James F. Bowring

Debugging in Parallel

The presence of multiple faults in a program can inhibit the ability of fault-localization techniques to locate the faults. This problem occurs for two reasons: when a program fails, the number of faults is, in general, unknown; and certain faults may mask or obfuscate other faults. This paper presents our approach to solving this problem that leverages the well-known advantages of parallel work flows to reduce the time-to-release of a program. Our approach consists of a technique that enables more effective debugging in the presence of multiple faults and a methodology that enables multiple developers to simultaneously debug multiple faults. The paper also presents an empirical study that demonstrates that our parallel-debugging technique and methodology can yield a dramatic decrease in total debugging time compared to a one-fault-at-a-time, or conventionally sequential, approach.

An undergraduate degree in data science: curriculum and a decade of implementation experience

We describe Data Science, a four-year undergraduate program in predictive analytics, machine learning, and data mining implemented at the College of Charleston, Charleston, South Carolina, USA. We present a ten-year status report detailing the programs origins, successes, and challenges. Our experience demonstrates that education and training for big data concepts are possible and practical at the undergraduate level. The development of this program parallels the growing demand for finding utility in data sets and streaming data. The curriculum is a seventy-seven credit-hour program that has been successfully implemented in a liberal arts and sciences institution by the faculties of computer science and mathematics.

A new paradigm for programming competitions

The annual ACM International Collegiate Programming Contest produces a competitive paradigm that is at odds with the pedagogical goals of modern computer science and software engineering degree programs. This paradigm stresses the fast completion of a programming task and evaluates the results solely with black-box testing specified by the judges. In contrast, the pedagogical goals of contemporary college degree programs in computing emphasize the quality of processes inherent in software development and implementation. In 2007, the College of Charleston student chapter of the ACM hosted its annual high school programming competition by turning the conventional programming paradigm on its head to focus on quality-of-process rather than time-to-complete. The judging criteria included both technical and artistic merit. The implementation of the competition emphasized success by giving students working skeleton solution programs. This paper presents the motivation for the new paradigm, the details of its implementation for the 2007 competition, and the details of the new techniques for judging technical and artistic merit.

Improving Consistency in Laser Ablation Geochronology; Workshop on Data Handling in LA‐ICP‐MS U‐Th‐Pb Geochronology; San Francisco, California, 12–13 December 2009

The use of uranium-thorium-lead (U-Th-Pb) laser ablation—inductively coupled plasma mass spectrometry (LA-ICP-MS) geochronology involves rapid analysis of U- and Th-rich accessory minerals. It routinely achieves 1–2% precision for U-Th-Pb dates constituting detrital mineral age spectra and for dating igneous and metamorphic events. The speed and low setup and analysis cost of LA-ICP-MS U-Th-Pb geochronology has led to a proliferation of active laboratories. Tens of thousands of analyses are produced per month, but there is little agreement on how to transform these data into accurate U-Th-Pb dates. Recent interlaboratory blind comparisons of zircon samples indicate that resolvable biases exist among laboratories and the sources of bias are not fully understood. Common protocols of data reduction and reporting are essential for scientists to be able to compare and interpret these data accurately. Members of the international community met prior to the 2009 AGU Fall Meeting in San Francisco to address these issues. Funded by the U.S. National Science Foundation (NSF), this collaboration between the Working Group on LA-ICP-MS U-Th-Pb Geochronology of the International Association of Geoanalysts (IAG) and the EARTHTIME and EarthChem communities was attended by 34 scientists from nine countries and multiple geochronological specialties. Attendees sought to compare and contrast the wide array of data reduction software currently used, agree on a common data reduction strategy and reporting protocol, and discuss funding agency-driven initiatives to create community databases for the wealth of data produced.

Algorithms and software for U-Pb geochronology by LA-ICPMS

The past 15 years have produced numerous innovations in geochronology, including experimental methods, instrumentation, and software that are revolutionizing the acquisition and application of geochronological data. For example, exciting advances are being driven by Laser-Ablation ICP Mass Spectrometry (LA-ICPMS), which allows for rapid determination of U-Th-Pb ages with 10s of micrometer-scale spatial resolution. This method has become the most commonly applied tool for dating zircons, constraining a host of geological problems. The LA-ICPMS community is now faced with archiving these data with associated analytical results and, more importantly, ensuring that data meet the highest standards for precision and accuracy and that interlaboratory biases are minimized. However, there is little consensus with regard to analytical strategies and data reduction protocols for LA-ICPMS geochronology. The result is systematic interlaboratory bias and both underestimation and overestimation of uncertainties on calculated dates that, in turn, decrease the value of data in repositories such as EarthChem, which archives data and analytical results from participating laboratories. We present free open-source software that implements new algorithms for evaluating and resolving many of these discrepancies. This solution is the result of a collaborative effort to extend the U-Pb_Redux software for the ID-TIMS community to the LA-ICPMS community. Now named ET_Redux, our new software automates the analytical and scientific workflows of data acquisition, statistical filtering, data analysis and interpretation, publication, community-based archiving, and the compilation and comparison of data from different laboratories to support collaborative science.

Resolving Bias in Laser Ablation Geochronology

Increasingly, scientific investigations requiring geochronology utilize laser ablation (LA)–inductively coupled plasma mass spectrometry (ICPMS), taking advantage of the efficiency and throughput possible for uranium-thorium-lead (U-Th-Pb) dating. A number of biases exist when comparing data among laboratories and an ongoing community-based effort is working to resolve and eliminate these biases to improve the accuracy of scientific interpretation based on these data.

SAM BOWRING - PIONEERING COLLABORATION BETWEEN EARTH SCIENCE AND COMPUTER SCIENCE

Sam Bowring anticipated and pioneered the development of a first of-its-kind collaboration between geochronologists and computer scientists to develop what he called “cradle to tomb” cyber infrastructure to support the flow of data for geochronology from the field to the laboratory to publicly accessible online databases. He first approached Jim Bowring in 1996 to discuss the problems and to explore solutions, and the work continued to advance from that point. Sam was adamant that earth scientists should not need to engage in computer science to develop tools to support their work, and that there was a great opportunity instead for collaboration with computer scientists to advance science, working together to create software that drives improvements in precision, accuracy, reproducibility, availability, and education. The word “Cyberinfrastructure” would not be coined until 1998, yet Sam Bowring foresaw the need for its key elements and processes. Over the last twenty years, Sam led the efforts to reify these ideas in concert with the authors and others. He worked with colleagues to establish EARTHTIME in 2001 as a community driven initiative with the goal of calibrating Earth history and developing the geochronological techniques necessary to produce high precision dates. These techniques include the collaborative development of robust open source software tools to support the scientific workflows of geochronologists including data reduction, analysis, and archiving. The resulting tools Tripoli and ET_Redux, developed with the authors and others, now play a key role in U-Pb geochronology. One of the most important aspects of his vision and these efforts was his anticipation of open data and the integration of these tools with EarthChem data repositories, especially Geochron.org, developed with author Doug Walker. Sam and Doug understood the power of open access to data and Sam insisted early on that ET_Redux be able to compile archived analyses from data repositories to potentially support novel advances. The overarching theme of Sam Bowring’s vision for collaborative development of cyber infrastructure is the potential to improve education at all levels by insisting on transparency and reproducibility.

EarthCube's Governance Working Group Steering Committee presents roadmap

June 2012 EarthCube Charrette;Washington, D. C., 12–14 June 2012 EarthCube is a U.S. National Science Foundation (NSF) initiative sponsored by the Directorate for Geosciences and the Office of Cyberinfrastructure to transform the conduct of research through open, community- guided development of cyberinfrastructure across the geosciences. EarthCube recently held its second organizational charrette (collaborative design event), with the objective of engaging its 190 physical and 60 remote attendees in discussions and workshops on developing EarthCube. One goal of the charrette was to review and integrate draft roadmaps produced by four NSF- funded Community Groups (Governance, Data, Semantics, and Workflow) and five Concept Awards (Brokering, Earth System Models, Layered Architecture, Interoperability, and Web Services), which emerged from the first charrette, held in November 2011. The roadmaps are the culmination of 6 months of research, community outreach, and deliberations in virtual and physical meetings; they identify initial EarthCube stakeholders and cyberinfrastructure components, in addition to key issues related to advancing EarthCube.