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Methods, Models, Tools, and Databases for Ecosystems Research


  • Biological Methods and Manual Development
    EPA's research in stream and source monitoring indicators includes fish, macroinvertebrates, periphyton, zooplankton, functional ecosystem indicators, water and sediment toxicity, and fish tissue contaminants. EPA exposure scientists regularly prepare and update field and laboratory protocol and methods manuals. They also provide technical assistance to EPA regions, program offices and states on the implementation and interpretation of these manuals. This website lists currently available manuals and protocols.
  • Regional Vulnerability Assessment (ReVA) Search EPA Archive
    ReVA is an approach to regional scale, priority-setting assessment by integrating research on human and environmental health, ecorestoration, landscape analysis, regional exposure and process modeling, problem formulation, and ecological risk guidelines.


  • Bioaccumulation in Aquatic Systems Simulator (BASS)
    BASS simulates population and bioaccumulation dynamics of age-structured fish communities. While BASS was designed to investigate bioaccumulation of chemicals within community or ecosystem contexts, it also allows EPA to evaluate various dimensions of fish health associated with non-chemical stressors. Accurate bioaccumulation estimates help predict realistic dietary exposures to humans and fish-eating wildlife.
  • Community Multi-scale Air Quality (CMAQ) Model
    CMAQ is an air quality model and software suite designed to model multiple pollutants at multiple scales. CMAQ allows regulatory agencies and state governments to evaluate the impact of air quality management decisions, and gives scientists the ability to probe, simulate, and understand chemical and physical interactions in the atmosphere.
  • Exposure Analysis Modeling System (EXAMS)
    EXAMS is a modeling system that supports development of aquatic ecosystem models for rapid evaluation of the fate, transport, and exposure concentrations of synthetic organic chemicals like pesticides, industrial materials, and leachates from disposal sites. The system is able to generate and summarize data critical for ecological risk assessments. Much of the data required for EXAMS to function has been collected historically. This allows data needs to be met for some projects without intensive field sampling.
  • Food and Gill Exchange of Toxic Substances (FGETS)
    FGETS predicts temporal dynamics of fish whole body concentration (ug chemical/(g live weight fish)) of non ionic, non metabolized, organic chemicals that are bioaccumulated from either water only or water and food jointly.
  • Framework for Risk Analysis of Multi-Media Environmental Systems (FRAMES) - Visit linked site to request  a copy. Exit
    FRAMES takes collections of models and modeling tools and applies them to real world problems. It facilitates communication between models, supporting the passage of data that helps simulate complex environmental processes. The tool has been used in EPA assessments in support of the Hazardous Waste Identification Rule, which establishes contaminant concentration levels in industrial waste streams that are considered safe for disposal.
  • Markov Chain Nest Productivity Model (MCnest)
    The Markov Chain Nest Productivity Model (or MCnest) integrates existing toxicity information from three standardized avian toxicity tests with information on species life history and the timing of pesticide applications relative to the timing of avian breeding seasons, to quantitatively estimate the impact of pesticide-use scenarios on the annual reproductive success of bird populations. 
  • PRZM
    PRZM is a one-dimensional, finite-difference model that accounts for pesticide and nitrogen fate in the crop root zone. The software includes modeling capabilities for such phenomena as soil temperature simulation, volatilization and vapor phase transport in soils, irrigation simulation, microbial transformation, and a method of characteristics algorithm to eliminate numerical dispersion.
  • Regional Vulnerability Assessment (ReVA) Search EPA Archive
    ReVA is an approach to regional scale, priority-setting assessment by integrating research on human and environmental health, ecorestoration, landscape analysis, regional exposure and process modeling, problem formulation, and ecological risk guidelines.
  • SPARC Performs Automated Reasoning in Chemistry (SPARC) Search EPA Archive
    SPARC estimates chemical reactivity parameters and physical properties for a wide range of organic molecules. This information is needed to be able to predict the fate and transport of pollutants in the environment. SPARC is being designed to incorporate multiple mathematical approaches to estimate important chemical reactions and behavior. It will then interface directly with air, water, and land models to provide scientists with data that can inform risk assessments and help prioritize toxicity-testing requirements for regulated chemicals.
  • Storm Water Management Model (SWMM)
    SWMM is a hydrology and hydraulics model that aids in the design of green and grey stormwater infrastructure alternatives
    Research question: How can urban stormwater and combined sewer overflows be best managed through some combination of conventional structural controls & non-structural BMP and low-impact development controls?
  • Supercomputer for Model Uncertainty and Sensitivity Evaluation (SuperMUSE) Search EPA Archive
    SuperMUSE enhances quality assurance in environmental models and applications. With SuperMUSE, EPA can now better investigate new and existing uncertainty analysis (UA) and sensitivity analysis (SA) methods. EPA can also more easily achieve UA/SA of complex, Windows-based environmental models, allowing scientists to conduct analyses that have, to date, been impractical to consider.
  • Vadose zone LEACHing (VLEACH)
    VLEACH is a one-dimensional, finite difference model for making preliminary assessments of the effects on groundwater from the leaching of volatile, sorbed contaminants through the vadose zone. The program models four main processes: liquid-phase advection, solid-phase sorption, vapor-phase diffusion, and three-phase equilibration.
  • Virulo
    Virulo is a probabilistic screening model for predicting leaching of viruses in unsaturated soils. Monte Carlo is employed to generate ensemble simulations of virus attenuation. The probability of failure is generated to achieve a user-chosen degree of attenuation.


  • Analytical Tools Interface for Landscape Assessments (ATtILA)
    ATtILA is an easy-to-use ArcView extension that calculates many commonly used landscape metrics. 
  • Causal Analysis/Diagnosis Decision Information System (CADDIS)
    CADDIS helps scientists and engineers conduct causal assessments in aquatic systems. It is organized into five volumes:
    • Volume 1: Stressor Identification provides a step-by-step guide for identifying probable causes of impairment in a particular system, based on the U.S. EPA's Stressor Identification process. If you are interested in conducting a complete causal assessment, learning about different types of evidence, or reviewing a history of causal assessment theory, start with this volume.
    • Volume 2: Sources, Stressors & Responses provides background information on many common sources, stressors, and biotic responses in stream ecosystems. If you are interested in viewing source- and stressor-specific summary information (e.g., for urbanization, physical habitat, nutrients, metals, pH and other stressors), start with this volume.
    • Volume 3: Examples & Applications provides examples illustrating different steps of causal assessments. If you are interested in reading completed causal assessment case studies, seeing how Stressor Identification worksheets are completed, or examining example applications of data analysis techniques, start with this volume.
    • Volume 4: Data Analysis provides guidance on the use of statistical analysis to support causal assessments. If you are interested in learning how to use data in your causal assessment, start with this volume.
    • Volume 5: Causal Databases provides access to literature databases and associated tools for use in causal assessments. If you are interested in applying literature-based evidence to your causal assessment, start with this volume.
  • EnviroAtlas
    EnviroAtlas provides interactive tools and resources for exploring the benefits people receive from nature or "ecosystem goods and services". Ecosystem goods and services are critically important to human health and well-being, but they are often overlooked due to lack of information. Using EnviroAtlas, many types of users can access, view, and analyze diverse information to better understand the potential impacts of various decisions.
  • EnviroAtlas Eco-Health Relationship Browser
    The Eco-Health Relationship Browser illustrates the linkages between human health and ecosystem services—benefits supplied by Nature. This interactive tool provides information about our nation's ecosystems, the services they provide, and how those services, or their degradation and loss, may affect people.
    Research question: What goods or services does a certain ecosystem provide and how do those goods and services affect human health and well-being?
  • Enhancing CMAQ Air-Surface Exchange for Ecosystems
    While EPA's Community Multiscale Air Quality (CMAQ) is a state of the science one-atmosphere model, it needs to have state-of-the-science connections to ecosystem models for multimedia analyses. The emphasis of this ecosystem research to enhance air-surface exchange capabilities in CMAQ is to add, modify, and evaluate CMAQ components for better ecosystem model linkage and land-use change study.  The research objective is to improve uni-directional and bi-directional exchange process descriptions in CMAQ and reduce uncertainty in the model estimates of dry and wet deposition, especially for sulfur and nitrogen compounds.  Bi-directional air-surface exchange parameterizations represent state-of-the-science capabilities for regional air quality modeling.  The objective is also to incorporate missing processes in CMAQ and to make the characterization of land use models more flexible.
  • Exposure Model for Soil-Organic Fate and Transport (EMSOFT)
     EMSOFT is used
    • To determine concentrations of contaminants remaining in the soil over a given time (when the initial soil concentration is known);
    • To quantify the mass flux (rate of transfer) of contaminants into the atmosphere over time; and
    • To subsequently calculate contaminant air concentrations by inputting mass flux values into atmospheric dispersion models.
      EMSOFT can also calculate average chemical concentrations at a given depth over time.
  • Integrated Climate and Land-Use Scenarios (ICLUS)-Online
    Initial set of housing density scenarios to assist in integrated assessments of the impacts of climate and land-use change
  • Multi-Resolution Land Characteristics (MRLC) Consortium
    Digital land cover products that can be used for change and trend analysis, and to support environmental assessments. The MRLC products were developed collectively by EPA and other federal agencies.
  • Report on the Environment (ROE)
    ROE presents the best available indicators of information on national conditions and trends in air, water, land, human health, and ecological systems that address 23 questions EPA considers mission critical to protecting our environment and human health.
  • ReVA - Environmental Decision Toolkits under development and ReVA Tools and Projects 
    ReVA is designed to create the methods needed to understand a region's environmental quality and its spatial pattern. Impacts of human activities are not uniformly distributed across landscapes and regions (defined here as a multi-state area) and are often interacting in complex ways.
  • Risk Assessment Guidance & Tools
    EPA has developed help for assessing and managing environmental risks, including guidance and tools which are the models and databases used in risk assessments.
  • Sanitary Sewer Overflow Analysis & Planning (SSOAP) Toolbox
    The SSOAP toolbox is a suite of computer software tools used for quantification of RDII and facilitating capacity analysis of sanitary sewer systems. This toolbox includes the Storm Water Management Model Version 5 (SWMM5) for performing dynamic routing of flows through the sanitary sewer systems.
  • Spatial Allocator
    The Spatial Allocator is used by the air quality modeling community to perform commonly needed spatial tasks without the use of a commercial Geographic Information System (GIS).
  • Spreadsheet-based Ecological Risk Assessment for the Fate of Mercury (SERAFM)
    SERAFM is a steady-state, process based mercury cycling model designed specifically to assist a risk assessor or researcher in estimating mercury concentrations in the water column, sediment, and fish tissue for a given water body for a specified watershed. SERAFM predicts mercury concentrations in these media for the species Hg0, HgII, and MeHg.
  • System for Urban Stormwater Treatment and Analysis Integration (SUSTAIN)
    SUSTAIN is a decision support system to facilitate selection and placement of Best Management Practices (BMPs) and Low Impact Development (LID) techniques at strategic locations in urban watersheds. It was developed to assist stormwater management professionals in developing implementation plans for flow and pollution control to protect source waters and meet water quality goals. From an understanding of the needs of the user community, SUSTAIN was designed for use by watershed and stormwater practitioners to develop, evaluate, and select optimal BMP combinations at various watershed scales on the basis of cost and effectiveness. 
    Research questions:
    • How effective are BMPs in reducing runoff and pollutant loadings?
    • What are the most cost-effective solutions for meeting water quality and quantity objectives?
    • Where, what type of, and how big should BMPs be?
  • Watershed Health Assessment Tools Investigating Fisheries (WHATIF) 
    WHATIF is software that integrates a number of calculators, tools, and models for assessing the health of watersheds and streams with an emphasis on fish communities. The toolset consists of hydrologic and stream geometry calculators, a fish assemblage predictor, a fish habitat suitability calculator, macro-invertebrate biodiversity calculators, and a process-based model to predict biomass dynamics of stream biota. WHATIF also supports screening analyses, such as prioritizing areas for restoration and comparing alternative watershed and habitat management scenarios.
  • Web-based Interspecies Correlation Estimation (WEB-ICE)
    WEB-ICE estimates acute toxicity to aquatic and terrestrial organisms for use in risk assessment.
  • Wildlife Contaminants Exposure Model (WCEM)
    WCEM estimates wildlife exposure to substances through inhalation and through ingestion of food, water, and soil in North American environments. It is suitable for any screening-level risk assessment exercise requiring an estimate of wildlife exposure to organic or inorganic compounds but can also support more detailed risk characterizations.
  • Wildlife Exposure Factors Handbook
    The Wildlife Exposure Factors Handbook provides data, references, and guidance for conducting exposure assessments for wildlife species exposed to toxic chemicals in their environment. The goals of this Handbook are
    • To promote the application of risk assessment methods to wildlife species,
    • To foster a consistent approach to wildlife exposure and risk assessments, and
    • To increase the accessibility of the literature applicable to these assessments.
  • Ubertool: Ecological Risk Web Application for Pesticide Modeling
    Ubertool supports ecological risk decisions.  The dashboard infrastructure integrates the processing of model results for over a dozen commonly-used EPA aquatic and terrestrial regulatory models and supporting datasets.


  • CADLit Database
    CADLit contains stressor-response information for multiple stressor exposures reported in the peer-reviewed scientific literature. As part of a causal analysis, CADLit can help:
    • To identify potential causes of impairment by providing information that may support or negate causal pathways in conceptual model diagrams.
    • To support or negate the contribution of a specific stressor to an impairment by providing qualitative and quantitative data from other studies of similar stressor scenarios.
  • Database of Sources of Environmental Releases of Dioxin-like Compounds in the United States
    The database is a repository of certain specific chlorinated dibenzo-p-dioxin/dibenzofuran (CDD/CDF) emissions data from all known sources in the US. The database contains information that can be analyzed to track emissions of CDD/CDF over time, compare specific profiles between and among source categories, and develop source specific emission factors that can then be used to develop emission estimates.
  • EcoService Models Library (ESML)
    The EcoService Models Library (ESML) is an online database for finding, examining and comparing ecological models that may be useful for quantifying ecosystem goods and services. 
  • ECOTOX Databases
    ECOTOX is a comprehensive database, which provides information on adverse effects of single chemical stressors to ecologically relevant aquatic and terrestrial species. ECOTOX includes more than 910,000 test records covering 12,500 aquatic and terrestrial species and 11,500 chemicals. 
  • EnviroAtlas
    EnviroAtlas provides interactive tools and resources for exploring the benefits people receive from nature or "ecosystem goods and services". Ecosystem goods and services are critically important to human health and well-being, but they are often overlooked due to lack of information. Using EnviroAtlas, many types of users can access, view, and analyze diverse information to better understand the potential impacts of various decisions.
  • Health & Environmental Research Online (HERO)
    HERO provides access to scientific literature used to support EPA’s integrated science assessments.
    Research question: How can EPA increase transparency and provide access to the scientific literature behind scientific assessments?
  • Landscape Ecology Data Browsers
  • ReefLink Database Search EPA Archive
    This scientific and management information database utilizes systems thinking to describe the linkages between decisions, human activities, and provisioning of reef ecosystem goods and services.
  • Virtual Field Reference Database (VFRDB) Search EPA Archive
    The VFRDB provides in situ reference measurement data for statistically rigorous accuracy assessments of land-cover maps derived from satellite and airborne remote sensing platforms.
  • Watershed Deposition Tool Data
    Deposition components available from CMAQ

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