Our Program and Focus Areas

Innovative technology driving science solutions

The SFEI Environmental Informatics Program utilizes the latest technology and design concepts to deliver scientific information to a wide range of stakeholders in dynamic, expressive, and cogent ways. Web-based tools, such as EcoAtlas, California Rapid Assessment Method, and Contaminant Data Display and Download, form a lynchpin of SFEI’s success as a communicator of timely and salient scientific information.

  • Our Geographic Information Systems team rigorously describes and analyzes the world as it is, as it once was, and as it could be.
  • Our Data Services team, forming the core of SFEI’s Regional Data Center, offers a suite of analytical services for the Bay RMP, the California Environmental Data Exchange Network, and various local agencies and programs.
  • Using innovative data visualizations, our Application Development team produces tools that integrate disparate data sources to serve the needs of decision-makers and the public.
  • Our Design and Communications team provides the bridge between science and its intended audience through creative and thoughtful methods.
  • Our Systems team ensures the Institute’s computing infrastructure is robust, secure, and accessible to meet the growing requirements of our databases, websites, and tools.

The Environmental Informatics Program is unique among the programs and departments at SFEI, in that it has a dual role. The first role is to provide the basic computing infrastructure and technical support necessary for any functioning organization; the second is to seek opportunities to apply information technology to promote informed stewardship of the Estuary, both for SFEI and for groups outside the Institute.


  • Continue to increase SFEI’s stature as the place to go for Bay region environmental data, evidenced by:
    • Growth in traffic to all SFEI websites
    • Growth in the number of websites SFEI hosts
    • Growth in the number of external requests for information
  • Increase the number of funded projects to manage and/or host Bay environmental data
  • Continue to break ground on providing clear, understandable, relevant information products to a variety of audiences
  • Maintain a high level of staff satisfaction with internal computing infrastructure and technical support

SFEI’s Environmental Informatics team, working in collaboration with its scientists, explores the frontiers of geodesign and alternative future planning, and facilitates discovery to inform decision-making at all levels of natural resource management.

For additional information, please contact Program Director Tony Hale or Program Manager Cristina Grosso.


Geographic Information Systems, or GIS, is a powerful dynamic tool that allows complex analyses to be applied to the landscape. The department uses this technology to create practical tools that support better decision-making and promote smart solutions for environmental problems. 

How GIS Enhances the Institute

SFEI’s GIS department supports the Institute’s mission through data production, mapping expertise, spatial analysis, and application development. The department serves four major functions:
  1. Creates, maintains and acts as a repository for local environmental data sets
  2. Provides cartographic support to convey complex conditions and presents science based solutions
  3. Develops custom GIS tools and applications to address and analyze environmental problems
  4. Presents potential solutions to different partners in order to promote environmental connections between different audiences

Audience and Stakeholders

The environmental applications of GIS are varied in terms of potential users, environmental fields, and the specific issue being investigated. In response to this need, SFEI’s GIS group is composed of professionals from various academic backgrounds with diverse specialties which promotes flexibility and innovation. (View the Data Center and Project pages for a sample of our GIS work.)

Our technologists work in concert with SFEI’s scientists and project managers to reach a wide array of audiences. We collaborate with such people and organizations as local landowners, city and county governments, California Regional Water Quality Control Boards, as well as other science based institutes and organizations, all to forge the connections necessary to inform accurate, useful and relevant GIS analysis and tool creation. .


One of the department’s distinguishing characteristics is the strength of the wetland mapping expertise. In order to protect and conserve the sensitive wetlands across the state of California, aquatic features must be cataloged and analyzed in a comprehensive and detailed database. CARI, an amalgam of a number of intensive regional aquatic resource mapping efforts, is merely one prominent achievement for our mapping expertise.

Broad Sustainability through Innovation

The Institute is often working on complex issues that have a broad impact for environmental sustainability on a regional scale. Such issues and ideas must be conveyed to different audiences in ways that are both visual and intuitive. Example environmental applications range from the Landscape Profile Tool, which allows users to summarize different environmental and social characteristics of custom areas of interest, to SFEI’s GreenPlanIT toolbox, which allows municipalities to create ranked maps of where future green infrastructure could be placed within their cities, using local priorities and datasets.

Special Project: Data Collection and Enhanced Analysis via Unmanned Aerial Vehicles


SFEI has invested in novel, cost-effective solutions to costly problems. Most recently, our work with Unmanned Aerial Vehicles (UAVs) has yielded some very promising results. We have collaborated with colleagues at the Southern California Coastal Water Research Project (SCCWRP) to field test a UAV and apply it to a number of scientific challenges. In the course of this research, we have derived some useful analysis on the use of the technology.


  • Repeatability of flights before and after events (autonomous flight paths)
  • Sensing of sensitive and hard to reach areas (marshes, water, native plants etc.)
  • Quick turnaround (12 hour processing)
  • High resolution and comprehensive datasets

More on this intriguing research is available on our Unmanned Aerial Vehicle Project page.

The Data Services (DS) team, forming the core of SFEI’s Regional Data Center (RDC), offers a suite of analytical services for the Bay RMP, the California Environmental Data Exchange Network (CEDEN), and various agencies and programs serving local and regional interests.

Subject Matter Expertise

The DS team helps organizations within the San Francisco Bay-Delta and northern montane regions prepare their data for regulatory compliance. The DS team also manages analytical data generated by staff scientists in support of SFEI programs and projects.

Accordingly, the DS team specializes in managing data associated with a variety of environmental sample types including: analytical chemistry, ancillary, water toxicity, sediment toxicity, benthic assessment, habitat, pathogen, and continuous data. All data records are standardized using standard data vocabulary and business rules.

SFEI’s Quality Assurance Officer and associated DS staff perform a thorough quality assurance and quality control (QA/QC) review of environmental results.  Each dataset is reviewed for accuracy, precision, sensitivity, contamination and completeness.

For more details on our services, please consult this reference.

Modern Tools

Over 2.1 million environmental data records are maintained by the DS team in SFEI’s RDC database. Data that has been approved for public release is disseminated through SFEI’s Contaminant Data Display and Download tool (CD3).

SFEI is also a regional data center for CEDEN, the State Water Board's data system for surface water quality in California. As such, the DS team works to upload data for CEDEN clients throughout northern California. In addition to CD3, CEDEN clients can download their data through CEDEN’s Advanced Query Tool (AQT).

Members of the Data Services team integrate with other Environmental Informatics focus areas by contributing to custom web programming and database design, programming and technology maintenance.

Data Services Team


The Application Development team is responsible for creating data visualizations and mapping resources that support the ongoing scientific efforts of the Institute. They innovate to bring the latest technologies to projects in service of greater efficiency, deeper impact, and more effective communication. Over the last 15 years, application development has gained prominence with successful completion of ambitious and meaningful efforts. These tools display not only data hosted and collected by SFEI and its partners, but also facilitate new mode of community interaction to promote broad-based data stewardship.

As they collaborate with the science teams, the Application Development team creates a public face for our data and strives to provide accurate, understandable tools that are useful and informative for scientists, policymakers, and public stakeholders alike.

The Institute's Design and Communications team exercises tasks vital to effective public information distribution. 

Our designers work closely with project stakeholders and collaborate with internal scientists and technologists to maximize impact for new tools, solve communications problems in project outputs, and lend a distinctive style to reports.

Over the years, this talented team has come to define the look and feel of SFEI's most notable output. EcoAtlas, a tool for visualizing aquatic resources, has benefited from the work of the Design and Communications team. Furthermore, the Pulse, RMP's flagship publication, offers a visually compelling view on the Bay's status as the state's most critical estuary. 

SFEI's Information Technology Systems team forms the backbone of the technology productivity at the Institute. Through careful planning and coordination, they keep a complex network operating smoothly and facilitate continuous innovation through adaptation and renewal.

Website Hosting and Management

SFEI continues to expand website hosting and management services, both for SFEI projects and for external partners. Notable sites include:



  • 16 physical servers; Over 10 terabytes of raided storage

Database technologies used at SFEI

  • Microsoft SQL Server; PostgreSQL/PostGIS; mySQL

Web servers, application frameworks and libraries used at SFEI

  • Apache; Tomcat; Grails; jQuery

GIS Software

  • ArcGIS; ArcSDE

Web GIS technologies

  • ArcGIS Server; GeoServer; Mapserver; Openlayers Google Maps API

Offsite backup

  • LTO-3 tape autoloader; LTO-4 tape autoloader; Self-starting diesel backup generator for all servers and desktops


  • 6 networked printers and printer-copiers; 42" large format poster & map printer


  • 50Mbps fiberoptic


  • Cloud-based companion features on Amazon Web Services for web hosting, disaster resilience, and recovery

Software Development SOP

Since 2008 a standard operating procedure for the development of software has been in effect. The SOP emphasizes fully planning software features and interactions in mockups and software specifications prior to initiating programming. This way, the programming task is well defined, costs and schedule can be better estimated, and all members of the project can align on needs and expectations.

Projects Related to the Environment Informatics Program

Advancing Performance Measures

This project consists of an effort to enhance EcoAtlas to serve as the shared and primary point of collection for project data, then actively transfer the data to Delta View.

Developing a Sustainable Business Model for the EcoAtlas Toolset

This project is funded by a USEPA wetland development grant (2015-2017) to develop a recommended funding and business model for the EcoAtlas toolset.   EcoAtlas is a framework and toolset recommended in the State's Wetland and Riparian Area Monitoring Plan (WRAMP) of the California Wetland Monitoring Workgroup (CWMW). The tools enable users to visualize and assess the distribution, abundance, diversity, and condition of surface waters in a landscape or watershed context.  The Business Plan project is developing several overview and planning memos and a final, compiled recommendation for an EcoAtlas business plan. Those documents are made available here as they are completed.

Visualizing and Sharing Intensive Data Assessments

With California's drought rapidly changing the outlook for natural resources, decision-makers must be equipped with information and tools that facilitate clear and rapid decisions. The proposed grant would fund the standardization, visualization, and sharing of Level 3 data. 

Satellite Imaging to Detect Cyanobacterial Blooms

Satellite remote sensing will aid the State of California in assessing cyanobacterial bloom threats to animal and human health across the state’s numerous large lakes. 

Habitat Restoration Project Tracking

This project expands the current capabilities of the wetland project tracking system for the monitoring and assessment of California’s aquatic resources to meet the project tracking, assessment, and reporting needs for current and planned habitat restoration in the San Francisco Bay-Delta and Central Valley.

U.S. Coast Survey Maps of California (South Coast)

Until the advent of this new map viewer, a valuable resource was largely unavailable to coastal planners. Now, US Coastal Survey maps are free for broad use.

Healthy Streams Portal

Healthy streams, rivers, and lakes provide safe drinking water, recreational opportunities, and important habitat for species ranging from the red-shouldered hawk to steelhead to crayfish and dragonflies. Maintaining healthy streams, rivers, and lakes can reduce the need for water treatment and water supply costs and make landscapes more resilient to climate change.

Archive Sample Tool

The Archive Sample Tool provides a web interface that SFEI researchers can use to browse the RMP archives when considering using archive material for a study. The RMP has been collecting archive samples during each sampling event for sediment, bivalve, fish and birds since the early 1990's. These samples are available to SFEI researchers with RMP Program Manager approval, and can be requested directly from the tool. 

RMP Update

The Regional Monitoring Program for Water Quality in San Francisco Bay is an innovative collaboration of the San Francisco Bay Regional Water Quality Control Board, the regulated discharger community, and the San Francisco Estuary Institute. It provides water quality regulators with information they need to manage the Bay effectively. The Program issues a report each year, the Pulse of the Bay in odd years and the RMP Update in even years.

Evaluation of CRAM performance for assessing wetland stress, small wetlands, and wetland habitat development

Caltrans funded this wetlands research to fill important gaps in knowledge about the ability of the California Rapid Assessment Method (CRAM) to assess small wetlands, wetlands stress, and the rate at which wetland restoration projects develop into mature habitats. Caltrans proposed specific tasks based on the research priorities provided by the CRAM Commitee of the statewide California Wetlands Monitoring Workgroup.

Publications Issued by the Environment Informatics Program

The Institute has collectively produced more than 1300 reports, articles, and other publications over the course of its 24-year existence. The following list represents those publications associated with this individual program and its focus areas.

Year of Publication: 2017

Year of Publication: 2016

Hale T, Grosso C. An Introduction to EcoAtlas: Applied Aquatic Science. Richmond, CA: San Francisco Estuary Institute; 2016 p. 16 pages.  (5.84 MB)
Doehring C, Beagle J, Lowe J, Grossinger RM, Salomon M, Kauhanen P, et al.. San Francisco Bay Shore Inventory: Mapping for Sea Level Rise Planning. Richmond, CA: San Francisco Estuary Institute; 2016 . Report No.: 779.  (20.33 MB)

Year of Publication: 2015

Hale T, Azimi-Gaylon S, Fong S, Goodwin P, Isaac G, Osti A, et al.. Enhancing the Vision for Managing California's Environmental Information. Sacramento, CA: Delta Stewardship Council; 2015 . Report No.: 792.  (1.16 MB)

Where Our Environment Informatics Program Works