HydroDS: Data Services in Support of Physically Based, Distributed Hydrological Models

Physically based distributed hydrologic models require geospatial and time-series data that take considerable time and effort in processing them into model inputs. Tools that automate and speed up input processing facilitate the application of these models. In this study, we developed a set of web-based data services called HydroDS to provide hydrologic data processing ‘software as a service.’ HydroDS provides functions for processing watershed, terrain, canopy, climate, and soil data. The services are accessed through a Python client library that facilitates developing simple but effective data processing workflows with Python. Evaluations of HydroDS by setting up the Utah Energy Balance and TOPNET models for multiple headwater watersheds in the Colorado River basin show that HydroDS reduces the input preparation time compared to manual processing. It also removes the requirements for software installation and maintenance by the user, and the Python workflows enhance reproducibility of hydrologic data processing and tracking of provenance

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

SPATIO-TEMPORAL VARIATION OF MERCURY IN BIDYADHARI RIVER OF SUNDARBAN DELTA, INDIA

Bidyadhari river originates in Nadia district of West Bengal, India and then flows through North 24 Parganas district and now serves as a sewage and excess rainwater outlet from the city of Kolkata and adjacent area, which ultimately empties at the Bay of Bengal through the Indian Sundarban delta. Four different stations situated around the course of the river at considerable distances have been selected from the outfall of sewage canals at Kulti-Ghushighata (S1), where metropolitan sewages discharged and mixed up into water of Bidyadhari river, which ultimately carried through this river via stations Malancha (S2), Kanmari (S3) to Dhamakhali (S4), just before the river confluences with the larger Raimangal river at northern Sundarban delta. This study was conducted to estimate total mercury (Hg) concentration in waters (during high tides and ebb tides) and sediments of Bidyadhari river in pre-monsoon, monsoon and post-monsoon seasons during the period from March, 2012 to February, 2013 at those stations. It is revealed from the estimated data that agricultural runoff, sewage, effluents from various industries and Kolkata metropolitan, Salt Lake City and adjacent areas of North 24 Parganas district carried and discharged in Bidyadhari river through sewage canals are not so high in mercury content for sediment contamination but alarming in respect of water quality, which crosses the permissible limit of Hg for consumption (0.001 ppm) in wide range of areas at Kanmari and Dhamakhali around the estuary. Enhancement of Hg level in this river water and transportation of the metal through tidal effects to and fro mangrove land of Sundarban may be dangerous for aquatic lives and supposed to be grave concern for the ecology of the Sundarban delta including human

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

HydroShare – A Case Study of the Application of Modern Software Engineering to a Large Distributed Federally-Funded Scientific Software Development Project

HydroShare is an online collaborative system under development to support the open sharing of hydrologic data, analytical tools, and computer models. With HydroShare, scientists can easily discover, access, and analyze hydrologic data and thereby enhance the production and reproducibility of hydrologic scientific results. HydroShare also takes advantage of emerging social media functionality to enable users to enhance information about and collaboration around hydrologic data and models. HydroShare is being developed by an interdisciplinary collaborative team of domain scientists, university software developers, and professional software engineers from ten institutions located across the United States. While the combination of non–co-located, diverse stakeholders presents communication and management challenges, the interdisciplinary nature of the team is integral to the project’s goal of improving scientific software development and capabilities in academia. This chapter describes the challenges faced and lessons learned with the development of HydroShare, as well as the approach to software development that the HydroShare team adopted on the basis of the lessons learned. The chapter closes with recommendations for the application of modern software engineering techniques to large, collaborative, scientific software development projects, similar to the National Science Foundation (NSF)–funded HydroShare, in order to promote the successful application of the approach described herein by other teams for other projects

Isorhapontigenin, a resveratrol analogue selectively inhibits ADP-stimulated platelet activation

Isorhapontigenin is a polyphenolic compound found in Chinese herbs and grapes. It is a methoxylated analogue of a stilbenoid, resveratrol, which is well-known for its various beneficial effects including anti-platelet activity. Isorhapontigenin possesses greater oral bioavailability than resveratrol and has also been identified to possess anti-cancer and anti-inflammatory properties. However, its effects on platelet function have not been reported previously. In this study, we report the effects of isorhapontigenin on the modulation of platelet function. Isorhapontigenin was found to selectively inhibit ADP-induced platelet aggregation with an IC50 of 1.85µM although it displayed marginal inhibition on platelet aggregation induced by other platelet agonists at 100µM. However, resveratrol exhibited weaker inhibition on ADP-induced platelet aggregation (IC50>100µM) but inhibited collagen induced platelet aggregation at 50µM and 100µM. Isorhapontigenin also inhibited integrin αIIbβ3 mediated inside-out and outside-in signalling and dense granule secretion in ADP-induced platelet activation but interestingly, no effect was observed on α-granule secretion. Isorhapontigenin did not exert any cytotoxicity on platelets at the concentrations of up to 100µM. Furthermore, it did not affect haemostasis in mice at the IC50 concentration (1.85µM). In addition, the mechanistic studies demonstrated that isorhapontigenin increased cAMP levels and VASP phosphorylation at Ser157 and decreased Akt phosphorylation. This suggests that isorhapontigenin may interfere with cAMP and PI3K signalling pathways that are associated with the P2Y12 receptor. Molecular docking studies emphasised that isorhapontigenin has greater binding affinity to P2Y12 receptor than resveratrol. Our results demonstrate that isorhapontigenin has selective inhibitory effects on ADP-stimulated platelet activation possibly via P2Y12 receptor

Design and implementation of a web service-oriented gateway to facilitate environmental modeling using HPC resources

Environmental researchers, modelers, water managers, and users require access to high-performance computing (HPC) resources for running data and computationally intensive models without being an HPC expert. To address these challenges, we have developed a web-service oriented gateway to HPC storage and computational resources. This gateway software (that we have named HydroGate) is a CGI based http web service that takes input via HTTP methods then transmits commands to the HPC system using SSH in a secure manner. The gateway abstracts away many details and complexities involved in the use of HPC systems including authentication, authorization, data and job management – transferring the data back and forth as well as creation, monitoring and scheduling of the jobs without installing any third-party software on the HPC systems. The web services we have developed may be called from a web server, or desktop client. The contribution of this study is the realization of the gateway service exposing an interface to the client applications that require access to the resources and services on the HPC centers in a secure and straightforward manner. The design and implementation are described, and the computational experience gained while developing the gateway is reported

Collaborative Sharing of Multidimensional Space-tie Data Using HydroShare

HydroShare is a collaborative environment being developed for sharing hydrological data and models. It includes capability to upload data in many formats as resources that can be shared. The HydroShare data model for resources uses a specific format for the representation of each type of data and specifies metadata common to all resource types as well as metadata unique to specific resource types. The Network Common Data Form (NetCDF) was chosen as the format for multidimensional space-time data in HydroShare. NetCDF is widely used in hydrological and other geoscience modeling because it contains self-describing metadata and supports the creation of array-oriented datasets that may include three spatial dimensions, a time dimension and other user defined dimensions. For example, NetCDF may be used to represent precipitation or surface air temperature fields that have two dimensions in space and one dimension in time. This presentation will illustrate how NetCDF files are used in HydroShare. When a NetCDF file is loaded into HydroShare, header information is extracted using the ncdump utility. Python functions developed for the Django web framework on which HydroShare is based, extract science metadata present in the NetCDF file, saving the user from having to enter it. Where the file follows Climate Forecast (CF) convention and Attribute Convention for Dataset Discovery (ACDD) standards, metadata is thus automatically populated. Users also have the ability to add metadata to the resource that may not have been present in the original NetCDF file. HydroShare\u27s metadata editing functionality then writes this science metadata back into the NetCDF file to maintain consistency between the science metadata in HydroShare and the metadata in the NetCDF file. This further helps researchers easily add metadata information following the CF and ACDD conventions. Additional data inspection and subsetting functions were developed, taking advantage of Python and command line libraries for working with NetCDF files. We describe the design and implementation of these features and illustrate how NetCDF files from a modeling application may be curated in HydroShare and thus enhance reproducibility of the associated research. We also discuss future development planned for multidimensional space-time data in HydroShare