Kelly Keating and James Myers Pacific Northwest National Laboratory Environmental Molecular Sciences...

Kelly Keating and James Myers

Pacific Northwest National Laboratory

Environmental Molecular Sciences LaboratoryWilliam R.Wiley

Remote Research Using the EMSL Virtual NMR Facility


Environmental Molecular Sciences LaboratoryWilliam R. Wiley

Outline• EMSL

– Mission

– NMR capabilities

• Supporting remote collaborators– User proposal process

– Collaboratory software

• Using the EMSL NMR Virtual Facility– First project

– Demo

• Developing Collaboratories

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

• Summary



Our Location...



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.



NMR Capabilities at EMSL

Instrument Magnet

(Oxford) Liquids Solids µ-imagingVarian (on order) 900WB Varian (November) 800 Varian Unity 750 Varian Inova 600 Varian Unity 600 Chemagnetics 500 NB Varian Unity Plus 500 NB Varian Unity Plus 500 WB home-built 400 WB Chemagnetics 300 WB Varian Unity Plus 300 WB

Details: http://www.emsl.pnl.gov:2080/docs/msd/mrf_guide/homepage.html



Supporting Scientific Collaboration

• Discovery

• Contact / Setup

• Training

• Remote experiment monitoring

• Remote analysis

• Remote consultation

• Joint authoring of papers

NMR Facility Information and Proposal Form on the Web

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



User Proposal Process• Two proposal calls per year, November 1 and May 1, due dates of January

1 and July 1, start dates are April 1 and October 1

• Request NMR time in 1- or 2-week blocks

• Three months for proposal review, by EMSL staff and an outside advisory board

• Review criteria include– Quality of the proposed science

– Appropriateness of the requested instrumentation

– Relevance to the EMSL Mission

– The contribution the EMSL can have in bringing that science to fruition

• Spectrometer time is free (except proprietary use)

• Costs to user - travel & lodging

The primary objective is to facilitate the best possible science.



Running Remote Experiments

• 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

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

• Group WWW based access to data/metadata

• Modular / Extensible

–New data types and data views

• Automation of data/metadata input from instruments and calculations

• Export/Import

• Interactive input of results from the WWW

• Simple, secure access to full datasets

–e.g. 2D, 3D, 4D NMR

• Rich media types (text, images, files, 3D structures, voice, animations, video, ...)

• Querying/Searching

• Digital Signatures, witnessing, timestamps

Electronic Laboratory Notebook



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



Demonstration



Heat Shock Factor (HSF)

• HSF is a transcription factor that enhances cellular production of heat shock proteins in response to environmental stresses

• HSF trimerizes and binds DNA

• Each HSF monomer has a 92 amino acid residue DNA-binding head linked by a 25 residue linker to a coiled-coil trimerization domain

• N- and C-terminal domains serve regulatory functions

We are studying a 112 residue HSF monomer, and are interested in the structure of the linker conformation for insight into how the three DNA-binding heads of an HSF trimer are oriented with respect to DNA.

Today’s Live Demo

You will see the Collaboratory tools used for communication between this conference room and EMSL in Richland, Washington. The tools are shown on the next 9 pages.

• Audio/video “vat”/“vic”

• Remote NMRcam

• Televiewer

• Chatbox

• Whiteboard

• Electronic notebook

Audio / Video

“vat” “vic”

NMRcam

Televiewer

Consulting on data acquisition and analysis via TeleViewer

Chatbox

Whiteboard

Analyzing Crosspeaks in the whiteboard

EMSL Collaborative Research Environment CORE2000

•Real-time collaboration

•Java-based

•Multi-platform (Unix, PC, Mac)

•Extends NCSA’s Habanero

•Extensible

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

Electronic Laboratory Notebook

• Group WWW based access to data and metadata

• Interactive input of results into notebook from the WWW

• Simple, secure access to full datasets

– e.g. 2D, 3D, 4D NMR

• Rich media types (text, images, files, 3D structures, voice, animations, video, ...)

• Querying/Searching

Adding New Notes



End Demonstration



DOEDOE 22000000

• 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



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



Secure access to the NMR Console

secure, encrypted control

open audio/ video/ whiteboard/ shared screen

ssh



Notebook Extensions

Editors, and

Viewers

for new data types



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

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

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



Customizing the Collaborative Environment

Existing Scientific Application or Applet

Collaborative Multi-user Scientific Application

Electronic Notebook Data Viewer

DOE2000 Programming Interfaces



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?



New Personal Opportunities:

• Expose students to ‘real world’ science and the latest scientific techniques

• Access colleagues and expensive instrumentation from small institutions

• Increased specialization (instrument design, analysis software, lecturing, …)

• Cross-disciplinary focus - follow a scientific question across disciplines



New Organizational Opportunities

• Develop Virtual Facilities - buy 1/4 of an NMR spectrometer

• Assemble a “Scientific SWAT Team” to address a new problem/ teach a cross-disciplinary subject

• Develop Virtual Institutes - one stop shopping for related techniques

• Build a Community



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 work across institutional

boundaries?

• What good is second best? (What’s software and what’s

plumbing?)

• What is the best division of work (what scales) ?

• What’s the right size unit for dividing work?

• When is research work and when is it education?



If travel were free:Live where you wantBuy clothes in New YorkBask on a beach in Bora Bora

How much of our concept of the roles of • students• teachers• researchers• buildings• institutions

is an artifact of communication costs?

Removing Distance (and Time) From the Equation

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



• 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

In Summary...

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

Ray Bair George ChinBrett Didier

Shawn Merriman James Myers Tom Valdez

EMSL Collaboratory Researchers

David W. Hoyt, EMSL

Jeffrey G. Pelton, LBNL

Thanks to...



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/

Kelly Keating and James Myers Pacific Northwest National Laboratory Environmental Molecular Sciences...

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