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

2. Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory William 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

3. Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory William R. Wiley Our Location...

4. Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory William 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.

5. Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory William R. Wiley NMR Capabilities at EMSL Details: http://www.emsl.pnl.gov:2080/docs/msd/mrf_guide/homepage.html

6. Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory William R. Wiley Supporting Scientific Collaboration Discovery Contact / Setup Training Remote experiment monitoring Remote analysis Remote consultation Joint authoring of papers

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

8. Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory William 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.

9. Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory William R. Wiley Running Remote Experiments Involves complex, multidimensional data No routine data handling Discovery/Learning Intermittent

10. Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory William 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

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

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

13. 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

14. Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory William 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

15. Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory William R. Wiley Demonstration

16. Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory William 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.

17. 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

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

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. Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory William R. Wiley End Demonstration

31. Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory William R. WileyDOE 2000 R&D –Inter-operability Framework* –Collaboration Management* –Electronic Notebooks* –Security Architecture –Floor Management –Quality of Service –Shared VR PiloPilotsts –Diesel Collaboratory –Materials Micro- Characterization (M 2 C) –(EMSL) –(Fusion) Pilots

32. Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory William R. Wiley Hardware Requirements “Minimum” Hardware –Modern computer –Camera –Echo canceller –Extras: Tablet, Pan/tilt/zoom camera, Video switch Conference room- whiteboard, projector, etc.

33. Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory William R. Wiley Network Requirements “Minimum” Bandwidth Security (Quality of service)

34. Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory William R. Wiley Secure access to the NMR Console secure, encrypted control open audio/ video/ whiteboard/ shared screen ssh

35. Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory William R. Wiley Notebook Extensions Editors, and Viewers for new data types

36. Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory William 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

37. 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

38. 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-PeerMentor-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

39. Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory William R. Wiley Mapping Collaboration Archetypes to Capabilities Producer-Consumer Interdisciplinary Mentor-Student Peer-to-Peer Instruments & Raw Data Software Audio/ Video White Board Shared Work ResultsNotebookLecture CriticalUseful

40. Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory William R. Wiley Customizing the Collaborative Environment Existing Scientific Application or Applet Collaborative Multi-user Scientific Application Electronic Notebook Data Viewer DOE2000 Programming Interfaces

41. Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory William 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?

42. Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory William 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

43. Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory William 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

44. Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory William 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?

45. Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory William R. Wiley 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? Removing Distance (and Time) From the Equation

46. 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

47. Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory William 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...

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

49. Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory William R. Wiley Shelly Harris Kelly Keating Elena Mendoza Ray Bair George Chin Brett Didier Shawn Merriman James Myers Tom Valdez EMSL Collaboratory Researchers David W. Hoyt, EMSL Jeffrey G. Pelton, LBNL Thanks to...

50. Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory William 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

51. Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory William R. Wiley Web sites… EMSL Collaboratoryhttp://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/