MEME (Multiple EM for Motif Elicitation) is one of the most widely used tools for searching for novel ‘signals’ in sets of biological sequences. Applications include the discovery of new transcription factor binding sites and protein domains. MEME works by searching for repeated, ungapped sequence patterns that occur in the DNA or protein sequences provided by the user. Users can perform MEME searches via the web server hosted by the National Biomedical Computation Resource () and several mirror sites. Through the same web server, users can also access the Motif Alignment and Search Tool to search sequence databases for matches to motifs encoded in several popular formats. By clicking on buttons in the MEME output, users can compare the motifs discovered in their input sequences with databases of known motifs, search sequence databases for matches to the motifs and display the motifs in various formats. This article describes the freely accessible web server and its architecture, and discusses ways to use MEME effectively to find new sequence patterns in biological sequences and analyze their significance.

Biomedical applications have become increasingly complex, and they often require large-scale high-performance computing resources with a large number of processors and memory. The complexity of application deployment and the advances in cluster, grid and cloud computing require new modes of support for biomedical research. Scientific Software as a Service (sSaaS) enables scalable and transparent access to biomedical applications through simple standards-based Web interfaces. Towards this end, we built a production web server (http://ws.nbcr.net) in August 2007 to support the bioinformatics application called MEME. The server has grown since to include docking analysis with AutoDock and AutoDock Vina, electrostatic calculations using PDB2PQR and APBS, and off-target analysis using SMAP. All the applications on the servers are powered by Opal, a toolkit that allows users to wrap scientific applications easily as web services without any modification to the scientific codes, by writing simple XML configuration files. Opal allows both web forms-based access and programmatic access of all our applications. The Opal toolkit currently supports SOAP-based Web service access to a number of popular applications from the National Biomedical Computation Resource (NBCR) and affiliated collaborative and service projects. In addition, Opal’s programmatic access capability allows our applications to be accessed through many workflow tools, including Vision, Kepler, Nimrod/K and VisTrails. From mid-August 2007 to the end of 2009, we have successfully executed 239 814 jobs. The number of successfully executed jobs more than doubled from 205 to 411 per day between 2008 and 2009. The Opal-enabled service model is useful for a wide range of applications. It provides for interoperation with other applications with Web Service interfaces, and allows application developers to focus on the scientific tool and workflow development. Web server availability: http://ws.nbcr.net.

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SUMMARY Airborne laser altimetry has proved useful in recent years in examining volcanic landforms and glacial ice sheets. With the advent of accurate differential GPS aircraft tracking, we believe that airborne lasers will also prove useful in monitoring timevarying topographic uplift, with rates as low as several centimetres of vertical motion per year. The Long Valley, California, caldera provides an excellent testing ground for this new technology. The region has a history of extensive volcanism, and its central dome has recently been undergoing resurgent uplift of up to 4 cm per year. In September 1993 we conducted three aircraft topographic surveys over the caldera and resurgent dome, utilizing a NASA T39 jet aircraft outfitted with a nadir‐profiling altimetric laser (ATLAS), two P‐code GPS receivers, a Litton LTN92 inertial unit for attitude, and aerial cameras. In addition, we operated two base‐station GPS receivers for post‐flight differential navigation and conducted a kinematic automobile survey of roads crossing the dome. The aircraft flew at a mean altitude of 500 m above ground, and at speeds of 80‐100 m s‐1. The laser had a divergence of 1.7 mrad, and output 50 pulses per second, yielding footprints of 0.9 m diameter separated by about 2 m along track. Precision flying yielded multiple profiles along nearly identical paths, including crossing profiles over the resurgent dome, off the dome, and along a nearby highway. The surveys included daily flights over Mono Lake for roll and pitch bias calibrations, and over the well‐surveyed Lake Crowley to provide an independent check of estimated elevations. Much progress has been made in developing analysis procedures for the laser timing and attitude corrections. Crossover points from repeated profiles over the dome and the lake indicate that although some profiles contain relative bias errors of up to 10 cm, most are substantially more accurate. The accuracy of the measurements will increase as the various sources of error are better defined and dealt with. Even with the present analysis level, the distribution of crossovers near the centre of the dome is roughly Gaussian, with a mean of 2.6 cm and a standard deviation of 11 cm. The standard error of the mean is low (1 cm), due to the high number of crossover points, which holds promise for measuring systematic changes in the dome height from year to year. Also, comparison of laser heights of Lake Crowley to tidal gauge heights yields only a 1–4 cm difference in absolute height. These encouraging results serve to confirm further the concept of using aircraft laser surveys for geodetic tectonic monitoring.

We describe the development of automated workflows that support computed-aided drug discovery (CADD) and molecular dynamics (MD) simulations and are included as part of the National Biomedical Computational Resource (NBCR). The main workflow components include: file-management tasks, ligand force field parameterization, receptor-ligand molecular dynamics (MD) simulations, job submission and monitoring on relevant high-performance computing (HPC) resources, receptor structural clustering, virtual screening (VS), and statistical analyses of the VS results. The workflows aim to standardize simulation and analysis and promote best practices within the molecular simulation and CADD communities. Each component is developed as a stand-alone workflow, which allows easy integration into larger frameworks built to suit user needs, while remaining intuitive and easy to extend.