COLLABORATORIES: BRINGING NATIONAL LABORATORIES INTO THE UNDERGRADUATE CLASSROOM AND LABORATORY VIA THE INTERNET

Copyright 1996 Council on Undergraduate Research. Published in the Council on Undergraduate Research Quarterly vol. 17, number 3, March 1997. Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution to servers or lists, or to reuse any copyrighted component of this work in other works, must be obtained from the Council on Undergraduate Research.

Jim Myers, Norman Chonacky, Thom Dunning, and Eric Leber

Introduction

Advances in computing and communications technologies, and particularly those related to the Internet, are reducing the barriers to collaboration and making it easier to access a variety of scientific resources, from research instruments and data sets to the scientific literature. That these changes might be much more than a convenience to researchers, that they might fundamentally change the structure and processes of research organizations was recognized early by Professor William A. Wulf (1989), subsequently chair of a National Research Council panel which published a study of the Collaboratory concept (1993). He coined the term Collaboratory to describe the concept of a meta-laboratory, spanning multiple geographical areas, with collaborators remotely accessing instruments, sharing data and literature, attending lectures and holding discussions, and analyzing data and writing papers, all via electronic means. The DOE's William R. Wiley Environmental Molecular Sciences Laboratory (EMSL), at the Pacific Northwest National Laboratory (PNNL), has embraced this concept of a Collaboratory as a means to help fulfill its mission as a collaborative user facility and is actively developing and pilot testing ways to share its unique research instrumentation and expertise via the Internet.

During the last year, the EMSL has begun working with a consortium of northwest colleges and universities under joint NSF and DOE sponsorship to develop a Collaboratory for Undergraduate Research and Education (CURE) that would provide a model for linking undergraduate institutions with national laboratories and other major research facilities (and with each other) to bring state-of-the art instruments and techniques, and real-world applications of science into the undergraduate experience. Starting with a series of workshops, and proceeding now with some "simple" collaborative interactions, the project's goal is to identify solutions to the technological, cultural, institutional, and other issues that arise in creating large (scalable), diverse, multi-institutional Collaboratories to enhance the education and research experience of undergraduate students, improve scientific literacy, provide faculty development opportunities, and help train the next generation of scientists.

Background

The William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) is a new research facility at the Pacific Northwest National Laboratory, funded by the Office of Health and Environmental Research in the U.S. Department of Energy (DOE). PNNL is near the Hanford site (formerly a DOE site for plutonium production) in southeastern Washington state. The EMSL mission is to develop a molecular level understanding of physical, chemical, and biological processes in areas such as contaminated soils and groundwater; waste analysis, characterization, processing, and storage; and human and ecological health effects, and to help apply this knowledge to the development of innovative, cost-effective technologies for environmental remediation. The EMSL is a National Scientific User Facility, providing unique resources to scientists from DOE and government laboratories, universities and industry. Major facilities include a complementary array of next generation instruments, including an ultra high field Nuclear Magnetic Resonance (NMR) spectrometer, a high field Fourier Transform Ion Cyclotron Resonance Mass Spectrometer, and a 472 processor IBM Scalable PowerParallel supercomputer. EMSL also houses many smaller instruments with unique capabilities, from benchtop electrochemistry instruments to laser systems and a near field optical microscope. For more information see http://www.emsl.pnl.gov:2080/.

The Collaboratory program within the EMSL is working to understand the communication needs of collaborating scientists and to design and integrate collaborative software to allow EMSL researchers and their collaborators to perform nearly all of their joint tasks via the Internet. Through this program, the EMSL is a participant in Department of Energy-wide (DOE) efforts to develop effective research Collaboratories (specifically, the Distributed Collaborative Experiment Environment (DCEE) project and the new DOE2000 Collaboratory program).

Research Collaboratory Requirements

The recent paper on "Collaboratories: Doing Science on the Internet" (Kouzes et. al., 1996) describes some of the sociological and technological issues related to research collaboratories and computer mediated communications that the EMSL and many others are solving. Scientific collaborations do not consist of work on a single task, e.g., acquiring data on a remote spectrometer, but a host of related tasks (contact, planning, training, acquiring data, analyzing and discussing results, writing papers, etc.) that have different communications requirements. Some of these tasks can be handled asynchronously, perhaps with a text note in e-mail, while others require media-rich real-time interaction, as when two researchers work to elucidate a 3-dimensional molecular structure using a computer visualization package, discussing their reasoning and watching for facial expressions and body language to determine each other's comprehension and agreement. To allow collaborations that are as deep, and as fruitful, as those with colleagues down the hall, collaborators need a rich communications environment and direct access to project specific scientific resources (research instruments, databases, visualization software) that allow a remote researcher to become directly involved in the project, recommending and/or making changes to experimental parameters during the experiment, before valuable instrument time is wasted, or iteratively adjusting a molecular structure model to fit both their theoretical results and their colleagues' results from complementary experiments. Also, one must remember that collaborations are based on a foundation of trust and friendship derived from non-science interactions, e.g., telling jokes in the coffee room. Remote colleagues will need the means to have off-topic, personal, interactions like this, perhaps in new forms, to keep their collaborations vital, interesting, and effective.

EMSL's Collaborative Research Environment (CORE)

The EMSL has developed a prototype collaborative environment (CORE) that provides a wide range of communications tools to which remote instruments and other scientific resources can be added as they are developed. This environment, consisting of commercial, public domain, and EMSL developed tools, is being used in pilot test and demonstrations now. It will eventually be replaced by the product of the multi-national-laboratory DOE2000 program.

To start or join a collaborative session using CORE, researchers simply click the appropriate buttons on the WWW page, and all required software is launched on their machines. Hidden from the users' view are a central session manager and a desktop executive that coordinate communications between participants, sending IP addresses and port numbers between computers, and configuring the various components. CORE currently runs under Windows (3.1 and 95) and a variety of UNIXs (SunOS, Solaris, Irix, ...), and will soon be ported to the Macintosh.

Figure 1 (Graphic displaying "What the User Sees")

CORE users can select a variety of tools for their session:

Audio/video Conferencing: allows collaborators to see and hear each other, as well as to monitor instruments and laboratories.
Shared Whiteboard: augments videoconferencing by providing a shared space where users can write and draw.
WWW Browser Synchronization: allows users to hold lectures or discussions, using materials on the WWW. When one user goes to a new URL, all linked browsers automatically go to the new document. Lecture (only the leader's browser is echoed) or discussion (peer-to-peer) modes are possible.
EMSL TeleViewer: allows users to view any program run by colleagues, including word processors, spreadsheets, instrument control software, and scientific computations, simulations, and visualizations. All participants can show their mouse cursors and create whiteboard-style annotation on top of the live image.
Shared Electronic Notebook: provides users with a shared version of the traditional paper laboratory notebook. In addition to distributed access, which benefits the group, the electronic notebook provides automated data entry, searching, and other information processing capabilities not possible with a paper notebook. The current EMSL notebook dynamically creates a notebook consisting of a set of WWW pages that can display experiment information and accept multi-media user annotations to the existing material.
File Sharing: enables the drag and drop transfer of files between multiple collaborators.
Chat: allows simple text communication

On-line Instruments, Computation, and Visualization

One of the first on-line instruments in the EMSL, developed by Dr. John Price and colleagues, is a radio-frequency ion-trap mass spectrometer that can be launched from CORE and save the data directly into the EMSL electronic notebook. The instrument software also includes pan and tilt controls for a laboratory video camera that can be included in a videoconference. Similarly, other instruments and analysis, modeling, and visualization software, including the EMSL Extensible Computational Chemistry Environment (ECCE, developed by Dr. Don Jones et al.), can be enhanced to work with CORE and allow multiple users to simultaneously view and interact with them. It is this direct integration of collaboration capability with daily scientific work processes that allows natural, informal, and effective, scientific communication.

Using CORE for Education

As a simple first step toward an education oriented Collaboratory, the EMSL and the CURE consortium are using CORE to support several pilot collaborations between EMSL researchers and student/faculty groups at several colleges and universities. The CURE consortium includes representatives from Bellevue Community College, The Evergreen State College, Heritage College, Montana and Wyoming EPSCoR (DOE Experimental Program to Stimulate Competitive Research), Northwest Academic Computing Consortium, Portland State University, Reed College, and the University of Washington.

The projects vary both in duration and focus, stressing different capabilities of CORE. Four of the most challenging were begun after the October CURE workshop:

Project: Student research investigating the kinetics and mechanism of CCl₄ degredation in groundwater, with students remotely running samples prepared at Heritage College on the EMSL's ion-trap mass spectrometer and using video-conferencing to view the mass spectroscopy lab and interact with researchers at the EMSL.

Participants: Heritage College: Hossein Divanfard, and Elsa Camacho and Jerrad Roetger(students)

EMSL: John Price, Jim Amonette

Project: Curriculum development in subsurface coupled fluid flow and transport with chemical and biological reactions, with EMSL researchers supporting a WWW based curriculum with remote lectures, discussions, and live display of transport simulations conducted on the EMSL supercomputer.

Participants: The Evergreen State College: Ken Tabbott

Bellevue Community College: Melodye Gold

EMSL: Steve Yabusaki

Project: Study of porphyrin compounds using FTICR mass spectroscopy, relying on the EMSL electronic notebook to let students, faculty and researchers share mass spectroscopy results and the subsequent analysis and interpretation of the data.

Participants: Portland State University: Carl Wamser and students

EMSL: Gordon Anderson, Jim Bruce

Project: Remote lectures, and open discussions/"brownbag lunches" between researchers and students on a variety of scientific topics, including the Collaboratory project itself, the EMSL and its environmental mission, and reports from EMSL research projects. These sessions will involve participants from three or more institutions simultaneously, relying on videoconferencing, shared WWW browsing, and the TeleViewer display sharing software. The first of these, held in early December, allowed one the authors (Dr. Jim Myers, an Associated Western Universities (AWU) 1996-97 Distinguished Lecturer) to present the Collaboratory project to faculty and students at Eastern Oregon State University without leaving his office.

Participants: All

Figure 2) U.W. Honors Chemistry Lab - Live from the EMSL.
Students use a variety of resources to learn about the effect of isotopic distributions on mass spectra.
Students from Prof. Jim Callis' class at U.W. access Jim's notes and spreadsheets from the WWW to
calculate the mass spectrum of a chlorine containing compound. The students visit Dr. John Price in
his ion-trap mass spectroscopy lab at the EMSL via videoconference and receive a short lecture based
on materials on the WWW. The students are then given permission to control the spectrometer and
take data to compare with their calculations. Saving the data in a WWW based notebook allows the
entire class to access the data files from anywhere on the Internet.

Moving toward a Collaboratory for Undergraduate Research and Education

These early projects provide a background for connecting a national research facility with a group of undergraduate institutions. The CURE workshops have raised a number of issues, beyond the basic technology and connectivity issues that have already been solved, that must be addressed to fulfill the true promise of the Collaboratory. Typical of these are:

Which aspects of partnership with a national laboratory are most important for different types of colleges and universities? Student access to advanced instruments and techniques? Development of faculty and their relationships with EMSL researchers? Demonstration and documentation of real-world, multi-disciplinary research in forms accessible to non-science as well as science students?
Where will electronic access to a facility such as the EMSL have the greatest impact? In promoting science literacy for general undergraduates, demonstrating the application of basic, interdisciplinary research to real world problems? Providing access to the latest tools and techniques to science majors as part of laboratory courses? As in-depth research projects for advanced undergraduates? Engaging undergraduate science faculty in the latest scientific developments and techniques?
How should projects in these areas be structured to take advantage of the limited resources (researcher and instrument time, etc.) at the laboratory? How can publishing information and data on the WWW help? How can faculty at multiple institutions work together to support EMSL related projects? How can we organize data that are generated so they can be 'recycled' to serve multiple learning needs of students across programs and time?
What effect will the cultural differences between primarily undergraduate institutions, large research universities, and a national laboratory have on projects? Can departmental barriers be overcome to allow projects that combine biology, chemistry, physics, geology, etc.? How can differences in customary pace, goal-orientation, and focus be melded into working relationships that serve the common good and the individual purposes of all those involved in a collaboration?
Can projects be made sustainable? Can they be structured to provide benefits to EMSL researchers, faculty, and students? Are the maintenance costs for Collaboratory programs consistent with the benefits they provide to students?

These, and a host of other issues must be solved before the Collaboratory approach can have a powerful impact on the undergraduate experience. The EMSL and CURE consortium are committed to cooperatively developing the educational Collaboratory model in pursuit of the joint goal of science literacy and the training of the next generation of scientists. We hope to be able to report on the progress from this work and to share ideas from both CURE workshops and a series of progressively more sophisticated projects, in future articles.

For further information on CURE and the EMSL Collaboratory project

Visit our WWW site or contact us directly:

URL: http://www.emsl.pnl.gov:2080/docs/collab/

Jim Myers manages the Collaboratory Development Project at the Pacific Northwest National Laboratory, William R. Wiley Environmental Molecular Sciences Laboratory and is a co-PI on the NSF-DOE CURE project.
email: jim.myers@pnl.gov
phone: 509/376-9558
fax: 509/376-0420

Norman Chonacky is a resource faculty at The Evergreen State College and a co-PI on the NSF-DOE CURE project.
email: chonacky@elwha.evergreen.edu
phone: 360/866-6000, ext. 5028
fax: 360/866-6823

Thom Dunning is the Director of the William R. Wiley Environmental Molecular Sciences Laboratory.
email: thom.dunning@pnl.gov
phone: 509/375-6863
fax: 509/375-6916

Eric Leber is the Manager of the University and Science Education Programs office, Pacific Northwest National Laboratory
email: eric.leber@pnl.gov
phone: 509/375-2730
fax: 509/375-2576

Acknowledgments

The authors would also like to thank all of the researchers, faculty, administrators, and students, who have participated in CURE workshops and projects.

The development of the Collaboratory and associated systems is supported by the U. S. Department of Energy through the Office of Health and Environmental Research, through the Mathematical, Information and Computational Sciences Division of the Office of Energy Research, and through the Laboratory Directed Research and Development program at Pacific Northwest National Laboratory (PNNL). PNNL is a multiprogram national laboratory operated by Battelle Memorial Institute for the U.S. Department of Energy under Contract DE-AC06-76RLO 1830.

We would also like to note a related effort, led by the non-profit corporation, Alliance for the Advancement of Science Through Astronomy and two of the authors (Leber, Myers), that will use the Collaboratory concept to change the shape and content of education at the pre-college level initially in connection with the Battelle telescope in the Rattlesnake Mountain Observatory of southeastern Washington. AASTA's "Stars On-line," project will provide Internet access to the research-grade Battelle telescope for schools that otherwise would not be able to provide comparable experiences in science and mathematics to their students and teachers. Information on the project is available at

URL: http://www.emsl.pnl.gov:2080/docs/RMO/

References

Kouzes, R.T., Myers, J.D., and Wulf, W.A., "Collaboratories: Doing Science On The Internet" IEEE Computer, Vol. 29:8, August 1996.

Wulf, W.A., "The National Collaboratory - A White Paper," in Towards a National Collaboratory, the unpublished report of a workshop held at Rockefeller University, March 17-18, 1989.

"National Collaboratories: Applying Information Technology for Scientific Research," National Research Council, National Academy Press (1993).