Methods, Models, Tools, and Databases for Ecosystems Research


  • Biological Condition Gradient (BCG)
    BCG is conceptual framework to allow biological condition to be interpreted independently of assessment methods. It evaluates biological conditions as they respond to varying levels of stressors, relative to an anchored baseline condition. This framework has been successfully applied nationally to management of freshwater streams. BCG can be used by states for more uniform and direct assessment of streams, and to communicate the status of aquatic resources and their potential for restoration to the public. This framework is being expanded to estuaries and other complex environments. 


  • AQUATOX: Linking water quality and aquatic life
    AQUATOX is a simulation model for aquatic systems. AQUATOX predicts the fate of various pollutants, such as nutrients and organic chemicals, and their effects on the ecosystem, including fish, invertebrates and aquatic plants. This model is a valuable tool for ecologists, biologists, water quality modelers and anyone involved in performing ecological risk assessments for aquatic ecosystems.
  • 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.
  • Coastal Gulf Ecology Model (CGEM)
    CGEM is a state-of-the-art complex model for nutrient dynamics and eutrophication processes and hypoxia. CGEM can assist states in the assessment of how much nutrient reduction is needed to achieve Gulf Hypoxia Task Force goals to improve water quality and reduce the Gulf hypoxic zone. It may be used to model harmful algal blooms (HABs), taking into consideration phytoplankton community dynamics. Technical expertise and high level computing resources are needed to run the three-dimensional (x, y, z) versions of the model, however, a one-dimensional version is available that can be run on a desktop computer. 
  • 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.
  • Environmental Fluid Dynamics Code (EFDC Hydro)
    EFDC Hydro is a state-of-the-art hydrodynamic model that can be used to simulate aquatic systems in one, two, and three dimensions. It has evolved over the past two decades to become one of the most widely used and technically defensible hydrodynamic models in the world. EFDC is a surface water modeling system that includes hydrodynamic, sediment-contaminant and eutrophication components. EFDC has been used for more than 80 modeling studies of rivers, lakes, estuaries and wetlands in the United States and abroad. The public domain EFDC model is currently maintained by Tetra Tech, Inc. with support from EPA.
  • 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.
  • 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. 
  • Multimedia, Multi-pathway, Multi-receptor Exposure and Risk Assessment (3MRA)
    3MRA takes collections of models and modeling tools and applies them to real world problems. It is designed to support the Hazardous Waste Identification Rule (HWIR), which establishes contaminant concentration levels in industrial waste streams that are considered safe for disposal. 3MRA conducts screening-level risk-based assessment of potential human and ecological risks from long-term exposure to HWIR chemicals.
  • 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.
  • SPARC Performs Automated Reasoning in Chemistry (SPARC)
    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)
    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 Tolls Interface for Landscape Assessments (ATtILA)
    The Analytical Tools Interface for Landscape Assessments (ATtILA) is an easy-to-use ArcView extension that calculates many commonly used landscape metrics. By providing an intuitive interface, the extension provides the ability to generate landscape metrics to a wide audience, regardless of their GIS knowledge level. 
  • Better Assessment Science Integrating Point & Non-point Sources (BASINS)
    BASINS is a multipurpose environmental analysis system designed to help regional, state, and local agencies perform watershed- and water quality-based studies. It was developed to assist in watershed management and TMDL development by integrating environmental data, analysis tools, and watershed and water quality models. A geographic information system (GIS) organizes spatial information so it can be displayed as maps, tables, or graphics. Through the use of GIS, BASINS has the flexibility to display and integrate a wide range of information (e.g., land use, point source discharges and water supply withdrawals) at a scale chosen by the user.
  • BASINS 4.0 Climate Assessment Tool (CAT): Supporting Documentation and User's Manual (Final Report)
    BASINS and WEPP Climate Assessment Tools (CAT): Case Study Guide to Potential Applications (Final Report)
    BASINS CAT provides flexible capabilities for creating climate change scenarios allowing users to quickly assess a wide range of what if questions about how weather and climate could affect their systems.  The report presenting a series of short case studies illustrating the capabilities of the BASINS CAT  (and a second Water Erosion Prediction Project (WEPP) Climate Assessment Tool) is for conducting scenario-based assessments of the potential effects of climate change on water resources.
  • BMP GeoPlatform
    EPA’s BMP GeoPlatform integrates geospatial technology and environmental data to from the International Stormwater BMP Database so that users can conduct data searches pertinent to a specific region or site. Information for each site includes the type of BMP or LID approach utilized, the amount of stormwater volume reduction achieved, and select soil, land cover, water table and climatic properties. The BMP GeoPlatform provides states with a tool to assist local communities in identifying cost-effective green infrastructure technologies to control stormwater runoff and combined sewer overflows.
  • BMP Siting Tool (ArcGIS 10.1) (Zip file)
    The BMP Siting Tool enables the selection of select suitable locations for different types of low impact development (LID) techniques or conventional best management practices (BMPs). Using GIS analysis and up to nine base data layers, the tool can help states identify suitable sites for placing structural BMPs according to suitability criteria, including slope, soil type, urban land use, land ownership, roads, water table depth, stream location, and drainage area. To conceptualize the physical function of BMPs with regard to their associated landscape, four categories (or types) of BMPs are presented in the BMP Siting Tool: point LID, point BMP, linear BMP and area BMP.
  • Causal Analysis/Diagnosis Decision Information System (CADDIS)
    CADDIS is a web-based technical support system for implementing the stressor identification process for determining environmental causes. Biological indices are the principal monitoring tool for evaluating the biological condition of water bodies in all 50 states, many territories and tribal lands. Yet when a biological assessment indicates a problem, it may not be readily apparent what caused the problem. CADDIS provides states a causal assessment framework by which data and other information are organized and evaluated, using quantitative and logical techniques, to determine the likely cause of an observed condition needed to identify appropriate remediation or restoration actions.
  • Coastal Biodiversity Risk Analysis Tool (CBRAT) Exit
    One of the challenges in responding to the effects of climate change on near-coastal systems is their rich biodiversity. CBRAT is a web-based database that displays the taxonomy and ecology of select groups of near-shore marine invertebrates, including distribution, life history and relative abundances. Using this generally available information, CBRAT can help states identify and predict the relative vulnerability of large numbers of near-coastal species to climate alterations in the marine environment. 
  • Eco-Health Relationship Browser
    This interactive tool provides information about major ecosystems, the services they provide, and how those services, or their degradation and loss, may affect 30+ specific health outcomes. The tool helps illustrate the linkages between human health and ecosystem services--benefits supplied by nature. Includes extensive bibliography.
  • EPA’s Estuary Data Mapper (EDM)
    EDM is a downloadable application that can help states view and access data for estuary-scale geographical regions of interest. Data types include nitrogen sources and loads for coastal watersheds and estuaries, including atmospheric deposition, point source loads and nonpoint source loads as well as response endpoints such as seagrass and chlorophyll a.
  • Exposure Model for Soil-Organic Fate and Transport (EMSOFT)
    • 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 is usedEMSOFT can also calculate average chemical concentrations at a given depth over time.
  • Fertilizer Emission Scenario Tool for CMAQ (FEST-C) 
    The FEST-C tool simulates daily fertilizer application information and facilitates the creation of N and P loss maps over a small region up to a national domain. These maps can use year-specific weather data and atmospheric deposition as input or average files available with the download. FEST-C can be used by states to assess not only the impacts of agricultural fertilization and management practices on the air quality (NH3) and climate (N2O), but also the impacts of meteorology/climate and air quality (N deposition) on crop yield, soil erosion and overall nitrogen, carbon and phosphorus biogeochemical status of the agricultural ecosystem.
  • 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.
  • Mercury Geospatial Assessments for the New England Region (MERGANSER)
    MERGANSER relates atmospheric mercury deposition and lake and watershed characteristics to Hg concentrations in fish and fish-eating wildlife (common loons). The tool provides predicted mercury levels in fish and loons via a web-based interactive tool for 4,404 lakes in New England. States can use MERGANSER to assess the risk of Hg contamination in fish and loons throughout New England and to help plan Hg-pollution reduction efforts.
  • 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.
  • N-Sink (PDFs)
    N-Sink is a web-based tool that uses the best available biogeochemical data and nationally available land cover to estimate nitrogen retention along water flow paths within a hydrologic unit code (HUC) 12 watershed. The approach can help states by generating heat maps of susceptibility and sensitivity of nitrogen deposition within a watershed that is highly valued by decision makers. Two case study watershed examples are available for use online and in an EPA report. EPA is working with the University of Connecticut and University of Rhode Island to apply the tool to multiple watersheds in EPA Region 1 to help support decision making.
  • National Stormwater Calculator with Climate Scenarios (SWC)
    SWC is a desktop application designed to help support local, state, and national stormwater management objectives using GI practices. The primary focus of the SWC is to inform site developers on how well they can meet a desired stormwater retention target, but it can also be used by landscapers and homeowners. In January 2014, it was updated to include the ability to analyze different future climate change scenarios. Users can apply these different scenarios to determine how well GI increases the resiliency of stormwater management approaches to a changing climate. The SWC is now a resource for LEED Project Credit 16 (Rainwater Management) certification by the U.S. Green Building Council for projects that are designed to reduce runoff volume and improve water quality of a site.
  • Net Zero
    Conserving water, reducing energy use, and eliminating solid waste can improve the environment, save money, and help communities become more sustainable and resilient. EPA researchers are helping by developing and implementing Net Zero strategies, approaches and technologies. Simply put, Net Zero means consuming only as much energy as produced, achieving a sustainable balance between water availability and demand, and eliminating solid waste sent to landfills. EPA's research will focus on pooling federal, state and local expertise and resources to make a positive impact on a grand scale while fostering economic growth and promoting citizen health and well-being.
    Under this cross-agency, transdisciplinary partnership, EPA scientists and engineers are working with the U.S. Army, the U.S. Department of Energy, U.S. Army Corp. of Engineers, U.S. Geological Survey, Kansas State University, and private industry to identify and demonstrate innovative water technologies and approaches for achieving net zero goals on the Fort Riley, Kansas Army installation. Results and lessons learned should be available in 2016 to assist states that have specific quantitative goals of reducing energy and water use, and waste generation.
  • 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.
  • 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.
  • Sequence alignment to predict across-species susceptibility (SeqAPASS)
    SeqAPASS is a web-based tool that allows the user to begin to understand how broadly High Throughput Screening (HTS) data or Adverse Outcome Pathways (AOP) constructs may plausibly be extrapolated across species, while describing the relative intrinsic susceptibility of different taxa to chemicals with known modes of action (e.g., pharmaceuticals and pesticides). The tool was designed to automate and streamline the relatively complex and time-consuming process of comparing protein sequences in a consistent, logical, and criteria driven manner intended for predicting across species susceptibility to a chemical perturbation. To define the domain of applicability and enhance the utility of the SeqAPASS tool, multiple case studies have been explored, including the derivation of predictions for across species susceptibility to chemicals that target the human estrogen receptor, bovine androgen receptor, mosquito voltage-gated sodium channel, fungus cytochrome P450 51, and honey bee nicotinic acetylcholine receptor. SeqAPASS is will be released later this year under as open-source program.
  • 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.
  • Stable Isotope Mixing Models for Estimating Source Proportions
    Stable isotope analysis can be used in ecological studies to trace chemical movement through the environment.  A common application is to use the isotopic composition of a mixture to determine the proportions of various sources in the mixture, using mathematical mixing models.  Examples include quantifying the importance of various pollutant sources to contaminated water, or the importance of various prey species in a predator's diet.
  • Stormwater Management Model - Climate Adjustment Tool (SWMM CAT)
    SWMM, first released in 1971, models hydrology and hydraulics to simulate the movement of water through the landscape and into and through sewer systems. The most recent version of this model includes a green infrastructure module to simulate the integration of green infrastructure practices, ranging from green roofs to permeable parking lots, into a community’s stormwater management plan. SWMM is  widely used throughout the world and considered the "gold standard" in the design of urban wet-weather flow pollution abatement approaches, and allows users to include any combination of low impact development/green infrastructure controls to determine their effectiveness in managing stormwater and sewer overflows. The new CAT update for SWMM is particularly useful to states, as it is a simple to use software utility that applies monthly climate adjustment factors onto historical precipitation and temperature data to consider potential impacts of future climate on stormwater.
  • Tool for the Reduction and Assessment of Chemical and Other Environmental Impacts (TRACI)
    TRACI is a software tool that allows for the translation of Life Cycle Assessment (LCA) inventories into quantitative environmental impacts. This process is called life cycle impact assessment. TRACI is designed to be used in conjunction with LCA methods or tools and requires life cycle inventory data to support characterization. The output provides characterized results within respective impact categories. These results may then be further analyzed to determine which stressors provided the primary inputs within each impact category. To demonstrate its widespread use, TRACI has been incorporated into numerous software systems used within the LCA research community and used by academic, industrial, and government personnel that are interested in evaluating the sustainability of a process or product.
  • Ubertool
    Ubertool is a cloud-based web application platform that integrates ten EPA regulatory models and supporting datasets into an automated system that improves the efficiency and transparency of modeled data informing ecological risk assessments. Models in the übertool web platform include a range of aquatic, terrestrial, and atmospheric deposition fate and transport models used to estimate pesticide exposures and effects to ecological receptors. They are used to determine if a pesticide can be approved, provide labeling information to determine safe levels of pesticide application, and, in certain situations, assess impacts to endangered species. 
  • Visualizing Ecosystems for Land Management Assessments (VELMA) (PDF)
    VELMA predicts the effectiveness of alternative green infrastructure scenarios for protecting water quality, and also estimates potential ecosystem service co-benefits and tradeoffs. VELMA is a spatially distributed, eco-hydrological model that links a land surface hydrology model with a terrestrial biogeochemistry model for simulating the integrated responses of vegetation, soil, and water resources to interacting stressors. For example, VELMA can be used by states to analyze the effects of climate and land use on the capacity of ecosystems to provide clean water, flood protection, food and fiber, greenhouse gas regulation, habitat for fish and wildlife, and other services. VELMA is being linked to a variety of other models – fish and wildlife populations, air quality, among others – to support comprehensive environmental decision-making. Current applications include an assessment of forest management strategies for improving salmon habitat in the Pacific Northwest, and identification of rangeland prescribed burning strategies for balancing ecological, economic and human health tradeoffs for rural and urban stakeholders in the Central Great Plains.
  • 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.


  • Adverse Outcome Pathway (AOP) Wiki Exit
    The AOP Wiki is a conceptual framework that shows existing knowledge concerning the linkage between a chemical interacting with a biological process, a direct molecular initiating event, and an adverse human or environmental health risk. The goal of an AOP is to provide the framework that connects the events of the chemical interaction that starts a molecular initiating event and leads to an adverse health outcome. It is important to understand and map AOPs to be able to use high-throughput toxicological data, such as those available from the ToxCast program, for chemical risk assessments and regulatory decisions. Information used to help develop AOPs comes from in vitro data, animal toxicity studies and computational systems. AOPs allow scientists to connect results from the in-vitro tools and rapid screening protocols to actual adverse outcomes.  
  • 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 web-based database that provides information on effects of chemicals on ecologically relevant species. ECOTOX is the ecological counterpart to IRIS (Integrated Risk Information System), the human health effects database. Both ECOTOX and IRIS provide state risk assessors and researchers consistent information on toxic effects of chemical substances. ECOTOX provides information on adverse effects of chemicals to aquatic and terrestrial plant and animal species. Pertinent information on species, chemicals, test methods and toxicity results are encoded into the database. The system currently includes over 789,000 test results on the effects of more than 8,600 chemicals on over 10,000 terrestrial and aquatic species. The database is updated quarterly with new test data.
  • Environmental Decision Toolkits under development
    List of National, Regional, and Place Based ReVA toolkits in development
  • 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?
  • Virtual Field Reference Database (VFRDB)
    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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