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.

Goals

  • 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. SFEI uses this technology to create practical tools that support better decision-making and promote smart solutions for environmental problems.

SFEI’s GIS focus area supports the Institute’s mission through data production, mapping expertise, spatial analysis, and application development. The department serves three major functions:

  • Improve, maintain, and act as a repository for local environmental data sets
  • Provide cartographic services to convey complex conditions and present science based solutions to diverse stakeholders
  • Leverage the latest technology to develop custom GIS tools and applications to address and analyze environmental problems

Overview of Wetland Remote Sensing Technologies

SFEI has invested in novel, cost-effective solutions to costly problems by capitalizing on recent advances in remote sensing and GIS technology, such as the use of drones (Unoccupied Aerial Systems), machine learning, and other automated mapping methodologies to address environmental challenges.

We encourage you to review the above presentation, showing some of the work that our GIS team performs in the service of wetland resource management.

The Data Services (DS) team 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.

SFEI is the Regional Data Center (RDC) for the San Francisco Bay-Delta and northern montane regions. The Institute manages water quality, tissue, wetlands, historical, and spatial data, and develops tools for uploading, accessing, and visualizing data.

The DS team specializes in managing data associated with a variety of environmental sample types and standardizing results using consistent data vocabulary and business rules. SFEI’s Quality Assurance Officer and associated DS staff thoroughly review environmental results for accuracy, precision, sensitivity, contamination, and completeness.

Over 4 million environmental data records are maintained by the DS team in SFEI’s RDC database. Data approved for public release are disseminated through SFEI’s Contaminant Data Display and Download tool (CD3).

Learn more about our services, and please contact us if you would like help making your data publicly available.

The Software Engineering focus area provides broad support wherever code-based solutions are needed for SFEI’s projects. In addition to supporting other SFEI Programs’ efforts, we build unique tools in service of other organizations. These tools synthesise, analyze, and visualize data created by SFEI and other scientific organizations. The resulting information products inform decision-making regarding our natural resources found across the State of California.

The Software Engineering team accordingly develops tools that are instrumental to operationalizing the science that SFEI and partners cultivate. The tools form a cornerstone to the success of many projects at SFEI, and the expertise of our software engineers encompasses a range of technical disciplines. Tasks may span from low-level security and efficiency issues, to data modeling and analysis scripts, to the creation of engaging visualizations, maps, and websites. The focus area also provides maintenance for version control tools and consultation for projects that require coding finesse.

Over the years, the Software Engineering team has developed enduring products, ranging from EcoAtlas, an innovative geospatial tool, with a 20-year history, to GreenPlan-IT, a toolset designed to address new and emerging concerns related to urban greening. Whatever the specific project, product, and goals, the Software Engineering focus area values efficiency, modularity, reusability, and legibility and are always excited to engage with new technologies, solutions, and collaborations.

The Institute's Design and Communications team exercises tasks vital to effective public information distribution. The team ensures that the key messages developed through the course of the Institute's scientific reports and technological innovations reach the target audience in the most credible and effective way.

To achieve this primary goal, our designers work closely with both external stakeholders and 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. The team enjoys a reputation for excellence among science communicators and looks forward to working with you on your next project. 

SFEI's Information Technology Systems team forms the backbone of the technology productivity at the Institute. We support and maintain a wide breadth of hardware and software platforms to ensure staff have the tools they need to perform their work efficiently. Across both local and cloud-hosted servers, we host websites, tools and high performance computing systems to drive a multitude of scientific research objectives and products. The IT Systems team delivers regular training and communications to keep staff apprised about important changes to the technology on which they rely. We conduct full cycle change management processes from needs assessment to go-live implementation to ensure successful adoption of new systems. Through careful planning and coordination and, when necessary, deft troubleshooting, we 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:

  • sfei.org — Main SFEI site
  • ecoatlas.org — EcoAtlas, a tool for visualizing the condition and extent of California's aquatic resources
  • cd3.sfei.org — CD3, a tool for visualizing and downloading water quality data in the SFEI data center
  • enviz.org — Environmental Visualization, a dynamic time-series visualization tool
  • cramwetlands.org — CRAM wetland assessments
  • sfestuary.org — San Francisco Estuary Project site (partner site)
  • wrmp.org — Wetlands Regional Monitoring Program
  • southbayrestoration.org — South Bay Salt Ponds restoration (partner site)

Infrastructure

SFEI has assembled an array of hardware and software infrastructure to serve multiple needs. The resources include 16 physical servers; various database technologies; numerous web servers, application frameworks and libraries; GIS software including ArcGIS and ArcSDE; Web GIS technologies, including ArcGIS Server, GeoServer, Mapserver, Openlayers, Google Maps API; Offsite backup; Self-starting diesel backup generator to protect all servers and desktops; server colocation and cloud-based hosting options.

Projects Related to the Environment Informatics Program

The Pulse of the Bay

https://www.sfei.org/documents/2019-pulse-bay-pollutant-pathwaysDownload the Pulse of the Bay! This report from the Regional Monitoring Program for Water Quality in San Francisco Bay features articles on the four major pathways by which pollutants enter the Bay: municipal wastewater, industrial wastewater, stormwater, and dredging and dredged sediment disposal.  Each article provides a basic introduction to the pathway and discusses the regulatory framework, recent findings, and future challenges.  The report also includes some of the latest highlights from monitoring of important parameters such as nutrients, emerging contaminants, mercury, PCBs, and selenium.    
Shallow Groundwater Response to Sea Level Rise

The response of shallow groundwater to sea-level rise is a relatively new field of study. For low-lying coastal communities, sea-level rise adaptation efforts must consider the potential for groundwater rise to avoid maladaptation. The need to better understand this slow and chronic threat was identified as a critical data gap in the San Francisco Bay Area’s adaptation efforts during the Bay Area Groundwater and Sea-Level Rise Workshop in 2019.
RipZET: A GIS-based Tool for Estimating Riparian Zones

The Riparian Zone Estimator Tool (RipZET) is a decision support tool developed by the San Francisco Estuary Institute and Aquatic Science Center for the California Riparian Habitat Joint Venture and the California Water Resources Control Board to assist in the visualization and characterization of riparian areas in the watershed context.
California Aquatic Resource Inventory (CARI)

The California Aquatic Resources Inventory (CARI) is a Geographic Information System (GIS) based map of wetlands, streams, and riparian areas within California that is hosted online through EcoAtlas.
Statewide Plastics Monitoring Plan & Strategy

Plastics, in their various chemical composition and sizes, pose serious challenges to the vitality of California's ecosystems. Once escaped into the environment, plastic contamination persists for very long periods and breaks down into ever smaller pieces, becoming more readily available to wildlife and populations who live, work, and play in those same habitats.
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 RMP produces two types of summary reports: The Pulse of the Bay and the RMP Update. The Pulse focuses on Bay water quality and summarizes information from all sources.
Next Generation Urban Greening

SFEI is working with partners across the Bay Area to design tools to help cities achieve biodiversity, stormwater, and climate benefits through multifunctional green infrastructure.
Re-Oaking

“Re-Oaking” is an approach to reintegrating oaks and other native trees within the developed California landscape to provide a range of ecosystem services. The concept has emerged from SFEI's research into the distribution and characteristics of California's former valley oak savannas -- a distinctive, widespread habitat that was mostly lost a century ago. Now valley oaks and other native trees are being recognized for the benefits they did -- and could again – provide, as communities design the ecologically healthy and resilient landscapes of the future.
California Pesticides: A Data Visualization Tool to Link Pesticide Use and Management to Water Quality

Despite California's data-rich environment, there are still many obstacles when trying to access and understand pesticide data at the nexus of water quality, ecological effects, and human health. We recognize a need to fill data gaps, not necessarily by collecting new data, but by better leveraging information already technically in the public domain. The goal of this project is to bring pesticide reporting, occurrence, and toxicity data together in ways that yield insights and meet the expressed needs of stakeholders in clear, efficient, credible, and repeatable ways.
Perfluoroalkyl and Polyfluoroalkyl Substances (PFAS)

A recent analysis of PFAS in the surface waters of SF Bay was conducted to understand the occurrence, fate, and potential risks to ecological and human health. Eleven of 40 PFAS were detected at part per trillions (ppt) concentrations in ambient water collected in 2021 from 22 sites in the Bay. Seven PFAS (PFPeA, PFHxA, PFHpA, PFOA, PFBS, PFHxS, and PFOS), were found in at least 50% of samples. Concentrations of PFAS in the Bay were generally consistent with similar studies globally for surface water. Sustained, multi-matrix monitoring of this important class of contaminants of emerging concern is a high priority for the RMP.
More Projects

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.
All Publications

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Year of Publication: 2024

Grosso C, Lowe S, Pearce S. Factsheet: How to Generate a Watershed Profile in EcoAtlas. 2024.  (1.87 MB)
Factsheet: The Baylands Habitat Map 2020: Mapping progress towards habitat restoration goals. 2024.  (4.76 MB)
Braud A, Kauhanen P, Murray R, Palermo K. Mapping Methods And Standards For Bayland Habitats In The San Francisco Bay v1.0. 2024.  (8.95 MB)
Poster: Baylands Change Basemap: Mapping Progress Toward Habitat Restoration Goals. 2024.  (15.8 MB)
Palermo K, Kauhanen P. Robertson Park and Medeiros Parkway sUAS Surveys for the Sycamore Pilot Implementation Project. Prepared for Zone 7 Water Agency and US Environmental Protection Agency’s Water Quality Improvement Fund. In collaboration with San Francisco Estuary Institute. 2024 .  (27.86 MB)
Murray R, Kauhanen P, Pearce S. San Diego Aquatic Resource Inventory (SDARI) Mapping Methods and Standards for Channels, Wetlands and Riparian Areas in San Diego v1.0. 2024.  (14.1 MB)
Murray R, Kauhanen P, Pearce S. San Diego Aquatic Resource Inventory (SDARI) Mapping Methods and Standards for Channels, Wetlands and Riparian Areas in San Diego v1.1. 2024.  (14.1 MB)
Kauhanen P, Braud A. WRMP Baylands Habitat Map 2020 Classification Key. Toms C, Pearce S. 2024 .  (35.94 MB)

Year of Publication: 2023

Vaughn LSmith, Braud A. Adding Salinity Modifiers to CARI - Methods Brief. San Francisco Estuary Institute; 2023 .  (1.13 MB)
Weaver M, Wong A, Grosso C. Data Management Procedures: For Lake County Water Resources Department (LCWRD) and Habematolel Pomo Of Upper Lake (HPUL) Tribe Water Quality Monitoring Data. 2023 p. 18. Report No.: 1140.  (4.22 MB)
Kauhanen P, Grosso C, Salomon M, Braud A. Delta Aquatic Resources Inventory (DARI): Mapping Methods and Standards for Channels, Wetlands, and Riparian Areas in the Sacramento-San Joaquin River Delta v1.0. 2023.  (25.36 MB)
SFEI. Landscape Scenario Planning Tool User Guide v2.2.0. Richmond, Calif: San Francisco Estuary Institute; 2023 .  (5.27 MB)
Pearce S, Lowe S, Gilbreath A, Kauhanen P, Vaughn L, Symonds J, et al.. McCosker Creek Restoration and Public Access Project: Alder Creek Daylighting Additional Monitoring Elements - Final Report. Richmond, CA: San Francisco Estuary Institute; 2023 . Report No.: 1157.  (8.07 MB)
Grosso C, Lowe S, Pearce S, O'Connor K, Teunis L, Stein ED, et al.. WRAMP Training and Outreach Plan. 2023 p. 39. Report No.: 1136.  (5.8 MB)

Where Our Environment Informatics Program Works