Remote Research Using the EMSL Virtual NMR Facility

1. Kelly Keating and James Myers William R.Wiley Environmental Molecular Sciences Laboratory Pacific Northwest National Laboratory Remote Research Using the EMSL Virtual NMR Facility

2. 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 Outline

3. Our Location... EMSL

4. 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.

5. NMR Capabilities at EMSL Details:http://www.emsl.pnl.gov:2080/docs/msd/mrf_guide/homepage.html

6. Discovery Contact / Setup Training Remote experiment monitoring Remote analysis Remote consultation Joint authoring of papers Supporting Scientific Collaboration

7. NMR Facility Information and Proposal Form on the Web http://www.emsl.pnl.gov:2080/using-emsl/proposal.html

8. 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. User Proposal Process

9. Involves complex, multidimensional data No routine data handling Discovery/Learning Intermittent Running Remote Experiments

10. 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 The EMSL Collaborative Research Environment (CORE) Design Goals

11. Today’s Collaborative Tools Email Newsgroups Calendars File systems Electronic Notebook Real-Time Collaboration Multi White Board Audio/Video Conferencing Chat Box Shared Window Remote Instrument Shared Browsers Group Authoring Voting Tools Remote Camera And Analysis

12. Using CORE2000 1) View WWW/CORBA Session Directory 3) Launch Shared Applications 2) Launch the Manager

13. Electronic Laboratory Notebook • 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

14. 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 First Project Using the Virtual NMR Facility

15. Demonstration

16. 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 Heat Shock Factor (HSF) 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.

17. 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 Today’s Live Demo

19. Audio / Video “vat” “vic”

20. NMRcam

21. Televiewer

22. Consulting on data acquisition and analysis via TeleViewer

23. Chatbox

24. Whiteboard

25. Analyzing Crosspeaks in the whiteboard

26. EMSL Collaborative Research Environment CORE2000 • Real-time collaboration • Java-based • Multi-platform (Unix, PC, Mac) • Extends NCSA’s Habanero • Extensible

27. Dynamic cross platform application viewer Monitor experiments or analysis applications Differencing and compression of frames used to enhance performance 300ps 300ps 300ps 300ps EMSL TeleViewer MacOS Windows SGI/IRIX Solaris

28. 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

29. Adding New Notes

30. End Demonstration

31. R&D Inter-operability Framework* Collaboration Management* Electronic Notebooks* Security Architecture Floor Management Quality of Service Shared VR DOE 2000 • Pilots • PiloPilotsts • Diesel Collaboratory • Materials Micro-Characterization (M2C) • (EMSL) • (Fusion)

32. “Minimum” Hardware Modern computer Camera Echo canceller Extras: Tablet, Pan/tilt/zoom camera, Video switch Conference room- whiteboard, projector, etc. Hardware Requirements

33. “Minimum” Bandwidth Security (Quality of service) Network Requirements

34. Secure access to the NMR Console ssh secure, encrypted control open audio/ video/ whiteboard/ shared screen

35. Notebook Extensions Viewers Editors, and for new data types

36. 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 Building an NMR Spectroscopists’ Notebook

37. 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 Creating a Collaborative Environment:the EMSL NMR Virtual Research Facility

38. 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 Collaboration Archetypes • Bi-directional Mentor-Student • Can understand each others’ processed results • Share goals, samples • Consumer has problem / provides sample • Producer returns results Community • Shared Literature • Shared Databases • Shared Tools

39. Mapping Collaboration Archetypes to Capabilities Instruments& Raw Data Software Audio/Video WhiteBoard SharedWork Results Notebook Lecture Peer-to-Peer Mentor-Student Interdisciplinary Producer-Consumer Critical Useful

40. Customizing the Collaborative Environment DOE2000 Programming Interfaces Collaborative Multi-user Scientific Application Existing Scientific Application or Applet Electronic Notebook Data Viewer

41. 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 Electronic Collaboration: Worse, Better ... … or Different?

42. 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 Personal Opportunities:

43. 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 New Organizational Opportunities

44. 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? Collaboratories Raise “New” Questions:

45. Removing Distance (and Time) From the Equation • If travel were free: • Live where you want • Buy clothes in New York • Bask 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?

46. More than new technology A “new” paradigm for scientific research and education Will change the way we build, think, and do Collaboratories Borromean Rings - the synergy of collaboration

47. 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...

48. Cross-platform: UNIX, PC, (MAC) All clients and servers are freely available EMSL Collaboratory Software Available http://www.emsl.pnl.gov:2080/docs/collab/

49. Thanks to... EMSL Collaboratory Researchers David W. Hoyt, EMSL Jeffrey G. Pelton, LBNL Shelly Harris Kelly Keating Elena Mendoza Ray Bair George Chin Brett Didier Shawn Merriman James Myers Tom Valdez

50. 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 Acknowledgments-funding