User Access

EMSL's Response

EMSL has rolled out several new features within the last year to facilitate communication with users:

• EMSL website: a new website was rolled out in June 2008. The User Access pages were redesigned to communicate EMSL policies and procedures more concisely.
• EMSL User Portal: the User Portal was rolled out in 2007 and allows users to view their proposal and its status, upload publications and summaries, peer review other users’ proposals, and update their personal contact information.
• EMSL proposal submission site (within the User Portal): the proposal submission site was redesigned and will be rolled out in July 2008.
• In July 2008, EMSL established and opened the User Support Office to centralize and enhance user services. Terry Law, Barb Diehl, and Toni Quackenbush will manage this one-stop shop for users handling front-end user activities including proposal processing, access, and training.

EMSL's Response

To alleviate crowding in the EMSL, a new office pod was built and completed this spring. Beginning summer 2008, a dedicated space and new desktop computers will be available for users.

EMSL's Response

For safety reasons, users only are allowed extended-business prox card access to EMSL (6 am to 9 pm). If users need to work outside these hours, they must be accompanied by a PNNL or EMSL staff member.

EMSL's Response

The Guest House is operated by PNNL, not EMSL. We will forward the comments to PNNL.

PNNL is a national laboratory and does not have the appropriate funds to provide a shuttle service to and from the Guest House. However, bus and taxi services are available to users through Ben Franklin Transit.

EMSL's Response

We recognize, as some users pointed out, that electronics consoles for the instruments are no longer state of the art, and this imposes some limitations for implementing "windowless" sequences. They also lack the benefits from fully digital receivers. We are preparing estimates for upgrades to the new generation of consoles and software for our two highest-end NMR systems for consideration by upper management. In addition, we are considering organizing an NMR workshop to provide a forum for gathering user input for science-driven considerations for capital investments with the highest impact for the NMR capability.

We are proud of the many positive comments we received from users in this round regarding the high quality of data and staff expertise they received when using our 900-and 800-MHz NMR systems. Users expressed how these systems provided critical data that contributed to the success of their projects and publications. The custom-built or one-of-a-kind probes on these two systems are appreciated by our user base and offer unique opportunities for study.

EMSL's Response

The majority of users commented about the excellent support they received from staff members during their visits and their willingness to solve problems even in off hours and weekends. Some users commented that staff members/consultants are not always available for the complete user schedule visit.

We strive to give the best support possible to a visit. We are cross-training our staff members in the basics of experiment setup and support in experimental areas in which they traditionally are not involved (e.g., solids, low-temperature bio-solids, and high-resolution multidimensional liquid state experiments). This new training should help relieve some basic issues in setup/troubleshooting for the NMR when a more experienced staff member/consultant is temporarily unavailable.

EMSL's Response

We have been operating the instrument in 2008 in various modes (with test samples and samples from existing metabolomics-based user proposals), now that all components have arrived. Based on user requests from the recapitalization workshop and management’s receipt of advice from advisory committee members, we have focused the proposal efforts of this instrument to perform metabolomics-based science. The funds to purchase the instrument were received to target this emerging area. Indeed, of the 20 new Science Theme proposals received for the NMR capability, 7 were related to metabolomics interests. We anticipate this new instrument will be an asset to researchers as user support staff and users become more familiar with all aspects of its operation.

EMSL's Response

EMSL emphasizes complex large-scale problems in science and engineering where computation is integrated with theory and experiment. Our current queuing policy is to give priority to jobs using large numbers of processors that cannot be run on readily available small computer clusters. Smaller jobs, which require long execution times, tend to wait longer in the queue. Our new computer (Chinook) will start to be available in summer 2008. At this time, we are revisiting the queuing policy to provide our users with balanced support for large-scale jobs and small-scale jobs associated with multi-facility EMSL Science Theme projects.

EMSL's Response

EMSL is in the process of replacing the MPP2 with Chinook, which has a greater capacity but a similar balance of processor speed, memory bandwidth, and local scratch. The hardware started arriving in spring 2008. The new computer will be about 10 times the current capacity of MPP2. Scalability of third-party software (like molecular dynamics codes such as NAMD and AMBER) depends on hardware and software architecture. Choosing optimal compilation flags is the most we can do in these cases.

EMSL's Response

Molecular dynamics codes such as NAMD and AMBER are provided to users on an "as is" basis. We get the code running as best we can; however, if code modifications are necessary, these need to be done by the software developer and turn-around time can be slower than we would like.

EMSL's Response

EMSL is analyzing the drivers for upgrades and new capabilities. EMSL has engaged its users as well as advisory committees and DOE in its recapitalization plan. In support of recapitalization, EMSL's strategic plan outlines its science vision and drivers, investment strategy, and potential partnerships. In addition, EMSL's "Gold Book" outlines the high-level drivers and the plan for capital investments. Focused workshops were held to help identify specific investment opportunities and technical parameters.

EMSL has several capability development projects in progress:

• Focused Ion Beam/Scamming Electron Microscopy: We have completed the installation and testing of all the components associated with this system. The installation and testing of this instrumentation along with integration to the main system took some time. We apologize for any inconvenience associated with the installation. We have successfully overcome these issues and completed the development of this capability.
• Transmission electron microscopy (TEM) with heating holders and Z contrast: We are working on developing an aberration corrected high-resolution TEM/scanning TEM with an environmental cell for chemical studies. This capability should be available to users in 1 to 2 years. In addition, we are looking to develop probes that can be used with environmental cells and heating for the existing TEM. We have made very good progress in developing probes with closed environmental cells for the existing TEM.
• EMSL now has a novel, high-resolution hybrid Linear Trap Quadrupole/OrbitrapTM Mass Spectrometer dedicated to identification and chemical structure characterization of high molecular weight organic compounds in aerosol and cloud water samples. A desorption electrospray ionization source is used to produce ions of large non-volatile organic molecules with minimal fragmentation. This system is characterized by inherently high mass accuracy (0.1-5 ppm), high mass resolution (up to 100,000), and reliable high-sensitivity multiple-stage tandem mass spectrometry setup for analysis of ions with mass-to-charge ratios in the range of 20-2000 amu. Accurate mass measurements using high-resolution mass spectrometry are crucial for unique identification of the elemental composition of the constituents of organic aerosols. In addition, multiple stages of tandem mass spectrometry experiments are essential for structural characterization of complex molecules. In addition, the system is coupled with a high-performance liquid chromatography separation stage to enable better detection and confident, unequivocal identification of complex oligomeric constituents and humic-like substances in aerosols.
• Plans for the expansion of the Subsurface Flow and Transport Lab are underway. Both the need for a larger format gamma system and an X-ray-based system are recognized. Plans to include microfluidics capability are nearing completion and should be available to general users in FY09. The microfluidics capability will allow investigatation of the effects of fluid flow and transport at the microscale. This new capability will address fundamental scaling issues associated with fluid flow and reactive transport from both a combined experimental and theoretical approach at the micron scale. This capability will bridge the gap in experimental capabilities from the molecular scale within EMSL to the laboratory scales currently available in EMSL's Subsurface Flow and Transport Lab and eventually permit simultaneous spatially and time-resolved spectroscopic examination of geochemical and/or biogeochemical processes.
• EMSL is in the process of assembling the equipment and capabilities to perform STORM (stochastic optical reconstruction microscopy) imaging of fluorescent samples. This new technology has a resolving power more than 10 times better than conventional optical microscopy. The STORM imaging process consists of a series of imaging cycles in which only a fraction of fluorophores are switched on, such that each of the active fluorophores is optically resolvable from the rest. This allows the position of these fluorophores to be determined with high accuracy. Repeating this process with multiple cycles causes a stochastically different subset of fluorophores to be turned on, eventually leading to the reconstruction of an overall image. Work is also proceeding on improving the fluorescent probes necessary for the process and developing automation software. The equipment has been ordered and work is progressing. We expect the scope to be operational in January and be ready for users in Spring or Summer of 2009.
• The Systems Microbiology and Extremophile Research Facility workshop was held March 26, 2008, with more than 30 participants, including prominent microbiologists and systems biologists from around the nation. The meeting was held to identify those capabilities needed to build a systems-level understanding of microbes and microbial communities, especially those that can withstand extreme environments. Unique capabilities in cell growth and analysis were identified as well as important roles that EMSL can play in driving progress in the emerging field of systems microbiology. Implementing several pilot projects in systems microbiology was suggested as a way to most rapidly develop the facility, and implementing a data management system was considered critical to its success.