Remote Research using the EMSL Virtual NMR Facility
Kelly A. Keating, Travis Brooks, James D. Myers
Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory
MS K8-91, 3335 Q Avenue, Richland, WA 99352 USA
Kelly.Keating@pnl.gov Travis.Brooks@pnl.gov, Jim.Myers@pnl.gov
Abstract:
Pacific Northwest National Laboratory's Environmental Molecular Sciences Laboratory (EMSL) is a new national user facility housing a variety of state-of-the-art nuclear magnetic resonance (NMR) spectrometers. As part of our Collaboratory for Environmental and Molecular Sciences effort and, we have developed a 'Virtual NMR Facility' that combines secure remote operation of the EMSL's NMR spectrometers with real-time videoconferencing, real time computer display sharing, a Web based Electronic Notebook, and other capabilities. Users of the Virtual Facility have secure direct acquisition control of the EMSL spectrometers and can consult with EMSL staff for training and during setup to optimize the experiment. The electronic notebook allows organization of group notes, drawings, proposed molecular structures, etc. This paper describes the general requirements for a virtual scientific facility, details the specific capabilities available through the EMSL Virtual NMR Facility, and shows how they are being used in the Facility's first project.
Implementing remote control of a scientific instrument is often seen as both necessary and sufficient for enabling distributed research teams to effectively perform experiments on the instrument. In practice, many other capabilities are needed. Remote researchers need to be able to discover the existence of the instrument and learn about the process for requesting time on it. They need to be able to schedule their experiments and work with local technicians or collaborating researchers to receive training, learn local procedures, guide local sample preparation, consult on experiment setup, etc. Once the sample is in the machine, the remote researcher may wish to control the experiment directly or simply monitor progress. Once data exists, remote researchers need access to the data files and local analysis programs. Remote researchers may again wish to consult with their local counterparts during analysis or during the preparation of articles based on the work. Throughout this process, a central repository of background information, plans, ideas, progress, reports, decisions, etc. is needed to allow the team members to coordinate their actions. In summary, the development of remote capabilities for an instrument may be a small part of the overall effort required to make remote/collaborative experiments an effective alternative to travelling to a remote site and running an experiment in the traditional manner.
The EMSL NMR Facility houses several state-of-the-art spectrometers that, as part of the EMSL user facility, are available for use by external researchers (independently, or as part of a collaboration with EMSL researchers) on a competitive proposal basis. (See http://www.emsl.pnl.gov:2080/docs/msd/mrf_guide/). The EMSL Virtual NMR Facility (VNMRF) is designed to allow these researchers to complete their experiments more effectively by increasing their access to EMSL resources before, during, and after use of the spectrometers themselves. Perhaps the best way to describe the VNMRF is in the context of the first experiment conducted using its capabilities. This experiment, a collaboration between Jeff Pelton at Lawrence Berkeley National Laboratory (LBNL) and one of the authors (Kelly Keating, at the EMSL), is designed to elucidate the structure of Heat Shock Factor (HSF) protein molecule. (HSF is a transcription factor that enhances cellular production of heat shock proteins in response to environmental stresses.)
Initial sample preparation was done at LBNL. The collaborators, who had not met in person, used EMSL’s CORE2000 real-time collaboration environment to get acquainted. CORE2000 is an extension of the National Center for Supercomputing Applications (NCSA) Habanero environment that integrates audio and videoconferencing, whiteboards, shared computer screens, chat box, and several other tools. Pelton and Keating used EMSL’s electronic notebook to share literature references and sample preparation procedures prior to the NMR experiments. Other than sample preparation and the actual insertion of the sample into the spectrometer, all aspects of the experiment have been done collaboratively over the Internet. Jeff Pelton (at LBNL) is able to securely login to the EMSL 750 MHz NMR spectrometer from his office computer, run the data acquisition software, and access data files. Keating works with Pelton via CORE2000, discussing parameter settings and watching via CORE2000’s dynamic screen sharing software as Pelton enters changes. (Pelton’s access to the data acquisition software is via X-Windows. Secure shell (ssh, see http://www.cs.hut.fi/ssh/) is used to provide an authenticated encrypted tunnel across the Internet that protects the spectrometer from session hijacking and other hacker threats.) While Pelton controls the spectrometer directly, both participants see the NMR console display, and together make adjustments, collect trial spectra, and finally decide to start the experiment, as though they were sitting together in the laboratory. A series of complementary experiments on HSF have now been completed this way, and data analysis is proceeding, with both real-time and notebook-based exchanges occurring frequently.
Developing the VNMRF required considerable commitment from both the NMR researchers (Pelton and Keating) and the EMSL Collaboratory development team. The NMR researchers were asked to analyze the way they conducted experiments and identify the tasks that compose the experiment lifecycle. They were also asked to help identify which of these tasks would benefit most from close collaboration and what information needed to be shared to accomplish these tasks (data files, parameter sets, literature references, etc.) The developers worked to extend the existing tools (using programming interfaces designed for this purpose) to customize the collaboration tools for NMR. For example, the base electronic notebook was extended to display 3-D rotatable protein structures and contour plots of spectra. Links to the notebook were built within the data acquisition software to allow parameters sets to be automatically sent to the notebook. Thus, an "NMR Spectroscopists’ Notebook" emerged. As the experiments proceeded, the researchers’ input was used to help refine existing tools and to prioritize new developments. In many cases, simply using the electronic collaboration tools gave the researchers ideas for new ways to work together. We believe that this cooperative process - up front analysis, the deployment of extensible base collaboration tools, and iterative development, deployment, and feedback - has been critical to our success and that such an approach is necessary in adopting electronic collaboration tools because of the coupling between user expectations, scientific workflow, and collaboration technologies.
We have found the VNMRF to be an effective means for running NMR experiments with remote colleagues. With the very visible success of Pelton and Keating as motivation, more than half of the first round of EMSL NMR facility users have opted to conduct some or all of their experiments remotely. We are extending the virtual facility concept to other areas of the EMSL and anticipate that such facilities will quickly become a standard way for researchers to access expensive state-of-the-art high field instruments and to work with remote colleagues more efficiently.
Acknowledgements
This work was supported by the U. S. Department of Energy through the DOE2000 program sponsored by 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. 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. Special thanks to Jeff Pelton, and to Deb Agarwal, also at LBNL, for her help in supporting Jeff Pelton’s use of CORE2000 and in debugging network configurations. We gratefully acknowledge the contribution of many individuals to the EMSL Collaboratory project (see http://www.emsl.pnl.gov:2080/docs/collab/).