nanoHUB.org: A Gateway to Undergraduate Simulation-Based Research in Materials Science and Related Fields

Our future engineers and scientists will likely be required to use advanced simulations to solve many of tomorrow\u27s challenges in nanotechnology. To prepare students to meet this need, the Network for Computational Nanotechnology (NCN) provides simulation-focused research experiences for undergraduates at an early point in their educational path, to increase the likelihood that they will ultimately complete a doctoral program. The NCN summer research program currently serves over 20 undergraduate students per year who are recruited nationwide, and selected by NCN and the faculty for aptitude in their chosen field within STEM, as well as complementary skills such as coding and written communication. Under the guidance of graduate student and faculty mentors, undergraduates modify or build nanoHUB simulation tools for exploring interdisciplinary problems in materials science and engineering, and related fields. While the summer projects exist within an overarching research context, the specific tasks that NCN undergraduate students engage in range from modifying existing tools to building new tools for nanoHUB and using them to conduct original research. Simulation tool development takes place within nanoHUB, using nanoHUB’s workspace, computational clusters, and additional training and educational resources. One objective of the program is for the students to publish their simulation tools on nanoHUB. These tools can be accessed and executed freely from around the world using a standard web-browser, and students can remain engaged with their work beyond the summer and into their careers. In this work, we will describe the NCN model for undergraduate summer research. We believe that our model is one that can be adopted by other universities, and will discuss the potential for others to engage undergraduate students in simulation-based research using free nanoHUB resources

Practical Considerations in Cloud Utilization for the Science Gateway nanoHUB.org

nanoHUB.org is arguably the largest online nanotechnology user facility in the world. Just between July 2010 and June 2011 it served 177,823 users. 10,477 users ran 393,648 simulation jobs on a variety of computational resources ranging from HUBzero-based virtual execution hosts for rapid, interactive runs as well as grid-based resources for computationally-intense runs. We believe that as such our users experience a fully operational scientific “cloud”-based infrastructure even though it is not using “standard” computational cloud infrastructures such as EC2. In this paper we explore the use of standard computational cloud-based resources to determine whether they can deliver satisfactory outcomes for our users without requiring high personnel costs for configuration. In a science gateway environment, the assignment of jobs to the appropriate computational resource is not trivial. Resource availability, wait time, time to completion, and likelihood of job success must all be considered in order to transparently deliver an acceptable level of service to our users. In this paper, we present preliminary results examining the benefits and drawbacks of utilizing standard computational cloud resources as one potential venue for nanoHUB computational runs. In summary we find that cloud resources performed competitively with other grid resources in terms of wait time, CPU usage, and success in a multiple job submission strategy

LSST Science Book, Version 2.0

A survey that can cover the sky in optical bands over wide fields to faint magnitudes with a fast cadence will enable many of the exciting science opportunities of the next decade. The Large Synoptic Survey Telescope (LSST) will have an effective aperture of 6.7 meters and an imaging camera with field of view of 9.6 deg^2, and will be devoted to a ten-year imaging survey over 20,000 deg^2 south of +15 deg. Each pointing will be imaged 2000 times with fifteen second exposures in six broad bands from 0.35 to 1.1 microns, to a total point-source depth of r~27.5. The LSST Science Book describes the basic parameters of the LSST hardware, software, and observing plans. The book discusses educational and outreach opportunities, then goes on to describe a broad range of science that LSST will revolutionize: mapping the inner and outer Solar System, stellar populations in the Milky Way and nearby galaxies, the structure of the Milky Way disk and halo and other objects in the Local Volume, transient and variable objects both at low and high redshift, and the properties of normal and active galaxies at low and high redshift. It then turns to far-field cosmological topics, exploring properties of supernovae to z~1, strong and weak lensing, the large-scale distribution of galaxies and baryon oscillations, and how these different probes may be combined to constrain cosmological models and the physics of dark energy.Comment: 596 pages. Also available at full resolution at http://www.lsst.org/lsst/sciboo

Social Networks of Researchers and Educators on nanoHUB.org

The science gateway nanoHUB.org is the world’s largest nanotechnology user facility, serving 167,196 users in 2010 with over 2,300 resources including 189 simulation programs. Surveys of nanoHUB users and automated usage analysis find widespread simulation use in formal classroom education, thereby connecting recent research more rapidly and closely to education. Analysis of 719 citations in the scientific literature by over 1,300 authors to nanoHUB.org resources documents use of simulation programs by new research collaborations, by researchers outside of the community originating the program, and by experimentalists. The publication and author networks reveal research collaborations and capacity building through knowledge transfer. Analysis of secondary citations documents the quality of the conducted research with an h-index of 30 after just 10 years of operation. Our analysis proves with quantitative metrics that impactful research can be conducted by an ever growing research community. We argue that HUBzero technology and the user- focused design and operation of nanoHUB.org are success criteria that can be transferred to other science gateways

Automated Grid-Probe System to Improve End-To-End Grid Reliability for a Science Gateway

In 2010, the science gateway nanoHUB.org, the world’s largest nanotechnology user facility, hosted 9,809 simulation users who performed 372,404 simulation runs. Many of these jobs are compute-intensive runs that benefit from submission to clusters at Purdue, TeraGrid, and Open Science Grid (OSG). Most of the nanoHUB users are not computational experts but end-users who expect complete and uninterrupted service. Within the ecology of grid computing resources, we need to manage the grid submissions of these users transparently with the highest possible degree of user satisfaction. In order to best utilize grid computing resources, we have developed a grid probe protocol to test the job submission system from end to end. Beginning in January 2009, we have collected a total of 1.2 million probe results from job submissions to TeraGrid, OSG, Purdue, and nanoHUB compute clusters. We then utilized these results to intelligently submit jobs to various grid sites using a model for probability of success based in part on probe test history. In this paper we present details of our grid probe model, results from the grid probe runs, and a discussion of data from production runs over the same time period. These results have allowed us to begin assessing our utilization of grid resources while providing our users with satisfactory outcomes

nanoHUB-U: A Science Gateway Ventures into Structured Online Education

nanoHUB.org is arguably the largest online nanotechnology user facility in the world. From an initial user base of about 1,000 users, nanoHUB has grown to support over 250,000 users annually. nanoHUB supports users in 172 countries with materials for research and education, along with a wide variety of simulation tools covering many nano-related areas. Preliminary assessments of user behavior patterns have shown that nanoHUB’s open access approach enables published resources to be integrated directly into classrooms. However, there is an increasing demand for pedagogically sound, workforce-ready, advanced courses that allow users to gain depth in topical areas related to nanotechnology. This paper explores an initial case study where an evolving cyber environment, based on the powerful HUBzero platform, begins to offer structured online courses to its massive audience through an experiment known as nanoHUB-U. This paper describes the impetus for this new offering and discusses how new and cutting-edge content formats are being combined with online simulations in significant ways. Further, it explores in-depth the outcome

Design, Progress and Challenges of a Double-Blind Trial of Warfarin versus Aspirin for Symptomatic Intracranial Arterial Stenosis

Background and Relevance: Atherosclerotic stenosis of the major intracranial arteries is an important cause of transient ischemic attack (TIA) or stroke. Of the 900,000 patients who suffer a TIA or stroke each year in the USA, intracranial stenosis is responsible for approximately 10%, i.e. 90,000 patients. There have been no prospective trials evaluating antithrombotic therapies for preventing recurrent vascular events in these patients. The main objective of this trial is to compare warfarin [International Normalized Ratio (INR) 2–3] with aspirin (1,300 mg/day) for preventing stroke (ischemic and hemorrhagic) and vascular death in patients presenting with TIA or stroke caused by stenosis of a major intracranial artery. Study Design: Prospective, randomized, double-blind, multicenter trial. The sample sizerequired will be 403 patients per group, based on stroke and vascular death rates of 33% per 3 years in the aspirin group vs. 22% per 3 years in the warfarin group, a p value of 0.05, power of 80%, a 24% rate of ‘withdrawal of therapy’, and a 1% rate of ‘lost to follow-up’. Conduct of Trial: Patients with TIA or nondisabling stroke caused by ≧50% stenosis of a major intracranial artery documented by catheter angiography are randomized to warfarin or aspirin. Patients are contacted monthly by phone and examined every 4 months until a common termination date. Mean follow-up in the study is expected to be 3 years. Conclusion: This study will determine whether warfarin or aspirin is superior for patients with symptomatic intracranial arterial stenosis. Furthermore, it will identify patients whose rate of ischemic stroke in the territory of the stenotic intracranial artery on best medical therapy is sufficiently high to justify a subsequent trial comparing intracranial angioplasty/stenting with best medical therapy in this subset of patients