1. James Myers Computer and Information Sciences Environmental Molecular Sciences Laboratory Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory William R.Wiley Collaborative Research Facilities in the Environmental Molecular Sciences Laboratory

2. Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory William 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

3. 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.

4. Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory William R. Wiley Advanced Research Capabilities for Environmental Molecular Science Molecular Level Surface Chemistry Cluster Structure and Dynamics Facility Real Time Dynamics Facility High Performance Computing Facility Visualization and Graphics Laboratory Large Molecule Mass Spectrometry Ultrahigh Field NMR Chambers For Controlled Simulation Of Environmental Reactions Sensor, Design Fabrication and Testing Materials Synthesis Advanced Processing Interphase Chemistry

5. Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory William R. Wiley 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

6. Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory William R. WileyDOE2000 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

7. Diesel Combustion Collaboratory Diesel Combustion Research Program Validation Analysis Visualization Design & analysis of computer experiments Model data management Experiment Laser diagnostics Image processing Scientific data management Engine Design Concepts Optical engines & cells Industry engine design Integrated engine tests Physical Submodel Development Chemistry Multiphase fluid dynamics Combustion dynamics Comprehensive Modeling 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

8. Instrument Room Instrument Room Instrument Status Instrument Status Experimental Data Experimental Data On-Line Control On-Line Control Video Conferencing Video Conferencing Electronic Notebooks Electronic Notebooks Provides Access to: Materials Microcharacterization Collaboratory Argonne National Laboratory Argonne National Laboratory MMC Slide: Nestor Zaluzec, Argonne National Lab

9. Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory William R. Wiley Collaborative Electronic Notebook Systems Association (CENSA) Rich Lysakowski - www.censa.org Chemical and Pharmaceutical companies promoting the development of commercial electronic notebook systems End User Members Abbott Labs Bristol-Myers Squibb Boehringer Ingelheim Dow Chemical Dow AgroSciences GlaxoWellcome HB Fuller Monsanto Life Sci. Pfizer Pharm. Proctor & Gamble Purdue Pharm. Rohm & Haas US DoE UOP Supplier Members Adobe Systems DOXIS Documentum IceBreaker PSSoftware Scrip-Safe Security Products

10. Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory William R. Wiley Collaboratories Have Potential Roles in 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

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

12. 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

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

14. Audio / Video “vat”“vic”

15. 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

16. Analyzing Crosspeaks in the whiteboard

17. NMRcam

18. Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory William R. Wiley Secure access to EMSL Resources secure, encrypted control open audio/ video/ whiteboard/ shared screen ssh

19. Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory William R. Wiley Laboratory Notebooks: the Heart of Scientific Research

20. Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory William R. Wiley Functions of Lab Notebooks the 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

21. Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory William R. Wiley 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 Project PNNLJim Myers, Elena Mendoza LBNLSonia Sachs ORNLAl Geist, Noel Nachtigal

22. 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

23. 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.

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

25. 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?

26. Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory William R. Wiley The Nature of Scientific Research Involves complex, multidimensional data No routine data handling Discovery/Learning Intermittent

27. 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

28. 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

29. 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

30. Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory William R. Wiley Environmental Molecular Sciences Collaboratory Instrument Development Laboratory Computing Infrastructure Collaboratory Tools Virtual NMR Facility RF Ion Trap Mass Spectrometer CURE: Chem 245 at EOU

31. Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory William R. Wiley U.W. Chem 155 - Live from the EMSL WWW/ Excel Spreadsheet A/V, WebTour Lecture Remote Data Acquisition EMSL WWW Data Notebook John Price

32. 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

33. 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

34. 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

35. 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 Lessons Learned...

36. Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory William R. Wiley Collaborative Problem Solving

37. Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory William R. Wiley 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

38. Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory William R. Wiley 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

39. 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 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?

40. Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory William R. Wiley Requirements to Achieve the 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

41. 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

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

43. Pacific Northwest National Laboratory Environmental Molecular Sciences Laboratory William R. Wiley Shelly Harris Kelly Keating Elena Mendoza George Chin Brett Didier Shawn Merriman James Myers Tom Valdez EMSL Collaboratory Project Acknowledgements... Instrument Development Laboratory Computing and Network Services John Price Ken Swanson Jeff Mack Gordon Anderson Troy Thompson Kerry Steele Jeff Mauth John McCoy Ray Bair Computing and Information Sciences

44. 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

45. 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/