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Microbial Source Module (MSM): Documenting the Science and Software for Discovery, Evaluation, and Integration
Citation:
Whelan, G., R. Parmar, AND Gerry Laniak. Microbial Source Module (MSM): Documenting the Science and Software for Discovery, Evaluation, and Integration. U.S. EPA Office of Research and Development, Washington, DC, EPA/600/B-15/315, 2015.
Impact/Purpose:
Manual for Microbial Source Module (MSM)
Description:
The Microbial Source Module (MSM) estimates microbial loading rates to land surfaces from non-point sources, and to streams from point sources for each subwatershed within a watershed. A subwatershed, the smallest modeling unit, represents the common basis for information consumed and produced by the MSM which is based on the HSPF (Bicknell et al., 1997) Bacterial Indicator Tool (EPA, 2013b, 2013c). Non-point sources include numbers, locations, and shedding rates of domestic agricultural animals (dairy and beef cows, swine, poultry, etc.) and wildlife (deer, duck, raccoon, etc.). Monthly maximum microbial storage and accumulation rates on the land surface, adjusted for die-off, are computed over an entire season for four land-use types (cropland, pasture, forest, and urbanized/mixed-use) for each subwatershed. Monthly point source microbial loadings to instream locations (i.e., stream segments that drain individual sub-watersheds) are combined and determined for septic systems, direct instream shedding by cattle, and POTWs/WWTPs (Publicly Owned Treatment Works/Wastewater Treatment Plants). The MSM functions within a larger modeling system that characterizes human-health risk resulting from ingestion of water contaminated with pathogens. The loading estimates produced by the MSM are input to the HSPF model that simulates flow and microbial fate/transport within a watershed. Microbial counts within recreational waters are then input to the MRA-IT model (Soller et al., 2008, 2004) to estimate human exposure and risk.A new approach has been taken in the design and implementation of MSM documentation and software with the goal of enhancing the MSM’s potential for reuse and interoperability with modeling systems. Satisfying this goal requires the MSM to be easy to discover, understand, evaluate, access, and integrate: therefore, the strategy is to 1) facilitate discovery, understanding, and evaluation by documenting the module with an ontological framework, and 2) facilitate access and integration by implementing the software as a web service.The ontological framework is based on the Water Resources Component (WRC) ontology (Elag and Goodall, 2013). The WRC is a structured way to describe the ontology of an environmental system represented by a science software component such as the MSM. The MSM ontology is documented in Protégé (Protégé, 2014), an editor that implements the Web Ontology Language (OWL; W3C, 2013). The ontological framework also documents key aspects of the MSM including key words; module purpose, assumptions, and constraints; inputs; outputs; and internal variables. Finally, this document represents a traditional Theory Manual that accompanies the science; it has been structured to mirror the ontology, thus facilitating development in Protégé.To facilitate access and integration, MSM software has been designed with object-oriented principles and is “published” as a Representational State Transfer (REST, 2015) web service. The web service consumes XML input and produces XML output which can be accessed directly via browser add-ons such as Postman for Chrome. The most common way to consume the web service is through a custom desktop or web client program. The web service is platform and programming language agnostic.