Use of accounting concepts to study research: return on investment in XSEDE, a US cyberinfrastructure service.

This paper uses accounting concepts-particularly the concept of Return on Investment (ROI)-to reveal the quantitative value of scientific research pertaining to a major US cyberinfrastructure project (XSEDE-the eXtreme Science and Engineering Discovery Environment). XSEDE provides operational and support services for advanced information technology systems, cloud systems, and supercomputers supporting non-classified US research, with an average budget for XSEDE of US$20M+ per year over the period studied (2014-2021). To assess the financial effectiveness of these services, we calculated a proxy for ROI, and converted quantitative measures of XSEDE service delivery into financial values using costs for service from the US marketplace.

Improving access to geodetic imaging crustal deformation data using GeoGateway.

GeoGateway (http://geo-gateway.org) is a web-based interface for analysis and modeling of geodetic imaging data and to support response to related disasters. Geodetic imaging data product currently supported by GeoGateway include Global Navigation Satellite System (GNSS) daily position time series and derived velocities and displacements and airborne Interferometric Synthetic Aperture Radar (InSAR) from NASA's UAVSAR platform.

Clustering Analysis Methods for GNSS Observations: A Data-Driven Approach to Identifying California's Major Faults.

We present a data-driven approach to clustering or grouping Global Navigation Satellite System (GNSS) stations according to observed velocities, displacements or other selected characteristics. Clustering GNSS stations provides useful scientific information, and is a necessary initial step in other analysis, such as detecting aseismic transient signals (Granat et al., 2013, https://doi.

Buried Aseismic Slip and Off-Fault Deformation on the Southernmost San Andreas Fault Triggered by the 2010 El Mayor Cucapah Earthquake Revealed by UAVSAR.

We use UAVSAR interferograms to characterize fault slip, triggered by the Mw 7.2 El Mayor-Cucapah earthquake on the 1 San Andreas Fault in the Coachella Valley providing comprehensive maps of short-term geodetic surface deformation that complement in situ measurements. Creepmeters and geological mapping of fault offsets on Durmid Hill recorded 4 and 8 mm of average triggered slip respectively on the fault, in contrast to radar views that reveal significant off-fault dextral deformation averaging 20 mm.

TopPIC Gateway: A Web Gateway for Top-Down Mass Spectrometry Data Interpretation.

Top-down mass spectrometry-based proteomics has become the method of choice for identifying and quantifying intact proteoforms in biological samples. We present a web-based gateway for TopPIC suite, a widely used software suite consisting of four software tools for top-down mass spectrometry data interpretation: TopFD, TopPIC, TopMG, and TopDiff. The gateway enables the community to use heterogeneous collection of computing resources that includes high performance computing clusters at Indiana University and virtual clusters on XSEDE's Jetstream Cloud resource for top-down mass spectral data analysis using TopPIC suite.

Building a Science Gateway For Processing and Modeling Sequencing Data Via Apache Airavata.

The amount of DNA sequencing data has been exponentially growing during the past decade due to advances in sequencing technology. Processing and modeling large amounts of sequencing data can be computationally intractable for desktop computing platforms. High performance computing (HPC) resources offer advantages in terms of computing power, and can be a general solution to these problems.

Sharpening peripheral dose gradient via beam number enhancement from patient head tilt for stereotactic brain radiosurgery.

Sharp dose fall-off is the hallmark of brain radiosurgery for the purpose of delivering high dose radiation to the target while minimizing peripheral dose to regional normal brain tissue. In this study, a technique was developed to enhance the peripheral dose gradient by magnifying the total number of beams focused toward each isocenter through pre-programmed patient head tilting. This technique was tested in clinical settings on a dedicated brain radiosurgical system (GKPFX, Gamma Knife Perfexion, Elekta Oncology) by comparing dosimetry as well as delivery efficiency for 20 radiosurgical cases previously treated with the system.

Potential for a large earthquake near Los Angeles inferred from the 2014 La Habra earthquake.

Tectonic motion across the Los Angeles region is distributed across an intricate network of strike-slip and thrust faults that will be released in destructive earthquakes similar to or larger than the 1933 6.4 Long Beach and 1994 6.7 Northridge events.

Advances in cheminformatics methodologies and infrastructure to support the data mining of large, heterogeneous chemical datasets.

In recent years, there has been an explosion in the availability of publicly accessible chemical information, including chemical structures of small molecules, structure-derived properties and associated biological activities in a variety of assays. These data sources present us with a significant opportunity to develop and apply computational tools to extract and understand the underlying structure-activity relationships. Furthermore, by integrating chemical data sources with biological information (protein structure, gene expression and so on), we can attempt to build up a holistic view of the effects of small molecules in biological systems.

BioDrugScreen: a computational drug design resource for ranking molecules docked to the human proteome.

BioDrugScreen is a resource for ranking molecules docked against a large number of targets in the human proteome. Nearly 1600 molecules from the freely available NCI diversity set were docked onto 1926 cavities identified on 1589 human targets resulting in >3 million receptor-ligand complexes requiring >200,000 cpu-hours on the TeraGrid. The targets in BioDrugScreen originated from Human Cancer Protein Interaction Network, which we have updated, as well as the Human Druggable Proteome, which we have created for the purpose of this effort.

Web service infrastructure for chemoinformatics.

The vast increase of pertinent information available to drug discovery scientists means that there is a strong demand for tools and techniques for organizing and intelligently mining this information for manageable human consumption. At Indiana University, we have developed an infrastructure of chemoinformatics Web services that simplifies the access to this information and the computational techniques that can be applied to it. In this paper, we describe this infrastructure, give some examples of its use, and then discuss our plans to use it as a platform for chemoinformatics application development in the future.

Building messaging substrates for Web and Grid applications.

Grid application frameworks have increasingly aligned themselves with the developments in Web services. Web services are currently the most popular infrastructure based on service-oriented architecture (SOA) paradigm. There are three core areas within the SOA framework: (i) a set of capabilities that are remotely accessible, (ii) communications using messages and (iii) metadata pertaining to the aforementioned capabilities.