William Barnett - US grants

This study investigates the impacts of a retarded child on the family based on time diary data, other measures of family function, and characteristics of family members, family units, and their environment. A sample of families of retarded children will be obtained in cooperation with the Nation Down Syndrome Congress. A stratified random sample of 300 families will be selected and four waves of surveys will be administered. All four waves will collect surveys for mother (or other primary caregiver) and the retarded child. Two waves will be administered to fathers (or other adult) and a sibling. Time diary data will be obtained for two week days, Saturday and Sunday. These data will be collected by the same instruments and methods applied in 1982 to a national probability sample of American households. This will allow us to compare families of retarded children to other families on very detailed measures of family function, the most important of which is time allocation (level of time in 223 activities, place, others involved, and secondary activity for each family member). Major categories of activities include work, child care, house work, and active and passive leisure. Information will also be collected from each child's teacher. The information produced will be used to assess the effects on internal and external family function, interaction effects of other variables and the resources required (time, money, energy) to care for retarded children (and adults) at home. This information has significance for numerous research and policy issues including: the most appropriate measures of family function and stress; resources expended by family assistance needed to support deinstitutionalization; resources expended by families to care for retarded children compared to other children; demands and constraints placed on individual family members; effects on employment, earnings, education, social life, family life, aspirations, and perceived satisfaction with family and quality of life generally for each family member. The survey includes detailed demographic and social measures, as well as measures of the child's level of adaptive behavior, that can be used in multivariate analyses. Methods of analysis include simple and bivariate statistics, and single equation and structural equation models for multivariate analysis of the new data set and comparison to the 1982 national sample of families. In sum, the study will establish a new baseline of information on families of retarded children.

If there is risk aversion relative to current period prices or interest rates, the tracking properties of all statistical index numbers, including the Divisia and superlative index numbers, are unknown. Under the previous NSF grant, the investigator demonstrated that the tracking ability of the discrete time Divisia index is not seriously compromised by risk aversion. However, that study used data produced by the economy. The use of data from the economy leaves many problems unanswered. For example, it is possible that specification errors might be large and might coincidentally offset the tracking error in the Divisia index. If that were true, the conclusion that the Divisia index is robust to risk aversion might be wrong. This project uses a Monte Carlo approach to generate simulated data in which only one possible source of tracking error remains: the degree of risk aversion. The results of this project are important for monetary policy because monetary aggregates are used by monetary authorities to track the performance of the economy. The research is also methodologically significant because it requires computationally demanding replications of state of the art nonlinear rational expectations models.

9313720 Wheeler This award will support work to develop software for alignment of DNA sequences in a network of workstations. The alignment of DNA sequences has implications in systematic biology, where comparative studies give insight into relationships between organisms and the pattern and the process of evolution. These algorithms for alignment will be developed for the parallel processing environment offered by the network of workstations. The award will test the scalability of these algorithms as one moves to more processing units in the network. ***

We request funds to replace our aging scanning electron microscope (SEM) facility with new instrumentation that has the capabilities to meet the evolving research and educational requirements at the American Museum of Natural History (AMNH). The high magnification, great detail, depth of field, and analytical capabilities inherent to scanning electron microscopy are crucial to the investigation of systematics, mineralogy, and other research foci at the AMNH. The current SEM/EDS system, a Zeiss DSM 950 and Link AN10000, is in continuous use by a varied population of researchers. It was an innovative digital design at the time, but is now worn, outdated, and not upgradeable. This system does not meet research and educational requirements including: 1) imaging uncoated biological specimens, 2) high magnification imaging in both secondary and backscattered electron modes, 3) production and storage of high resolution digital image files, 4) separation of light elements, 5) ease of operation for a diverse user population, 6) industry-standard computing platforms that can be upgraded and have third party application support, 7) network and Internet operation for collaboration and education, and 8) publication quality printing. A new isolation system will suppress of vibrations at magnifications above 20,000x. Secondary electron imaging of uncoated biological specimens, particularly taxonomic types, is important in a museum setting because these specimens are unique and cannot be coated. Backscattered imaging at high magnification and high accelerating voltage operation are critical for mineralogical research. These diverse requirements can now be met by field emission FE) instruments. The ability to greatly increase magnification (FE scopes are rated to 600,00'0~ will extend the frontiers of scientific research at the AMNH. FE instruments have chamber sizes adequate for large specimens and are easy to operate. Current SEM and EDS systems are now migrating to standa rd computing platforms that are easy to use, produce high-resolution digital images, and operate with other instruments over networks and the Internet. The new facility will provide state-of-the-art instrumentation that will meet both new and longstanding research and educational requirements for a very large user population associated with some of the most important natural history collections in the world (in excess of 37 million specimens). The AMNH has committed, and will continue to commit, staff and resources to the operation of the SEM facility. The SEM will be available to all affiliated personnel who undertake research, research training, or education. 3

DESCRIPTION (provided by applicant): The Informatics Core is part of the Consortium for the "Collaborative Initiative on Fetal Alcohol Spectrum Disorders" (CIFASD). The theme of this collaborative initiative is a cross-cultural assessment of "fetal alcohol spectrum disorder" (FASD). The CIFASD will coordinate basic, behavioral, and clinical investigators in a multidisciplinary research project to better inform approaches aimed at developing effective intervention and treatment approaches for FASD. It will involve the input and contributions from basic researchers, behavioral scientists, and clinical investigators with the willingness to utilize novel and cutting-edge techniques so as not to simply replicate previous or ongoing work, but rather to try and move it forward in a rigorous fashion. The Informatics Core will develop and maintain the CIFASD Data Repository, which will be used to collect, maintain and distribute data generated by the various participants in the consortium. The Informatics Core will be responsible for working with the other consortium participants to define a Data Dictionary to be used in standardizing data collection, enabling the transfer of data to and from the CIFASD Data Repository, consulting on how to establish local data management systems, providing both software tools and consulting to consortium participants, and producing status reports about the progress of the various projects within the consortium. The Informatics Core draws on a wealth of resources, experience, and expertise at Indiana University in information technology infrastructure and data management, The CIFASD Data Repository will be developed on Indiana University's state-of-the-art central supercomputing facilities, taking advantage of Indiana University's strong commitment to institutional computational resources. Resources that will be used to implement the CIFASD Data Repository include multiple supercomputers, an array of readily available database and statistical software, and a high- speed, secure, robust data archiving system capable of storing duplicate copies in multiple physical locations separated by more than fifty miles. The Informatics Core will use these extraordinary computational resources to provide a single, highly secure location for consortium participants to obtain the cross-cultural data that will enable the CIFASD to meet its goals of developing novel techniques for intervention and treatment of FASD.

An InCommon Roadmap for NSF Cyberinfrastructure
Abstract
PI: William Barnett


The InCommon project describes activities to produce a guidance document for use by NSF Cyberinfrastructure (CI) projects, their researchers, their users, and campus policy makers, in adopting and using the technologies and policies that make up the identity federation among US campuses called InCommon. Working off existing InCommon documentation, this Roadmap document will focus as much on the motivations and policies as the technologies for joining and participating in the InCommon federation. The document will include advice to NSF as well. The document will be produced under the auspices of an editorial board of technical and policy experts with approval of a final version to be approved by the ACCI Campus Bridging Task Force. Metrics of success for the Roadmap document relate to increased membership and use of federated identity. These metrics therefore address quantitatively the criterion of Broader Impact. Intellectual merit is noted by the proposal as how to overcome the policy, technical, and social challenges in producing clear and concise guidance.


In reality, a single expert will be doing the vast majority of work on this document. The creator of GridShib, along with the identified members of the editorial board, are highly qualified to produce a sound Roadmap. A key driver for adoption and use of this document will be in the motivations for use of InCommon, properly situated as the first thrust area. The proposal includes a detailed timeline and defines the three thrust areas appropriately. The process of using a stellar editorial board with required approval of the ACCI Campus Bridging Task Force ensures the release of a Roadmap that is both technically sound and fully responsive to the needs of CI-centric projects and capabilities of campus CI. If successful, this document will be a cornerstone for wider scale adoption and use of federated identity as defined by the InCommon Federation, the predominant trust fabric in existence today across academic campuses, while providing NSF a reference for the community in defining a path toward achieving the goal of shared CI.

The scientific enterprise in America requires enterprise class security to assure competitive advantage and efficiently advance discovery and invention. Across NSF funded activities there is pervasive and increasing concern with the availability, integrity, and confidentiality of scientific workflows, resources, data, and personal information. Threats include data loss and corruption due to archive failures or malicious attacks, release of private data maliciously or accidentally, or loss of computational or network capacity due to system software failure or compromise. The good news is that there are a number of common security solutions that support NSF researchers today however support for these is limited and often left to the individual development or project teams

This NSF-sponsored workshop will explore the potential for a cross-disciplinary Scientific Software Security Innovation Institute (S3I2) to address the protection, integrity, and reliability of research software, systems, and information. The goal of this workshop is to identify the needs for, and models of, an S3I2 to address secure scientific cyberinfrastructure in the United States. To accomplish this goal, the workshop will bring together representatives from NSF funded projects, researchers, developers, and resource providers. The workshop will cover the topics of: research security needs; existing tools, systems, processes and organizations that secure research activities and data; outstanding issues to be addressed in research assurance; and organization and operational models for a future security institute targeting the identified security needs. The workshop will result in an analysis of these needs and solutions and discuss the advantages of potential models for a S3I2 to address America?s research assurance needs.

Intellectual Merit: This award to Indiana University (IU) is to establish the National Center for Genome Analysis Support (NCGAS) in partnership with the Texas Advanced Computing Center (TACC). The NCGAS will be an innovative service center (core facility) that supports the national community of NSF-funded researchers who use genome assembly software, particularly software suitable for assembly of data from next-generation sequencers; large-scale phylogenetic software; and other genome analysis software requiring large amounts of memory. This center will be a general source of software support and services that will be provided on the Mason large memory computer cluster at IU, on the TACC Gordon system, and on the San Diego Supercomputer Center Dash system. The NCGAS will provide services such as use of cluster-based genome analysis software, storage of submitted data sets, and a repository of open source genome analysis software. Services will particularly support analyses of next-generation sequencer output for de novo assembly, metagenomic projects, and resequencing.

Broader Impacts: The NCGAS will develop innovative solutions to current needs in genome assembly and analysis. It will establish a core of experts and software tools to support research on a variety of nationally funded cyberinfrastructure systems, and will add to the suite of available systems a large memory cluster ideal for this work. By developing a community of investigators and technologists and exploring new modalities of provisioning computational resources, such as "on demand" computing, this project aspires to become a sustainable model for the ongoing, and increasing, need for sequence analysis. The NCGAS website provides up-to-date information at http://pti.iu.edu/ncgas/.

DESCRIPTION (provided by applicant): The Informatics Core is part of the Consortium for the "Collaborative Initiative on Fetal Alcohol Spectrum Disorders" (CIFASD). The theme of this collaborative initiative is a cross-cultural assessment of "fetal alcohol spectrum disorder" (FASD). The CIFASD will coordinate basic, behavioral, and clinical investigators in a multidisciplinary research project to better inform approaches aimed at developing effective intervention and treatment approaches for FASD. It will involve the input and contributions from basic researchers, behavioral scientists, and clinical investigators with the willingness to utilize novel and cutting-edge techniques so as not to simply replicate previous or ongoing work, but rather to try and move it forward in a rigorous fashion. The Informatics Core will develop and maintain the CIFASD Data Repository, which will be used to collect, maintain and distribute data generated by the various participants in the consortium. The Informatics Core will be responsible for working with the other consortium participants to define a Data Dictionary to be used in standardizing data collection, enabling the transfer of data to and from the CIFASD Data Repository, consulting on how to establish local data management systems, providing both software tools and consulting to consortium participants, and producing status reports about the progress of the various projects within the consortium. The Informatics Core draws on a wealth of resources, experience, and expertise at Indiana University in information technology infrastructure and data management, The CIFASD Data Repository will be developed on Indiana University's state-of-the-art central supercomputing facilities, taking advantage of Indiana University's strong commitment to institutional computational resources. Resources that will be used to implement the CIFASD Data Repository include multiple supercomputers, an array of readily available database and statistical software, and a high- speed, secure, robust data archiving system capable of storing duplicate copies in multiple physical locations separated by more than fifty miles. The Informatics Core will use these extraordinary computational resources to provide a single, highly secure location for consortium participants to obtain the cross-cultural data that will enable the CIFASD to meet its goals of developing novel techniques for intervention and treatment of FASD.

DESCRIPTION (provided by applicant): The CIFASD Informatics Core provides a research data resource to be used by investigators to explore the relationships of face, brain, and behavior to improve the diagnosis of FAS and work towards therapies for alcohol exposed children. The Informatics Core has the following specific aims for the next five years: Aim 1: Continued cyber infrastructure support. The Informatics Core will consult and collaborate with CIFASD clinical projects, cores, and developmental projects to support the existing data submission to the CIFASD Central Repository, manage those data, and make those data available for use to accomplish CIFASD goals. Aim 2: Collection of additional data sets. The Informatics Core will securely bring new data sets into the CIFASD Central Repository for cross-study and cross-modality data analysis amongst CIFASD projects. Aim 3: Support of affiliated projects. The Informatics Core will develop technical solutions that will allow the comparison of data between CIFASD and affiliated projects. The Informatics core will use the following methods to support the goals of this project and CIFASD: The ongoing management of standardized data in the CIFASD Central Repository will provide core consortium resources including; data input and bulk upload tools, a data dictionary to standardize terms across studies, a cross query tool so that data from multiple studies can be integrated for synthetic studies, and data browsing tools that enable investigators to ensure data quality. Expert consultation will support the input, export, and integration of data in the Central Repository to lower the barrier of use for investigators and improve data quality of synthetic studies. This consultation will also regularly report on data in the Central Repository to track consortium progress goals. Expert software engineering will provide new input tools and modify existing tools to support the changing needs of CIFASD projects as well as new research projects that are added as part of the third Phase of the CIFASD program.

iSGTW (International Science Grid This Week) is a unique international weekly online publication that covers distributed computing and the research it enables. They report on all aspects of distributed computing technology, such as grids and clouds. They also regularly feature articles on distributed computing-enabled research in a large variety of disciplines, including physics, biology, sociology, earth sciences, archaeology, medicine, disaster management, crime, and art. (Note that they do not cover stories that are purely about commercial technology) In its current incarnation, iSGTW is also an online destination where you can host a profile and blog, and find and disseminate announcements and information about events, deadlines, and jobs. What many people outside of particle physics may not know is that distributed computing played a crucial role in the race towards the discovery of the Higgs Boson at the Large Hadron Collider (LHC) at the CERN laboratory in Geneva, Switzerland.

At present, each issue of iSGTW includes three feature articles, a visual, and a spotlight. Visuals present opportunities to showcase something graphic in nature, such as scientific visualizations, while spotlights feature a variety of links, news articles, papers, and so forth. Both items are typically written in a more casual style, with only a small amount of text. iSGTW feature articles are typically 500 - 1,500 words, but sometimes run longer. iSGTW coverage attempts to be rigorously neutral, never favoring projects affiliated with its funding source or Advisory Board, and maintaining balance across world regions.

The iSGTW website, re-launched in January 2011, also has a number of new and exciting community service features. Readers can post announcements, advertise jobs, and add events to the calendar and everything appears on the front page. News feeds on related topics also appeal to readers looking for more background. Similarly, the website has basic social networking functionality: visitors can leave comments, share content, create profiles, and blog.

A large proportion of the news stories covering cyberinfrastructure-enabled research do not mention the computational side of the story. By publishing well-written science stories that explain the computational aspects of the research, iSGTW ensures that taxpayers, policy makers, and other interested readers understand the role of cyberinfrastructure in scientific endeavors.

As a long-established publication, iSGTW has earned the trust of a range of audiences. Furthermore, as an international collaboration with the explicit support of diverse cyberinfrastructures (such as the Open Science Grid and XSEDE), iSGTW is better able to maintain impartiality and credibility, as compared to publications from individual institutions. The general public and members of the press are more likely to give weight to the stories iSGTW runs, and news outlets are more likely to pick them up.

This theory is supported by the growing number of journalists subscribing to iSGTW. In the July 2009 reader survey, only 3% of iSGTW readers identified as journalists. In the most recent survey, that rose to 7%. The subscription list currently includes approximately 130 journalists, not counting those affiliated with foreign-language media. Publications represented include The New York Times, NPR, Science/AAAS, and the Washington Post. iSGTW's email subscriber list has grown to approximately 8,180 today. Web readership is split evenly between the US and the EU, with approximately 40% of viewers hailing from each continent. Viewers from the Asia Pacific region constitute another 13%. Four percent are from the Central and South American sub-continents. The remainder are from Western Asia, the Middle East, and Africa.

The study of genomes is a critical and rapidly growing component in understanding the variability of life, biological functions, population dynamics, and how organisms respond to external influences. Genomics has qualitatively improved our ability to investigate biological dynamics and to make important discoveries that are the foundations for understanding topics such as environmental change, developing and protecting crops, and improving health outcomes. Genome analysis, however, is a significant challenge for the practicing biologist. Most biologists who need to undertake genome science are not sufficiently expert in the relevant analytical tools, or understand the complex workflows required to get from the initial data generated by sequencers to a biologically meaningful analyzed result. In addition, few have access to the supercomputing resources and large-scale storage required for processing and managing genomics data. The National Center for Genome Analysis Support (NCGAS) addresses these challenges by providing an integrated service comprised of expert consulting and educational services, hardened and optimized software available through easy to use web-based workflow management tools, large memory supercomputers, and large scale data storage and publishing facilities. These resources are particularly useful for researchers from smaller, and minority serving, institutions that typically do not have access to the required expertise and cyberinfrastructure, yet whose investigations are equally important. Since its inception in 2011, the NCGAS has supported over 80 research projects representing over $61M in funded research. It engaged in 51 training events that served 691 individuals, of which 241 were from traditionally underserved populations.

The NCGAS (http://ncgas.org) was established in 2011 through a National Science Foundation ABI development award to help the national research community complete genomics research that requires data management and computational infrastructures at scale. NCGAS is a partnership among the Indiana University Pervasive Technology Institute, the Pittsburgh Supercomputing Center, the Texas Advanced Computing Center, and the San Diego Supercomputing Center. It meets the technology challenges of modern genome science by providing excellent bioinformatics consulting services for genome analysis, particularly genome and transcriptome assembly, including research design, data analysis and visualization. It optimizes, supports, and delivers genome analysis software on national supercomputing systems such as those funded by the NSF eXtreme Digital (XD) program and coordinated by the eXtreme Science and Engineering Discovery Environment (XSEDE) and the Open Science Grid (OSG). The NCGAS maintains and supports easy-to-use gateways, including Galaxy web portals, for genome analysis workflows that lower barriers for scientist to create, execute, document, and share genomics analyses. It distributes software tools for genome analysis to research computing facilities and the general research community so that IT managers can more easily install these tools on their systems. It provides long-term archival storage services. The NCGAS provides a digital library resource for the dissemination of data sets, publications, reports, or collections of files that will allow research to be visible and data to be re-used for decades to come. It delivers education and outreach programs on genome analysis, interpretation, and data management to biology faculty and students nationally. These programs will enhance the technology literacy of practicing scientists and help grow the bioinformatics workforce. These services are particularly available to smaller institutions across the country without access to supercomputers, bioinformatics expertise, or training. The NCGAS will enable breakthroughs that would not be possible without advanced cyberinfrastructure support.