Sciunits: Reusable Research Objects

Science is conducted collaboratively, often requiring knowledge sharing about computational experiments. When experiments include only datasets, they can be shared using Uniform Resource Identifiers (URIs) or Digital Object Identifiers (DOIs). An experiment, however, seldom includes only datasets, but more often includes software, its past execution, provenance, and associated documentation. The Research Object has recently emerged as a comprehensive and systematic method for aggregation and identification of diverse elements of computational experiments. While a necessary method, mere aggregation is not sufficient for the sharing of computational experiments. Other users must be able to easily recompute on these shared research objects. In this paper, we present the sciunit, a reusable research object in which aggregated content is recomputable. We describe a Git-like client that efficiently creates, stores, and repeats sciunits. We show through analysis that sciunits repeat computational experiments with minimal storage and processing overhead. Finally, we provide an overview of sharing and reproducible cyberinfrastructure based on sciunits gaining adoption in the domain of geosciences

Utilizing Provenance in Reusable Research Objects

Science is conducted collaboratively, often requiring the sharing of knowledge about computational experiments. When experiments include only datasets, they can be shared using Uniform Resource Identifiers (URIs) or Digital Object Identifiers (DOIs). An experiment, however, seldom includes only datasets, but more often includes software, its past execution, provenance, and associated documentation. The Research Object has recently emerged as a comprehensive and systematic method for aggregation and identification of diverse elements of computational experiments. While a necessary method, mere aggregation is not sufficient for the sharing of computational experiments. Other users must be able to easily recompute on these shared research objects. Computational provenance is often the key to enable such reuse. In this paper, we show how reusable research objects can utilize provenance to correctly repeat a previous reference execution, to construct a subset of a research object for partial reuse, and to reuse existing contents of a research object for modified reuse. We describe two methods to summarize provenance that aid in understanding the contents and past executions of a research object. The first method obtains a process-view by collapsing low-level system information, and the second method obtains a summary graph by grouping related nodes and edges with the goal to obtain a graph view similar to application workflow. Through detailed experiments, we show the efficacy and efficiency of our algorithms.Comment: 25 page

Catalogue g\ue9n\ue9ral de v\ue9g\ue9taux fruitiers et d\u27Ornement /

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Adequacy of Treatments in the Case of the Melanoma of the Skin Controlling for Age and Stage

Objectives. Is surgery+adjuvant therapy a better treatment than surgery alone in the case of localized melanoma of the skin? Background. Melanoma of the skin is a cancer that begins in the melanocytes. The cells keep making melanin which often gives the tumor brown or black color. People with darker skin may have lower incidence of the disease, but may develop melanoma as well as people with white skin. Methods. We studied 18,550 individuals diagnosed for the first time with melanoma of the skin in the State of Florida from January 1st 1994 to December 31st 2002. The study design was a cross-sectional, with incident cases over the study period. We used the relative risk as a measure of association. The stratified Mantel-Haenszel methodology was used to assess confounders and/or effect modifiers of the main association between treatment (surgery vs surgery+adjuvant therapy) and vital status (dead vs alive). Results. We analyzed age groups, stage at diagnosis (i.e. localized vs. regionalized), ethnicity and histology. Age groups and stage were effect modifiers, while the latter two were not found to be neither effect modifiers nor confounders. Patients who had surgery alone in localized stage, age 37-50, were 7.39 times more likely to die than those who underwent surgery+adjuvant therapy. When comparing the surgery alone versus surgery+adjuvant we found that patients who underwent surgery alone were 4.6 times more likely to die than patients that underwent surgery + adjuvant therapy. Conclusion. According to age of patient and the stage of the disease, patients younger than 36 years old have higher chances of dying if they undergo surgery alone than older patients; patients between 37-50 years old have higher chances of dying from surgery alone in the localized stage than in regionalized stage. Surgery alone is not indicated in the localized melanoma of the skin. Grants and Acknowledgement. This study was funded in part through the HPD Research Grant for Florida Cancer Registry Analysis, 2004-2007. The views expressed herein are solely those of the authors and do not necessarily reflect those of FCDS, the contractor of FL-DOH