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Here you can find links to all information and videos of the 2022 DSOS/AEMON-J Virtual Workshop and Summit. All recordings are available on our OSF archive The organisers of this event were:
| Day 1: Remote Sensing -- Monday 25 July 2021 15:00-19:00 UTC |
| A brief introduction to remote sensing and earth observation |
| Nuria Sanchez Lopez (@Sanchez_LopezN; University of Idaho) |
| The use of remote sensing for environmental applications and ecosystem monitoring has exponentially grown in the last decades as it is one of the most powerful tools to understand the Earth’s processes from local to global scales. This trend is expected to continue as new data products, models, and sensors are being prototyped. This talk is oriented to provide unfamiliarized and potential new users with a brief introduction to the fundamentals of remote sensing, and give an overview of the main products and resources available for water resources and land management. |
| Operationalizing Moderate Resolution Satellite Remote Sensing of Water Quality |
| Tyler King (@TylerKingofNone; U.S. Geological Survey) |
| The United States Geological Survey has undertaken the development of an operational system to deliver remotely sensed water quality at Continental United States scale from Landsat and Sentinel-2 imagery. This multi-year project is focused on evaluating published methods of estimating water clarity, chlorophyll-a, colored dissolved organic matter, and water surface temperature. The products of the project will include 1) in-situ water quality observations matched with remote sensing imagery, 2) re-processed historic satellite imagery as well as ongoing data product production as new imagery is acquired. The project is centered around an ensemble approach to remotely sensing water quality parameters, incorporating the best performing image processing techniques in a final estimate. This approach allows for ensemble member selection to vary based on water quality conditions, and to estimate uncertainty based on ensemble member divergence. This presentation will focus on the framework used in the development of these products and initial results from three test watersheds in the Delaware, Illinois, and Colorado river basins. |
| 15:00-15:45 UTC Keynote: It’s a matter of time: harnessing the power of spectral-temporal data for monitoring aquatic ecosystem dynamics |
| Kate Fickas (@katefickas; U.S. Geological Survey) |
| The use of remote sensing data has historically been constrained to spectral and spatial information derived from a carefully selected image or set of images. However, advances in data storage, computing, analysis ready data, and analysis ready science products are revolutionizing how the temporal domain is used to map and monitor land surface properties and land cover change. Aquatic ecosystems such as wetlands and lakes present a unique challenge for remotely sensed spectral data as their physical and biological dynamics can vary so widely over different temporal scales. This talk will cover the power of the remote sensing temporal domain and how to use it to our advantage to characterize, map, and monitor aquatic ecosystems and capture their hydrologic dynamics over time. |
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A live stream of the pre-recorded keynote will begin at 17:00 UTC, followed immediately by a live Question and Answer session with Kate, Nuria, and Tyler. |
| 15:45-16:00 UTC Break |
| 16:00-18:00 UTC Workshop: Using Google Earth Engine for Remote Sensing of Water Quality |
| Victoria Stengel (@VictoriaStengel; U.S. Geological Survey) |
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This workshop will focus on aquatic remote sensing in the cloud geocomputational environment. Our panel of experts
will facilitate a collaborative discussion about aquatic remote sensing theory as we step through the implementation of water
quality spectral algorithms, time series, and time lapse geovisualization, utilizing analysis ready imagery in Google Earth Engine. This workshop will use Google Earth Engine, and in order to follow along, you will need an account. These accounts are free for academic purposes. You can request an account here. Note that it can can take a few days to be approved. You can access the materials for the workshop by forking or locally cloning the workshop's repo. |
| This workshop will be live and led by Victoria. |
| 18:00-19:00 UTC Breakout/Working Groups Sessions |
| A traditional part of AEMON-J meetings in the past has been to openly discuss ideas for new, joint projects. This time in the schedule is to bring up such ideas, perhaps inspired by the workshops earlier that day, and discuss. If no such ideas are pitched, this time can also be used for small talk, networking, and other social activities. |
| Day 2: Data Science Tuesday 26 July 2022 15:00-19:00 UTC |
| An introduction to workflow management software in ecology |
| Matthew Brousil (@mrbrousil; Washington State University) and Kaelin Cawley |
| Ecological research increasingly uses large, complex datasets and research methods that are intended to make science more reproducible. Workflow management software is a tool that can greatly increase the reproducibility and efficiency of research analyses, in part by providing options to make complex analytical routines more intelligible. In this talk I will outline what workflow management software is, why it is useful in ecological research, and what tools are available to implement it for projects using the R programming language. |
| 15:00-15:45 UTC Keynote: Making data analysis easier with workflow management software |
|
Alessandro Filazzola (@EcoFilazzola; ApexRMS) |
| Limnology, like other scientific disciplines, is facing a computational crisis, where the management, analysis, and reproducibility are becoming increasingly challenging. We all strive for analyses that are fast, accurate, and easy to update, but our projects are inherently complex, often using multiple data types or sources. Harmonizing many large datasets for analysis thus requires substantial computational resources, such as high-performance computing or cloud computing infrastructure. Workflow management software is a helpful tool that can be used for creating tractable data pipelines that identifies dependencies and selectively updates new changes. We demonstrate the power of applying a popular workflow management software in R, targets, to a limnology project. We describe the benefits of including a workflow management software into any limnology project and the potential limitations or challenges. Lastly, we present the role of workflow management software in the larger movement in science to be more technology driven. As computation requirements in limnology becoming increasingly complex, workflow management software is one of many tools that can facilitate our work. |
| 15:45-16:00 UTC Break |
| 16:00-18:00 UTC Workshop: Build a pipeline to analyze an aquatic NEON dataset using the targets R package for workflow management |
| Matthew Brousil (@mrbrousil; Washington State University) |
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Datasets from the National Ecological Observatory Network (NEON) offer plentiful opportunities for ecological (and limnological) analysis and forecasting on a large scale.
Their public accessibility and wide ranging topic matter make them ideal candidates for reproducible research, especially when paired with workflow management software.
In this workshop we will build a simple, fully functional data analysis pipeline for a NEON dataset using the targets package in R.
We will discuss how to build a targets pipeline that performs and links tasks such as downloading, cleaning, analyzing, and reporting results of an analysis. This workshop will use the Targets package, which requires R. You can download R here and RStudio here. Details on R packages, script templates, and general workshop information can be accessed from the GitHub Repo here. |
| This workshop will be live. |
| 18:00-19:00 UTC Breakout/Working Groups Sessions |
| A traditional part of AEMON-J meetings in the past has been to openly discuss ideas for new, joint projects. This time in the schedule is to bring up such ideas, perhaps inspired by the workshops earlier that day, and discuss. If no such ideas are pitched, this time can also be used for small talk, networking, and other social activities. |
| Day 3: Aquatic Ecosystem Modelling -- Wednesday 27 July 2022 15:00-19:00 UTC | The development and application of numerical aquatic ecosystem models has been a rapidly growing field in aquatic sciences. In an effort to understand the functioning of aquatic ecosystems and to aid in restoring and preserving water bodies, for instance by scenario analysis or in a forecasting framework, aquatic ecosystem models has emerged as powerful tools for science and management. In this workshop, we will learn more about the possibilities of numerical aquatic ecosystem models and how to configure, execute and apply the Water Ecosystems Tool model. |
| A brief introduction to aquatic ecosystem modelling |
|
Nicolas Azaña Schnedler-Meyer (niaz@aqua.dtu.dk; Technical University of Denmark) Tobias Kuhlmann Andersen (@TobiasKAndersen; Aarhus University) |
| Aquatic ecosystem models have evolved from the classical pelagic nutrient-phytoplankton- zooplankton models to increase in complexity in, among others, biogeochemical processes, food web, functional groups and behavior of modelled organisms. Also, the coupling to hydrodynamic models in 1- to 3-dimensions have deepened our understanding of the spatial dynamics of aquatic ecosystems. In this talk, we will introduce the concepts of ecosystem modelling while providing an overview of the current state-of-the-art in simulating lake ecosystem dynamics ranging from temperature and nutrients to macrophytes and fish. |
| 15:00-15:45 UTC Keynote: Application of lake models to lake management and stewardship |
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Dennis Trolle (@DennisTrolle; Aarhus University) |
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Lake models can be considered a virtual representation of a real lake ecosystem. This can be very
useful, as this allow us to conduct virtual full-scale experiments, which would otherwise not be
possible due to the temporal or spatial scales involved. The Water Ecosystems Tool (WET) is one
such model, which has undergone intensive development for the past decade.
Exemplified by recent model applications, this presentation will demonstrate how the model can be used to simulate: 1) long-term changes to an ecosystem; 2) the response of a lake ecosystem to an internal manipulation (e.g. removal of fish); 3) operational short-term water quality forecasts. |
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A live stream of the pre-recorded keynote will begin at 15:00 UTC, followed immediately by a live Question and Answer session with Dennis. |
| 15:45-16:00 UTC Break |
| 16:00-18:00 UTC Workshop: Configure and use the lake ecosystem model WET |
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Tobias Kuhlmann Andersen (@TobiasKAndersen; Aarhus University) Nicolas Azaña Schnedler-Meyer (niaz@aqua.dtu.dk; Technical University of Denmark) |
| In this workshop, participants will learn how to apply the process-based lake ecosystem model, Water Ecosystems Tool (WET), for a given lake. We will take you through each step in setting up and configuring the model with the user interface QWET. We will also explore calibration and validation, and you will learn how to make experiments with the model. At the end of the workshop, we will open up for a discussion of the applicability of WET, future model developments and the use of auto-calibration and sensitivity analysis with WET. |
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Software and material
To participate in the hands-on part of the workshop, you will need to have a working version of QGIS and the graphical user interface QWET. If you are a Mac user, we highly recommend you to apply a windows-partition on your system, as the QWET installer is only available in windows format. QGIS To run QWET you need to install QGIS3 64 bit version 3.16 or newer (available here: www.qgis.org). We recommend you install QGIS3 64 bit version 3.22. QWET QWET is an open source QGIS plugin for application and user adaptation of the Water Ecosystems Tool (WET). The QWET installer and the QWET source code is available through Gitlab: https://gitlab.com/WET . To download the installer or the source code, you first need to set up a (free) GitLab account. We recommend you install QWET version 3.4.2. Please read the download/ instructions and watch the associated video tutorial on how to download the software. Case study data for Lake Ravn For our case study, we will work with the Danish Lake Ravn that is located in the central part of Jutland. The lake is approx. 32 meters deep with a surface area of 1.8 square kilometers. You can download the case study here/ .The case study folder includes files to configure a GOTM-WET model to Lake Ravn with QWET with lake specific hypsography and inflow and weather forcing as well as in-lake observations and files calibrated parameters. PyNCView To visualize model output with contour plots, we recommend using the software PyNCView. You can download an installer (for Windows) at the bottom of this page (pyncview-0.99.8.msi): https://github.com/BoldingBruggeman/pyncview/releases. If you have problems installing the required software or downloading the case study, you are welcome to contact us. Also, if you have any other questions related to the workshop. |
| This workshop will be live and led by Tobias and Nicolas. |
| 18:00-19:00 UTC Breakout/Working Groups Sessions |
| A traditional part of AEMON-J meetings in the past has been to openly discuss ideas for new, joint projects. This time in the schedule is to bring up such ideas, perhaps inspired by the workshops earlier that day, and discuss. If no such ideas are pitched, this time can also be used for small talk, networking, and other social activities. |
| 28 July 2022 | |||||||||||
| 13:00-13:15 EDT Introduction, Welcome, and Ground Rules | |||||||||||
| 13:15-14:25 EDT Big Data | |||||||||||
| 13:15-13:25 EDT |
Patricia Q. Tran @patriciatran_ Mégadonnées pour des petits microbes: Utiliser la génomique afin de mieux comprendre comment les microbes vivant dans les lacs contribuent aux cycles biogéochimiques Big data for tiny organisms: using genomic data to understand the roles of microbes in biogeochemical cycling in lakes |
| 13:25-13:35 EDT |
Heloisa E. Macedo @heloisaemacedo Building a global database of wastewater treatment plants: applications, challenges and uncertainties |
| 13:35-13:45 EDT |
Safat Sidker The global lake drainage topology and catchment dataset: Lake-TopoCat |
| 13:45-13:55 EDT |
Sam Newall @srsnewall A Complete Dataset of Radiocarbon Age Estimates from Lake Baikal Sediments: Refining and Critiquing Estimates of Radiocarbon Age Offsets |
| 13:55-14:05 EDT |
Shannon Speir @ecospeir and Andrew Robison @werdrobison Biogeochemical controls on bacterial communities and gene diversity across US streams |
| 14:05-14:25 EDT | Live Q&A with the speakers |
| 14:25-14:45 EDT Break | |||||||||||
| 14:45-15:55 EDT Data Intensive Models | |||||||||||
| 14:45-14:55 EDT |
Heili Lowman @heili_lowman Predicting river resilience to disturbance in streams and rivers across the U.S. |
| 14:55-15:05 EDT |
Jianning Ren @ren_will How does water yield respond to mountain pine beetle infestation in a semiarid forest? |
| 15:05-15:15 EDT |
Jorrit P. Mesman @JorritMesman Modeling climate, groundwater, physics, and phytoplankton in a Spanish coastal lagoon |
| 15:15-15:25 EDT |
Azadeh Yousefi @YousefiAzadeh تاثیر عمق آب و عوامل جبری در عملکرد مدل فراگیری ماشین در مدلسازی دمای آب سطحی دریاچه The influence of water depth and forcing factors on the performances of Machine Learning approaches for the simulation of lake surface water temperature |
| 15:25-15:35 EDT |
Wayana Dolan @wayana_dolan Functional lake-to-channel connectivity impacts lake ice in an Arctic delta |
| 15:35-15:55 EDT | Live Q&A with the speakers |
| 15:55-16:10 EDT Break |
| 16:10-16:55 EDT Panel: Operationalizing Interoperability |
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Margaret O’Brien @EDIgotdata - Environmental Data Initiative Mathis L. Messager @messamat - McGill University & INRAE Lyon-Grenoble Auvergne-Rhône-Alpes Sarah McCord @mccord_se - U.S. Department of Agriculture Mike Kolian - U.S. Environmental Protection Agency Paul Julian @SwampThingPaul - Sanibel-Captiva Conservation Foundation Kait Reinl @KaitReinl - Lake Superior National Estuarine Research Reserve Martin Seul - Consortium of Universities for the Advancement of Hydrologic Science, Inc. Amanda Whitmire @AWhitTwit - Harold A. Miller Library at Stanford University |
| 16:55-17:00 EDT Closing Remarks |
| 29 July 2022 | |||||||||||
| 13:00-13:15 EDT Introduction, Welcome, and Ground Rules | |||||||||||
| 13:15-14:25 EDT Tools and Software | |||||||||||
| 13:15-13:25 EDT |
Tyler V. King @TylerKingofNone Spectral Mixture Analysis for Surveillance of Harmful Algal Blooms (SMASH): A Hybrid Laboratory and Satellite based approach to identify algal taxa in inland waterbodies via remote sensing |
| 13:25-13:35 EDT |
Qiusheng Wu @giswqs Automated surface water mapping with cloud computing and open-source software |
| 13:35-13:45 EDT |
Orhun Aydin @orhun_sow Mining Spatio-Temporal Patterns of Transshipment Activity in an Interoperable GIS: The R-ArcGIS Bridge and ESRI - R Integration |
| 13:45-13:55 EDT |
Matthew Conlon Harnessing USGS data and open-source tools to create dynamic data visualizations |
| 13:55-14:05 EDT |
Carolina C. Barbosa @carollcbarbosa Abordagem de modelagem integrada para prever mudanças de estado trófico de um reservatório subtropical An integrated modeling approach to predict trophic state changes of a subtropical reservoir |
| 14:05-14:25 EDT | Live Q&A with the speakers |
| 14:25-14:45 EDT Break | |||||||||||
| 14:45-15:55 EDT Applications of Open Science | |||||||||||
| 14:45-14:55 EDT |
Laura Soares Drought impacts on the water quality and trophic state of a Brazilian reservoir: evidence from GLM-AED2 model |
| 14:55-15:05 EDT |
Amber Jones @AmberWaves_USU Water Data Science and Hydroinformatics Instruction: Community Perspectives and Online Learning Resources |
| 15:05-15:15 EDT |
Amanda T Stahl @AmandaTStahl Broadening and streamlining access to remote sensing data for natural scientists and natural resource professionals |
| 15:15-15:25 EDT |
Joshua Culpepper @JoshCulpepper4 Leveraging Red-Band Reflectance to Detect Mountain Lake Ice Phenology |
| 15:25-15:35 EDT |
Abdou R Bah @AbdouRachidBah1 Downscaling GOES-R Land Surface Temperature over Urban Regions |
| 15:35-15:55 EDT | Live Q&A with the speakers |
| 15:55-16:10 EDT Break |
| 16:10-16:55 EDT Panel: Careers in Data Science and Open Science |
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Julian J. Reyes @julianjon - U.S. Department of Agriculture Alden Keefe Sampson @aldenks - Upstream Tech Cee Nell @cee_phd - U.S. Geological Survey Sylvia Lee @DrDiatomLee - U.S. Environmental Protection Agency Stephanie E. Hampton @se_hampton - Washington State University |
| 16:55-17:00 EDT Closing Remarks |
| 17:00-18:00 EDT Virtual Social Hour |
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