Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery最新文献

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OSC OnDemand: a web platform integrating access to HPC systems, web and VNC applications OSC OnDemand:一个集成访问HPC系统、web和VNC应用程序的web平台
D. Hudak, Thomas Bitterman, Patricia Carey, Douglas Johnson, Eric Franz, Shaun Brady, P. Diwan
{"title":"OSC OnDemand: a web platform integrating access to HPC systems, web and VNC applications","authors":"D. Hudak, Thomas Bitterman, Patricia Carey, Douglas Johnson, Eric Franz, Shaun Brady, P. Diwan","doi":"10.1145/2484762.2484780","DOIUrl":"https://doi.org/10.1145/2484762.2484780","url":null,"abstract":"In this paper, we describe the OnDemand web platform for providing OSC users integrated access to HPC systems, web applications and VNC services. We present the user experience and implementation of OnDemand and compare it with existing science gateway approaches.","PeriodicalId":426819,"journal":{"name":"Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery","volume":"66 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129007766","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 10
Human centered game design for bioinformatics and cyberinfrastructure learning 生物信息学和网络基础设施学习中以人为本的游戏设计
D. Perry, Cecilia R. Aragon, S. Cruz, M. Peters, J. Chowning
{"title":"Human centered game design for bioinformatics and cyberinfrastructure learning","authors":"D. Perry, Cecilia R. Aragon, S. Cruz, M. Peters, J. Chowning","doi":"10.1145/2484762.2484833","DOIUrl":"https://doi.org/10.1145/2484762.2484833","url":null,"abstract":"Engaging students in science, technology, engineering, and math (STEM) fields is critical to ensure the success of the next generation of scientists and engineers. Given that 97% of American teens play video games, there is a tremendous opportunity to facilitate interest in STEM topics through the design of engaging learning games. While a growing number of serious games have been developed for biological science and computer science learning, few address the communication and technical challenges that arise in cyberinfrastructure intensive projects, where multiple domain scientists and computer scientists collaborate. This paper describes empirical data collected during a year-long human centered game design process, in which design ideas generated by high school students were bridged with cyberinfrastructure and bioinformatics learning concepts. Our research shows that \"fun\" and engaging game elements are well suited for addressing the sociotechnical aspects of cyberinfrastructure projects. In this research we provide a human centered game design methodology for science educators and science game designers, as well as design implications for integrating game-based experiences into the use of large-scale shared computing resources and services.","PeriodicalId":426819,"journal":{"name":"Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery","volume":"30 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132015348","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 6
Developing a high-volume batch submission system for earthquake engineering 地震工程大批量批量提交系统的开发
A. Mohan, T. Hacker, Gregory P. Rodgers
{"title":"Developing a high-volume batch submission system for earthquake engineering","authors":"A. Mohan, T. Hacker, Gregory P. Rodgers","doi":"10.1145/2484762.2484784","DOIUrl":"https://doi.org/10.1145/2484762.2484784","url":null,"abstract":"NEES is a network of 14 earthquake engineering labs distributed across the United States. As a part of the NEES effort NEESComm operates a comprehensive cyberinfrastructure that consists of the NEEShub and the NEES Project Warehouse. NEESComm provides consistent access to several High Performance Computing (HPC) venues. These venues include XSEDE, the Open Science Grid (OSG), Purdue Supercomputers, and NEEShub servers. In this paper, we describe the system we developed, Batchsubmit, which allows NEES researchers to make use of all these venues through the NEEShub science gateway.","PeriodicalId":426819,"journal":{"name":"Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery","volume":"3 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124553855","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
Training, education, and outreach: raising the bar 培训、教育和推广:提高标准
L. Akli, S. Moore, L. Rivera, P. Teller
{"title":"Training, education, and outreach: raising the bar","authors":"L. Akli, S. Moore, L. Rivera, P. Teller","doi":"10.1145/2484762.2484807","DOIUrl":"https://doi.org/10.1145/2484762.2484807","url":null,"abstract":"This paper describes our efforts to help expand computational and data-enabled science and engineering by educating faculty, students, and staff at the University of Texas at El Paso (UTEP) to advance scientific discovery through the use of cyberinfrastructure. The best practices used to plan, execute, and evaluate the workshop are discussed, and the results of a professional assessment of the workshop are presented. The two-day regional workshop held at UTEP on February 19 and 20, 2013 attracted 100 registrants. It was the largest, most diverse, and most comprehensive workshop that XSEDE has conducted to date. Since the workshop was located at UTEP, it addressed the inclusion of communities that are traditionally under-represented and under-served in STEM, including women and minorities. Note that UTEP is a Hispanic-serving institution with a student population that mirrors the region, i.e., it serves 22,700 students, 77% of whom are Hispanic. In addition, because of its focus, this effort also is meaningful in terms of sustaining a large and diverse scientific, academic, and industrial workforce.","PeriodicalId":426819,"journal":{"name":"Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery","volume":"275 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114524487","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
Experiences in building a next-generation sequencing analysis service using galaxy, globus online and Amazon web service 使用galaxy、globus online和Amazon web服务构建下一代测序分析服务的经验
R. Madduri, Paul Dave, Dinanath Sulakhe, Lukasz Lacinski, Bo Liu, Ian T Foster
{"title":"Experiences in building a next-generation sequencing analysis service using galaxy, globus online and Amazon web service","authors":"R. Madduri, Paul Dave, Dinanath Sulakhe, Lukasz Lacinski, Bo Liu, Ian T Foster","doi":"10.1145/2484762.2484827","DOIUrl":"https://doi.org/10.1145/2484762.2484827","url":null,"abstract":"We describe Globus Genomics, a system that we have developed for rapid analysis of large quantities of next-generation sequencing (NGS) genomic data. This system is notable for its high degree of end-to-end automation, which encompasses every stage of the data analysis pipeline from initial data access (from remote sequencing center or database, by the Globus Online file transfer system) to on-demand resource acquisition (on Amazon EC2, via the Globus Provision cloud manager); specification, configuration, and reuse of multi-step processing pipelines (via the Galaxy workflow system); and efficient scheduling of these pipelines over many processors (via the Condor scheduler). The system allows biomedical researchers to perform rapid analysis of large NGS datasets using just a web browser in a fully automated manner, without software installation.","PeriodicalId":426819,"journal":{"name":"Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery","volume":"21 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114850076","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 19
XSEDE-enabled high-throughput lesion activity assessment 支持xsede的高通量病变活动性评估
Hui Zhang, M. Boyles, Guangchen Ruan, Huian Li, Hongwei Shen, M. Ando
{"title":"XSEDE-enabled high-throughput lesion activity assessment","authors":"Hui Zhang, M. Boyles, Guangchen Ruan, Huian Li, Hongwei Shen, M. Ando","doi":"10.1145/2484762.2484783","DOIUrl":"https://doi.org/10.1145/2484762.2484783","url":null,"abstract":"Caries lesion activity assessment has been a routine diagnostic procedure in dental caries management, traditionally employing subjective measurements incorporating visual and tactile inspections. Recently, advances in 2D/3D image processing and analysis methods and microfocus x-ray computerized tomography (μ-CT) hardware, together with increased power of high performance computing, have created a synergic effect that is revolutionizing many fields in dental computing. In this paper, we report such an XSEDE-enabled high-throughput lesion activity assessment workflow that exploits 2D/3D image processing, visual analytics, and high performance computing technologies. Our paper starts with a brief introduction of the image dataset in our dental studies. We then proceed to a family of 2D image analysis, ROI segmentation, and 3D geometric construction methods. By combining dental imaging technology and 2D/3D image processing algorithms, we transform the task of lesion activity assessment into a 3D-time series analysis of computer generated lesion models. Building on the computational algorithms and implementation models, we develop a high-throughput dental computing workflow exploiting MapReduce tasks to parallelize the image analysis of dental CT scans, the segmentation of region-of-interest (ROI), and the 3D construction of lesion volumes. We showcase the employment of 3D-time series analysis and several other information representations that are applied to our lesion activity assessment scenario focusing on large scale dental image data.","PeriodicalId":426819,"journal":{"name":"Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery","volume":"132 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122881622","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 5
The XSEDE ticket system: from concept to implementation XSEDE票证系统:从概念到实现
Michael Campfield, Mike Pingleton, Stephen McNally, Tabitha K. Samuel, M. Packard, T. Maiden
{"title":"The XSEDE ticket system: from concept to implementation","authors":"Michael Campfield, Mike Pingleton, Stephen McNally, Tabitha K. Samuel, M. Packard, T. Maiden","doi":"10.1145/2484762.2484792","DOIUrl":"https://doi.org/10.1145/2484762.2484792","url":null,"abstract":"In this paper we examine the process of designing and deploying a replacement for the old XSEDE ticket system. We look at each step, from initial concept to final deployment. The impact of XSEDE and service provider-specific policies and needs is outlined along with the final implemented global policies. We review the software and technologies under consideration along with a detailed analysis of the chosen solution. Deployed in May, 2013, the new ticket system is based on Request Tracker by Best Practical. We utilized distributed configuration management to speed deployment and arrange for rapid failover transitions providing increased uptime and ease of management between the National Institute for Computational Sciences and the Texas Advanced Computing Center. Novel high availability practices will deliver a near 100% uptime for the deployed system. We discuss future plans to deploy a federated interface that will allow the various Service Providers to update the central XSEDE ticket system directly from their local ticket systems. This federated interface will provide added functionality and will allow the XSEDE ticket system to tie into existing workflows at each Service Provider thus making it both a critical and agile service. Finally, we examine future directions the project can take in order to provide for the changing needs of the wider XSEDE community.","PeriodicalId":426819,"journal":{"name":"Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery","volume":"29 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127063153","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
SeedMe preview: your results from disk to device SeedMe预览:您的结果从磁盘到设备
A. Chourasia, M. Wong-Barnum, M. Norman
{"title":"SeedMe preview: your results from disk to device","authors":"A. Chourasia, M. Wong-Barnum, M. Norman","doi":"10.1145/2484762.2484764","DOIUrl":"https://doi.org/10.1145/2484762.2484764","url":null,"abstract":"Computational simulations have become an indispensible tool for a wide variety of science and engineering investigations. With the rise in complexity and size of computational simulations, it has become necessary to continually and rapidly assess simulation output. Visualization could play an even more important and critical role for qualitative assessment of raw data. The result of many visualization processes is a set of image sequences, which can be encoded as a movie and distributed within and beyond the research group. The movie encoding process is a computationally intensive, manual, serial, cumbersome and complicated process as well as one that each research group must undertake. Furthermore, sharing visualizations within and outside the research groups requires additional effort. On the other hand, the ubiquity of portable wireless devices has made it possible and oftentimes desirable to access information anywhere and at anytime, yet the application of this capability for use in computational research and outreach has been negligible. We are building a cyberinfrastructure SeedMe (Stream Encode Explore Disseminate My Experiments) to fill these gaps that will enable seamless sharing and streaming of visualization content on a variety of platforms from mobile devices to workstations making it possible to conveniently view and assess the results thus provide an essential yet missing component in computational research and current High Performance Computing infrastructure.","PeriodicalId":426819,"journal":{"name":"Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery","volume":"12 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128478399","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 6
'Spring through the gateway': deploying genomic workflows with XSEDE “Spring through the gateway”:使用XSEDE部署基因组工作流程
David Rhee, Joseph Hargitai, R. B. Calder, Pilib Ó Broin, Kevin R. Shieh, A. Golden
{"title":"'Spring through the gateway': deploying genomic workflows with XSEDE","authors":"David Rhee, Joseph Hargitai, R. B. Calder, Pilib Ó Broin, Kevin R. Shieh, A. Golden","doi":"10.1145/2484762.2484812","DOIUrl":"https://doi.org/10.1145/2484762.2484812","url":null,"abstract":"The use of sequencing technologies has revolutionized the field of genomics, allowing us to study structural and functional variations within the genome to base pair level. These technologies can also be used to probe the associated epigenome, where DNA-binding proteins alter the structural integrity of the genome, restricting or enabling localized gene expression in a heritable fashion. By using assays that identify the binding location of these proteins, so called 'epigenetic marks' can be used to discover and correlate molecular functions and phenotypes being studied. As such 'epigenetic marks' are inherently plastic in their nature, being easily perturbed by environmental stimuli, they are a compelling and important area of study in the context of human development and diseases. One of the most commonly studied epigenetic marks is DNA methylation: attachment of the methyl group to cytosines in CpG dinucleotides -- an occurrence where two cytosine nucleotides are immediately followed by two guanine nucleotides in tandem. This modification can directly block the binding of regulatory proteins to that specific location thus effectively 'silencing' transcriptional activities. There are roughly 2.8 million such CpG loci in a human genome, making it an excellent target for performing a genome-wide methylation assay using sequencing technologies.","PeriodicalId":426819,"journal":{"name":"Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery","volume":"26 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125932715","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Low-temperature isomers of the water hexamer as predicted by q-TIP4P/F and TTM3-F potentials 用q-TIP4P/F和TTM3-F势预测水六聚体的低温异构体
V. Babin, F. Paesani
{"title":"Low-temperature isomers of the water hexamer as predicted by q-TIP4P/F and TTM3-F potentials","authors":"V. Babin, F. Paesani","doi":"10.1145/2484762.2484768","DOIUrl":"https://doi.org/10.1145/2484762.2484768","url":null,"abstract":"The hexamer is the smallest non-planar water cluster exhibiting several isomeric forms whose equilibria are governed by the subtle interplay between energetic and entropic contributions affected significantly by nuclear quantum effects. The hexamer thus can serve as a sensitive test for model potential energy surfaces (PESs), probing both the relative depth and shape of the minima corresponding to the different isomers. Here we report on the equilibrium populations of the hexamer isomers in the temperature range from 30 K to 150 K as predicted by two popular flexible force fields (q-TIP4P/F and TTM3-F) and compare them against the results obtained recently for an ab initio-based potential (WHBB). The calculations were performed using path-integral molecular dynamics combined with the replica exchange method.","PeriodicalId":426819,"journal":{"name":"Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery","volume":"20 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125597994","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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