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

Open source GIS platform for water resource modelling: FREEWAT approach in the Lugano Lake

The FREEWAT platform is an innovative Free and Open Source water resource modelling platform integrated in the QGIS geospatial software, using the SpatiaLite database, and including globally-established simulation codes from the USGS MODFLOW models family. This paper demonstrates its application to the Lugano Lake basin case study, Switzerland and Italy. Two specific modules of the platform were used to execute data integration and analyses: the Observation Analysis Tool and the Lake Package. The first one is a newly developed module facilitating the integration of time-series observations into modelling by enabling pre- and post-processing in the model environment; the latter is an existing MODFLOW package allowing dynamic evaluation of groundwater/ lakes interaction. In the case study implementation, a participatory approach was adopted to enhance trust and acceptance of results. These show that integration of simulation codes within GIS is highly appreciated. Furthermore, its openness and freeness allow easily sharing of developed analysis and models. Stakeholders also positively evaluated the participatory process as it empowers decision making with a better understanding of model results and uncertainties. The combination of the FREEWAT platform and the participatory approach may constitute a valuable methodology to include scientifically based analysis to be used for policy design and implementation

Integrating Hydrologic Modeling Web Services With Online Data Sharing to Prepare, Store, and Execute Hydrologic Models

Web based applications, web services, and online data and model sharing technology are becoming increasingly available to support hydrologic research. This promises benefits in terms of collaboration, computer platform independence, and reproducibility of modeling workflows and results. In this research, we designed an approach that integrates hydrologic modeling web services with an online data sharing system to support web-based simulation for hydrologic models. We used this approach to integrate example systems as a case study to support reproducible snowmelt modeling for a test watershed in the Colorado River Basin, USA. We demonstrated that this approach enabled users to work within an online environment to create, describe, share, discover, repeat, modify, and analyze the modeling work. This approach encourages collaboration and improves research reproducibility. It can also be adopted or adapted to integrate other hydrologic modeling web services with data sharing systems for different hydrologic models

Design of a Metadata Framework for the Environmental Models with an Example Hydrologic Application in HydroShare

Environmental modelers rely on a variety of computational models to make predictions, test hypotheses, and address specific problems related to environmental science and natural resource management. Scientists and engineers must devote significant effort to preparing these computational models. While significant attention has been devoted to sharing and reusing environmental data, less attention has been devoted to sharing and reusing environmental models. A first step toward increasing environmental model sharing and reuse is to define a general metadata framework for models that is flexible and, therefore, applicable across the wide variety of models used by environmental modelers. This paper proposes a general approach for representing environmental model metadata that extends the Dublin Core metadata framework. The framework is implemented within the HydroShare system and applied for a hydrologic model sharing use case. This example application demonstrates how the metadata framework implemented within HydroShare can assist in model sharing, publication, reuse, and reproducibility

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

Advancing Cyberinfrastructure for Collaborative Data Sharing and Modeling in Hydrology

Hydrologic research is increasingly data and computationally intensive, and often involves hydrologic model simulation and collaboration among researchers. With the development of cyberinfrastructure, researchers are able to improve the efficiency, impact, and effectiveness of their research by utilizing online data sharing and hydrologic modeling functionality. However, further efforts are still in need to improve the capability of cyberinfrastructure to serve the hydrologic science community. This dissertation first presents the evaluation of a physically based snowmelt model as an alternative to a temperature index model to improve operational water supply forecasts in the Colorado River Basin. Then it presents the design of the functionality to share multidimensional space-time data in the HydroShare hydrologic information system. It then describes a web application developed to facilitate input preparation and model execution of a snowmelt model and the storage of these results in HydroShare. The snowmelt model evaluation provided use cases to evaluate the cyberinfrastructure elements developed. This research explored a new approach to advance operational water supply forecasts and provided potential solutions for the challenges associated with the design and implementation of cyberinfrastructure for hydrologic data sharing and modeling