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Kelly Keating and James Myers
Pacific Northwest National Laboratory
Environmental Molecular Sciences LaboratoryWilliam R.Wiley
Remote Research Using the EMSL Virtual NMR Facility
Pacific Northwest National Laboratory
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
Pacific Northwest National Laboratory
Environmental Molecular Sciences LaboratoryWilliam R. Wiley
Our Location...
Pacific Northwest National Laboratory
Environmental Molecular Sciences LaboratoryWilliam R. Wiley
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.
Pacific Northwest National Laboratory
Environmental Molecular Sciences LaboratoryWilliam R. Wiley
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
Pacific Northwest National Laboratory
Environmental Molecular Sciences LaboratoryWilliam R. Wiley
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
Pacific Northwest National Laboratory
Environmental Molecular Sciences LaboratoryWilliam R. Wiley
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.
Pacific Northwest National Laboratory
Environmental Molecular Sciences LaboratoryWilliam R. Wiley
Running Remote Experiments
• Involves complex,
multidimensional data
• No routine data
handling
• Discovery/Learning
• Intermittent
Pacific Northwest National Laboratory
Environmental Molecular Sciences LaboratoryWilliam R. Wiley
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
Pacific Northwest National Laboratory
Environmental Molecular Sciences LaboratoryWilliam R. Wiley
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
Pacific Northwest National Laboratory
Environmental Molecular Sciences LaboratoryWilliam R. Wiley
Demonstration
Pacific Northwest National Laboratory
Environmental Molecular Sciences LaboratoryWilliam R. Wiley
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
Pacific Northwest National Laboratory
Environmental Molecular Sciences LaboratoryWilliam R. Wiley
End Demonstration
Pacific Northwest National Laboratory
Environmental Molecular Sciences LaboratoryWilliam R. Wiley
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
Pacific Northwest National Laboratory
Environmental Molecular Sciences LaboratoryWilliam R. Wiley
Hardware Requirements
• “Minimum” Hardware– Modern computer– Camera– Echo canceller– Extras:
• Tablet,
• Pan/tilt/zoom camera,
• Video switch
• Conference room- whiteboard, projector, etc.
Pacific Northwest National Laboratory
Environmental Molecular Sciences LaboratoryWilliam R. Wiley
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
Pacific Northwest National Laboratory
Environmental Molecular Sciences LaboratoryWilliam R. Wiley
Secure access to the NMR Console
secure, encrypted control
open audio/ video/ whiteboard/ shared screen
ssh
Pacific Northwest National Laboratory
Environmental Molecular Sciences LaboratoryWilliam R. Wiley
Notebook Extensions
Editors, and
Viewers
for new data types
Pacific Northwest National Laboratory
Environmental Molecular Sciences LaboratoryWilliam R. Wiley
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
Pacific Northwest National Laboratory
Environmental Molecular Sciences LaboratoryWilliam R. Wiley
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
Pacific Northwest National Laboratory
Environmental Molecular Sciences LaboratoryWilliam R. Wiley
Customizing the Collaborative Environment
Existing Scientific Application or Applet
Collaborative Multi-user Scientific Application
Electronic Notebook Data Viewer
DOE2000 Programming Interfaces
Pacific Northwest National Laboratory
Environmental Molecular Sciences LaboratoryWilliam R. Wiley
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?
Pacific Northwest National Laboratory
Environmental Molecular Sciences LaboratoryWilliam R. Wiley
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
Pacific Northwest National Laboratory
Environmental Molecular Sciences LaboratoryWilliam R. Wiley
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
Pacific Northwest National Laboratory
Environmental Molecular Sciences LaboratoryWilliam R. Wiley
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?
Pacific Northwest National Laboratory
Environmental Molecular Sciences LaboratoryWilliam R. Wiley
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
Pacific Northwest National Laboratory
Environmental Molecular Sciences LaboratoryWilliam R. Wiley
• 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/
Pacific Northwest National Laboratory
Environmental Molecular Sciences LaboratoryWilliam R. Wiley
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...
Pacific Northwest National Laboratory
Environmental Molecular Sciences LaboratoryWilliam R. Wiley
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
Pacific Northwest National Laboratory
Environmental Molecular Sciences LaboratoryWilliam R. Wiley
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/