Collaborative Research Facilities in the Environmental Molecular Sciences Laboratory

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

2. EMSL Supporting remote collaborators EMSL Virtual Facilities Other DOE2000 Collaboratories Developing Collaboratories Understanding Scientific Collaboratories The changing roles of researchers and research organizations Summary Outline

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

5. 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. 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)

7. Experiment • Laser diagnostics • Image processing • Scientific data management • Physical • Submodel • Development • Chemistry • Multiphase fluid dynamics • Combustion dynamics • Engine • Design • Concepts • Optical engines & cells • Industry engine design • Integrated engine tests • Comprehensive • Modeling • Numerical & mathematical methods • MPP computing • 3D gridding • Validation Analysis • Visualization • Design & analysis of computer experiments • Model data management Diesel Combustion Collaboratory DCC Slides:Larry Rahn, Sandia National Lab Diesel Combustion Research Program Through computer and information technologies, the DCC aims to reduce geographical barriers to information transfer and increase the utilization of computational models and visualization

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

9. Collaborative Electronic Notebook Systems Association (CENSA)Rich Lysakowski - www.censa.orgChemical 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. Resource Discovery Planning and Organization Experiment Design Software Development Computation and Simulation Collaborative Remote Experiments Shared Analysis and Discovery Remote Consultation & Mentoring Joint Authoring Collaboratories Have Potential Rolesin All Phases of Research

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

12. 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

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

14. Audio / Video “vat” “vic”

15. 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 Windows SGI/IRIX MacOS Solaris

16. Analyzing Crosspeaks in the whiteboard

17. NMRcam

18. Secure access to EMSL Resources ssh secure, encrypted control open audio/ video/ whiteboard/ shared screen

19. Laboratory Notebooks: the Heart of Scientific Research

20. 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 Functions of Lab Notebooksthe primary record of the scientific process

21. 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 • PNNL Jim Myers, Elena Mendoza • LBNL Sonia Sachs • ORNL Al Geist, Noel Nachtigal

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

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

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

25. 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?

26. Involves complex, multidimensional data No routine data handling Discovery/Learning Intermittent The Nature of Scientific Research

27. 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

28. 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

29. 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

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

31. John Price U.W. Chem 155 - Live from the EMSL WWW/ Excel Spreadsheet A/V, WebTour Lecture Remote Data Acquisition EMSL WWW Data Notebook

32. 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

33. 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

34. 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

35. 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. Collaborative Problem Solving

37. 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 Scientific Collaboratory Drivers

38. 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. 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? Collaboratories Raise “New” Questions

40. 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 Requirements to Achievethe Promise of Collaboratories

41. 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

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

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

44. 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

45. 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/