Materials Micro-Characterization (M2C)

– (EMSL)

– (Fusion)

• Pilots

Diesel Combustion Collaboratory

Diesel CombustionResearch Program

Validation Analysis•Visualization•Design & analysis of computer experiments•Model data management

Experiment•Laser diagnostics•Image processing•Scientific data management

EngineDesignConcepts•Optical engines & cells•Industry engine design•Integrated engine tests

PhysicalSubmodel

Development•Chemistry

•Multiphase fluid dynamics

•Combustion dynamics

ComprehensiveModeling

•Numerical & mathematical methods

•MPP computing•3D gridding

Through computer and information technologies, the DCC aims to reduce geographical barriers to information transfer and increase the utilization of computational models and visualization

DCC Slides:Larry Rahn,Sandia National Lab

• • Instrument RoomInstrument Room

• • Instrument StatusInstrument Status

• • Experimental DataExperimental Data

• • On-Line ControlOn-Line Control

• • Video ConferencingVideo Conferencing

• • Electronic NotebooksElectronic Notebooks

Provides Access to:Provides Access to:

Materials Microcharacterization Materials Microcharacterization CollaboratoryCollaboratory

Materials Microcharacterization Materials Microcharacterization CollaboratoryCollaboratory

Argonne National Argonne National LaboratoryLaboratory

MMC Slide:Nestor Zaluzec,Argonne National Lab



Collaborative Electronic Notebook Systems Association (CENSA)

Rich Lysakowski - www.censa.org

Chemical and Pharmaceutical companies promoting the development of commercial electronic notebook

systemsEnd User MembersAbbott LabsBristol-Myers SquibbBoehringer IngelheimDow ChemicalDow AgroSciencesGlaxoWellcomeHB FullerMonsanto Life Sci.Pfizer Pharm.Proctor & GamblePurdue Pharm.Rohm & HaasUS DoEUOP

Supplier MembersAdobe SystemsDOXISDocumentumIceBreakerPSSoftwareScrip-Safe Security Products



Collaboratories Have Potential Rolesin All Phases of Research

• Resource Discovery

• Planning and Organization

• Experiment Design

• Software Development

• Computation and Simulation

• Collaborative Remote Experiments

• Shared Analysis and Discovery

• Remote Consultation & Mentoring

• Joint Authoring

Facility Information and Proposal Form on the Web

http://www.emsl.pnl.gov:2080/using-emsl/proposal.html

Electronic Notebook

Audio/Video Conferencing

Shared WindowChat Box

Multi White Board

Real-Time Collaboration

Remote InstrumentAnd Analysis

EmailNewsgroups

CalendarsFile systems

Shared BrowsersGroup Authoring

Voting ToolsRemote Camera

Today’s Collaborative Tools

Using CORE2000

1) View WWW/CORBA Session Directory

2) Launch the Manager

3) Launch Shared Applications

Audio / Video

“vat” “vic”

300ps

EMSL TeleViewer

WindowsSGI/IRIX

Solaris

MacOS

300ps

300ps

300ps

• Dynamic cross platform application viewer

• Monitor experiments or analysis applications

• Differencing and compression of frames used to enhance performance

Analyzing Crosspeaks in the whiteboard

NMRcam



Secure access to EMSL Resources

secure, encrypted control

open audio/ video/ whiteboard/ shared screen

ssh



Laboratory Notebooks: the Heart of Scientific Research



Functions of Lab Notebooksthe primary record of the scientific process

• Science Observations• Design Notebook• Instrument Log Book• Experiment Log Book• Legal Record• Notepad• Group Workspace

• Science Observations• Design Notebook• Instrument Log Book• Experiment Log Book• Legal Record• Notepad• Group Workspace

Sources of Notebook Information– Instruments – Software analyses, simulations,

visualizations– Data files in ‘native’ formats

(lossless)– Summaries - images, tables, …

(lossy)– Metadata, processing history,

parameter files– Text, sketches, diagrams, schematics,

by individuals– Presentations, conversations,

planning, by groups



DOE2000 Electronic Notebooks

• Shared web-based space • Interactive input• Rich media types• Querying and searching• Automated data/metadata input• Modular and extensible• Import / export• Legal defensibility• Preservation of electronic records • Notification / workflow• Mobile use

DOE 2000 Electronic Notebook ProjectPNNL Jim Myers, Elena MendozaLBNL Sonia SachsORNL Al Geist, Noel Nachtigal



Customizing the Collaborative Environment

Existing Scientific Application or Applet

Collaborative Multi-user Scientific Application

Electronic Notebook Data Viewer

DOE2000 Programming Interfaces



Hardware Requirements

• “Minimum” Hardware– Modern computer– Camera– Echo canceller– Extras:

• Tablet,

• Pan/tilt/zoom camera,

• Video switch

• Conference room- whiteboard, projector, etc.



Network Requirements• “Minimum” Bandwidth

• Security

• (Quality of service)

Interaction per person 3-5 people 20 groups(Kb/s) (Mb/s) (Mb/s)

Video 100+ 0.5 10Audio 25-50+ 0.2 4

Shared Apps 50+ 0.2 4

File Transfer 50-106 0.2 4Notebooks 50+ 0.3 6

Instruments 10-106 0.1 2Total 300 1.5 30



Electronic Collaboration: Worse, Better ...

• Lack of non-verbal cues

• Lack of presence

• Intrusion of technology

• Delays, network outages

• Rapidly changing technologies

• Remote access

• Scaling

• Desktop access to people, information and scientific resources

• Automation of recording and routing

• Translation/different views of data

• Media integration

• Anonymity / equality

… or Different?



The Nature of Scientific Research

• Involves complex,

multidimensional data

• No routine data

handling

• Discovery/Learning

• Intermittent



The EMSL Collaborative Research Environment (CORE) Design Goals

• Ubiquitous ~ cross-platform

• Integrated ~ single logon

• Simple ~ easy to use, no IP/port numbers

• Secure ~ for safety, intellectual property

• Flexible ~ supports different work processes

• Extensible ~ easily add needed scientific resources

• Reliable ~ guarantee quality of service

• Transparent ~ allow a natural social interaction

Collaboration Archetypes

• Can understand each others’ raw data• Share equipment (new source, new

detector)

• Unequal knowledge• Need reference material• Mentor needs to lecture, demonstrate• Mentor oversees student’s efforts

Peer-to-Peer Mentor-Student

Interdisciplinary Producer-Consumer

• Shared Literature

• Shared Databases

• Shared Tools

Community

• Bi-directional Mentor-Student• Can understand each others’

processed results• Share goals, samples

• Consumer has problem / provides sample

• Producer returns results



Mapping Collaboration Archetypes to Capabilities

Producer-Consumer

Interdisciplinary

Mentor-Student

Peer-to-Peer

Instruments& Raw Data

SoftwareAudio/Video

WhiteBoard

SharedWork

Results Notebook Lecture

Critical Useful



Environmental Molecular Sciences Collaboratory

Instrument DevelopmentLaboratory Computing Infrastructure

Collaboratory Tools

Virtual NMR FacilityRF Ion Trap Mass Spectrometer CURE: Chem 245 at EOU



U.W. Chem 155 - Live from the EMSLWWW/ Excel Spreadsheet A/V, WebTour LectureRemote Data Acquisition EMSL WWW Data Notebook

John Price



First Project Using the Virtual NMR Facility• Collaboration with Jeffrey Pelton and David Wemmer at

Lawrence Berkeley National Laboratory

• Sample: Heat Shock Factor protein from yeast

• All protein prep done at LBNL

• NMR experiments done at EMSL– 750, 600 MHz spectrometers operated remotely from

Berkeley– Collaboratory tools facilitated setting up the NMR

experiment together

• Audio/video communication

• Live screen sharing in Televiewer of the Varian console display

– Jeff’s setup: his office Sun computer, Berkeley

– Kelly’s setup: her office PC, Richland

Creating a Collaborative Environment:the EMSL NMR Virtual Research Facility

• Pilot project

• Deploy standard tools

• Provide secure remote

access to the NMR

• Instrument sends data

directly to notebook

• Notebook displays

– Instrument

parameters

– Protein structures

– NMR spectra



Building an NMR Spectroscopists’ Notebook

• Add new data types– 3D Protein Structures (PDB)– NMR Parameter files

• “Save to Notebook” macro in spectrometer software

• Visualization of large, multidimensional data– Efficient Client/Server design



• We have found “working together apart” to collect and analyze NMR data between

remote sites with the aid of Collaboratory tools is an efficient method of collaboration.

– Requires no additional NMR experiment setup time (except startup of the

Collaboratory software)

– The Televiewer tool is indispensable for the NMR experiment

• allows live consultation

– The Electronic Notebook

• Is a timesaver for exchange of data, notes, analyses

• NMR specific data visualization very helpful (e.g. PDB viewer)

• WWW does not mean public (access limited to collaborators)

• A real pilot project is a very effective way of introducing Collaborative technologies

– 4 of 7 first round proposals requested access via the Virtual NMR Facility

Lessons Learned...



Collaborative Problem Solving



Scientific Collaboratory Drivers

• Opportunity– to make more progress on a project

– to employ expertise, data, experiments or computations not otherwise available

– to be first to explore a research question or solve a problem (competitive advantage)

• Problem Complexity and Scale– need for large or multi-disciplinary research teams

– information exchange between research and application

• Economics– optimizing travel, equipment use, information value



• Personal– interesting work with colleagues– develop a new specialization (follow a

molecule)– expose more students to practicing

scientists and the latest techniques

• Scientific– exploit timely science opportunities– more cross-disciplinary contributions– assemble scientific “SWAT” teams

• Organizational– virtual institutes (disciplinary or topical)– shared research capabilities– connect researchers from smaller institutions, branch offices, etc., with scientists and

capabilities at larger facilities

Science Opportunities



Collaboratories Raise “New” Questions

• What’s more important - home or virtual institute affiliation?

• Who are your peers in cross-disciplinary work?

• What’s a paper?

• How do we evaluate and fund work across institutional boundaries?

• What is the best division of work (what scales)?– What’s software and what’s plumbing?

• When is it research work and when is it education?

• How can we preserve informal communications?



Requirements to Achievethe Promise of Collaboratories

• Cooperative development of science collaboratory capabilities– teams of domain scientists, computer scientists, and sociologists

• Research by doing– learn to deploy and support collaboratories– evaluate collaboratory science in action

• Technology Development– security and authentication– component frameworks– tools for representation and use of shared knowledge– contributions to industry standards

• Better networks, network standards, network management• Open software interfaces to instruments

Collaboratories

• More than new technology

• A “new” paradigm for scientific research and education

• Will change the way we build, think, and do

Borromean Rings - the synergy of collaboration

EMSL Collaboratory Software Available

• Cross-platform:

UNIX, PC,

(MAC)

• All clients and

servers are freely

available

http://www.emsl.pnl.gov:2080/docs/collab/



Shelly Harris Kelly Keating

Elena Mendoza

George ChinBrett Didier

Shawn Merriman James Myers Tom Valdez

EMSL Collaboratory Project

Acknowledgements ...

Instrument Development Laboratory

Computing and Network Services

John Price Ken Swanson

Jeff MackGordon Anderson

Troy ThompsonKerry Steele

Jeff MauthJohn McCoy

Ray Bair

Computing and Information Sciences



Acknowledgments-funding

U.S. Department of Energy– Mathematical, Information and Computational Sciences Division

of the Office of Energy Research • Distributed Collaboratory Experiment Environments (DCEE)

• DOE2000 project (Multi-institution project developing and piloting scientific collaboration technologies)

Pacific Northwest National Laboratory– Pacific Northwest National Laboratory is a multiprogram national laboratory

operated by Battelle Memorial Institute for the U.S. Department of Energy under Contract DE-AC06-76RLO 1830

– Laboratory Directed Research and Development (LDRD)• NMR Virtual Facility Project



Web sites…

EMSL Collaboratory http://www.emsl.pnl.gov:2080/docs/collab/

DOE2000 http://www.mcs.anl.gov/DOE2000/

NCSA Habanero http://www.ncsa.uiuc.edu/SDG/Software/Habanero/

WebMol (Java-based pdb file viewer in the Electronic Notebook, by Dirk Walther) http://www.embl-heidelberg.de/cgi/viewer.pl

ssh (secure shell) http://www.cs.hut.fi/ssh/

Documents

James Myers Computer and Information Sciences Environmental Molecular Sciences Laboratory Pacific Northwest National Laboratory Environmental Molecular