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 Services, 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.

Data Collection and Enhanced Analysis via Unoccupied Aerial Vehicles


SFEI has invested in novel, cost-effective solutions to costly problems. Most recently, our work with Unoccupied 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 Unoccupied 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

Healthy Watersheds Resilient Baylands

Through the EPA-funded Healthy Watersheds Resilient Baylands project, SFEI and sixteen partner organizations are developing multi-benefit tools to enhance climate change resilience in San Francisco Bay. Healthy Watersheds Resilient Baylands has two major components: Multi-benefit Urban Greening and Tidal Wetlands Restoration. Through both components, we have developed strategies that inform  policy, planning, and design of innovative implementation projects.

SediMatch Web Tool

SediMatch is a web tool for matching restoration projects that need sediment with navigational and flood protection dredging projects and other "sediment suppliers" throughout the region to meet current and future sediment supply needs.

Contaminant Data Download and Display (CD3)

Contaminant Data Display and Download Tool or CD3  is an innovative visualization tool for accessing water quality data for the San Francisco Bay-Delta and northern montane regions. It is the primary tool for accessing and downloading the San Francisco Bay Regional Monitoring Program’s (RMP) long-term dataset and other project data stored in SFEI's Regional Data Center (RDC).

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. 

Regional Data Center

SFEI is one of the state's Regional Data Centers that exchanges water quality data to the California Environmental Data Exchange Network (CEDEN). SFEI provides data management and visualization services to the San Francisco Bay-Delta and northern montane regions.

Wetlands Regional Monitoring Project

This Prop 50 - funded project was a three-year effort to monitor and track changes in Bay Area wetland condition. This wetland monitoring toolkit meets basic information needs for managing wetlands: to develop a scientific framework with standard methods for monitoring wetlands and for interpreting the results, and to regularly report the findings to the public. These monitoring tools are intended to help provide a public measure of the environmental costs or benefits of most wetland management actions.

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 the 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.

Shallow Groundwater Response to Sea Level Rise

As sea levels rise and extreme storms become more frequent, communities are developing climate adaptation plans to protect housing, jobs, ecosystems, and infrastructure from flooding. However, these plans often neglect an important potential flood hazard – emergent groundwater. Shallow groundwater in coastal communities will rise as sea levels rise, increasing the risk of flooding communities from below. The threat of rising groundwater levels was identified by the Coastal Hazards Adaptation and Resiliency Group as a critical data gap in regional climate resilience planning.

Resilient Silicon Valley

Tools for the creation of a resilient Silicon Valley ecosystem.

Historical Wetlands of the Southern California Coast: An Atlas of US Coast Survey T-Sheets 1851-1889

This project is the first regional assessment of the relative distribution and abundance of different wetland habitat types along the historical Southern California coastline ("South Coast"). The extent of South Coast wetlands has been dramatically reduced over the past 150 years, and there are now many large-scale efforts to recover some of these environments.

Publications related to 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: 2021

Moore S, Hale T, Weisberg SB, Flores L, Kauhanen P. California Trash Monitoring Methods and Assessments Playbook. Richmond, Calif.: San Francisco Estuary Institute; 2021 . Report No.: 1025.  (299.71 MB)
Moore S, Hale T, Weisberg SB, Flores L, Kauhanen P. Field Testing Report: California Trash Monitoring Methods. Richmond, Calif.: San Francisco Estuary Institute; 2021 . Report No.: 1026.  (14.2 MB)

Year of Publication: 2020

Year of Publication: 2019

Year of Publication: 2018

Hale T, Sim L, McKee LJ. GreenPlan-IT Tracker. Bradt J. Richmond, CA: San Francisco Estuary Institute; 2018.  (1.43 MB)

Year of Publication: 2017

Hale T, Grosso C. Applied Aquatic Science: A Business Plan for EcoAtlas. Richmond, CA: San Francisco Estuary Institue; 2017 .  (1.69 MB) (323.4 KB) (214.45 KB)

Where Our Environment Informatics Program Works