James D. Myers

Bio: James D. Myers is an academic researcher from University of Illinois at Urbana–Champaign. The author has contributed to research in topics: Metadata & Workflow. The author has an hindex of 26, co-authored 82 publications receiving 4480 citations. Previous affiliations of James D. Myers include Inter-university Consortium for Political and Social Research & Sandia National Laboratories.

Examining the Challenges of Scientific Workflows

Abstract: Workflows have emerged as a paradigm for representing and managing complex distributed computations and are used to accelerate the pace of scientific progress. A recent National Science Foundation workshop brought together domain, computer, and social scientists to discuss requirements of future scientific applications and the challenges they present to current workflow technologies.

Vibrational spectroscopy of the hydrated hydronium cluster ions H3O+·(H2O)n (n=1, 2, 3)

Abstract: The gas phase infrared spectra of the hydrated hydronium cluster ions H3O+·(H2O)n(n=1, 2, 3) have been observed from 3550 to 3800 cm^−1. The new spectroscopic method developed for this study is a two color laser scheme consisting of a tunable cw infrared laser with 0.5 cm^−1 resolution used to excite the O–H stretching vibrations and a cw CO2 laser that dissociates the vibrationally excited cluster ion through a multiphoton process. The apparatus is a tandem mass spectrometer with a radio frequency ion trap that utilizes the following scheme: the cluster ion to be studied is first mass selected; spectroscopic interrogation then occurs in the radio frequency ion trap; finally, a fragment ion is selected and detected using ion counting techniques. The vibrational spectra obtained in this manner are compared with that taken previously using a weakly bound H2 "messenger." A spectrum of H7 O + 3 taken using a neon messenger is also presented. Ab initio structure and frequency predictions by Remington and Schaefer are compared with the experimental results.

PROV-DM: The PROV Data Model

Abstract: Provenance is information about entities, activities, and people involved in producing a piece of data or thing, which can be used to form assessments about its quality, reliability or trustworthiness. PROV-DM is the conceptual data model that forms a basis for the W3C provenance (PROV) family of specifications. PROV-DM distinguishes core structures, forming the essence of provenance information, from extended structures catering for more specific uses of provenance. PROV-DM is organized in six components, respectively dealing with: (1) entities and activities, and the time at which they were created, used, or ended; (2) derivations of entities from entities; (3) agents bearing responsibility for entities that were generated and activities that happened; (4) a notion of bundle, a mechanism to support provenance of provenance; (5) properties to link entities that refer to the same thing; and, (6) collections forming a logical structure for its members. This document introduces the provenance concepts found in PROV and defines PROV-DM types and relations. The PROV data model is domain-agnostic, but is equipped with extensibility points allowing domain-specific information to be included. Two further documents complete the specification of PROV-DM. First, a companion document specifies the set of constraints that provenance should follow. Second, a separate document describes a provenance notation for expressing instances of provenance for human consumption; this notation is used in examples in this document.

Infrared spectra of the solvated hydronium ion: Vibrational predissociation spectroscopy of mass-selected H3O+.cntdot.(H2O)n.cntdot.(H2)m

Abstract: Infrared spectra of the mass-selected clusters H{sub 3}O{sup +}{sm bullet}(H{sub 2}O){sub n}{sm bullet}(H{sub 2}) and H{sub 3}O{sup +}{sm bullet}(H{sub 2}){sub n} (n = 1,2, and 3) were observed by vibrational predissociation spectroscopy The clusters were mass-selected and then trapped in a radio frequency ion trap Cluster dissociation by loss of H{sub 2} followed excitation of OH or H{sub 2} stretches Spectra were recorded by detecting fragment ions as a function of laser frequency From spectra of H{sub 3}O{sup +}{sm bullet}(H{sub 2}O){sub n}{sm bullet}(H{sub 2}), the authors were able to determine the spectrum of the hydrated hydronium ion H{sub 3}O{sup +}{sm bullet}(H{sub 2}O){sub n}, because the H{sub 2} formed weak complexes with the hydrates Spectra in the OH stretching region (3,000-4,000 cm{sup {minus}1}) were observed at a resolution of 13 cm{sup {minus}1} for clusters n = 1,2, and 3 The structure of the clusters and the perturbing effect of the H{sub 2} were inferred from a comparison with recent unpublished ab initio vibrational frequencies calculated by Remington and Schaefer

Open Babel: An open chemical toolbox

Abstract: A frequent problem in computational modeling is the interconversion of chemical structures between different formats. While standard interchange formats exist (for example, Chemical Markup Language) and de facto standards have arisen (for example, SMILES format), the need to interconvert formats is a continuing problem due to the multitude of different application areas for chemistry data, differences in the data stored by different formats (0D versus 3D, for example), and competition between software along with a lack of vendor-neutral formats. We discuss, for the first time, Open Babel, an open-source chemical toolbox that speaks the many languages of chemical data. Open Babel version 2.3 interconverts over 110 formats. The need to represent such a wide variety of chemical and molecular data requires a library that implements a wide range of cheminformatics algorithms, from partial charge assignment and aromaticity detection, to bond order perception and canonicalization. We detail the implementation of Open Babel, describe key advances in the 2.3 release, and outline a variety of uses both in terms of software products and scientific research, including applications far beyond simple format interconversion. Open Babel presents a solution to the proliferation of multiple chemical file formats. In addition, it provides a variety of useful utilities from conformer searching and 2D depiction, to filtering, batch conversion, and substructure and similarity searching. For developers, it can be used as a programming library to handle chemical data in areas such as organic chemistry, drug design, materials science, and computational chemistry. It is freely available under an open-source license from http://openbabel.org .

Linked Data - the story so far

Abstract: The term “Linked Data” refers to a set of best practices for publishing and connecting structured data on the Web. These best practices have been adopted by an increasing number of data providers over the last three years, leading to the creation of a global data space containing billions of assertions— the Web of Data. In this article, the authors present the concept and technical principles of Linked Data, and situate these within the broader context of related technological developments. They describe progress to date in publishing Linked Data on the Web, review applications that have been developed to exploit the Web of Data, and map out a research agenda for the Linked Data community as it moves forward.

Basis set exchange: a community database for computational sciences.

Abstract: Basis sets are some of the most important input data for computational models in the chemistry, materials, biology, and other science domains that utilize computational quantum mechanics methods. Providing a shared, Web-accessible environment where researchers can not only download basis sets in their required format but browse the data, contribute new basis sets, and ultimately curate and manage the data as a community will facilitate growth of this resource and encourage sharing both data and knowledge. We describe the Basis Set Exchange (BSE), a Web portal that provides advanced browsing and download capabilities, facilities for contributing basis set data, and an environment that incorporates tools to foster development and interaction of communities. The BSE leverages and enables continued development of the basis set library originally assembled at the Environmental Molecular Sciences Laboratory.

Velocity map imaging of ions and electrons using electrostatic lenses: Application in photoelectron and photofragment ion imaging of molecular oxygen

Abstract: The application of electrostatic lenses is demonstrated to give a substantial improvement of the two-dimensional (2D) ion/electron imaging technique. This combination of ion lens optics and 2D detection makes “velocity map imaging” possible, i.e., all particles with the same initial velocity vector are mapped onto the same point on the detector. Whereas the more common application of grid electrodes leads to transmission reduction, severe trajectory deflections and blurring due to the non-point source geometry, these problems are avoided with open lens electrodes. A three-plate assembly with aperture electrodes has been tested and its properties are compared with those of grid electrodes. The photodissociation processes occurring in molecular oxygen following the two-photon 3dπ(3Σ1g −)(v=2, N=2)←X(3Σg −) Rydberg excitation around 225 nm are presented here to show the improvement in spatial resolution in the ion and electron images. Simulated trajectory calculations show good agreement with experiment and ...

A survey of data provenance in e-science

Abstract: Data management is growing in complexity as large-scale applications take advantage of the loosely coupled resources brought together by grid middleware and by abundant storage capacity. Metadata describing the data products used in and generated by these applications is essential to disambiguate the data and enable reuse. Data provenance, one kind of metadata, pertains to the derivation history of a data product starting from its original sources.In this paper we create a taxonomy of data provenance characteristics and apply it to current research efforts in e-science, focusing primarily on scientific workflow approaches. The main aspect of our taxonomy categorizes provenance systems based on why they record provenance, what they describe, how they represent and store provenance, and ways to disseminate it. The survey culminates with an identification of open research problems in the field.