Property:CSDMS meeting abstract presentation
From CSDMS
This is a property of type Text.
P
Are you confused about the best way to make your models and data accessible, reusable, and citable by others? In this clinic we will give you tools, information, and some dedicated time to help make your models and data FAIR - findable, accessible, interoperable and reusable. Models in the CSDMS ecosystem are already well on their way to being more FAIR than models that are not. But here, you will learn more about developments, guidelines, and tools from recent gatherings of publishers, repository leaders, and information technology practitioners at recent FAIR Data meetings, and translate this information into steps you can take to make your scientific models and data FAIR. +
Are you interested in expanding the reach of your scientific data or models? One way of increasing the FAIRness of your digital resources (i.e., making them more findable, accessible, interoperable, and reproducible) is by annotating them with metadata about the scientific variables they describe. In this talk, we provide a simple introduction to the Scientific Variables Ontology (SVO) and show how, with only a small number of design patterns, it can be used to neatly unpack the definitions of even quite complex scientific variables and translate them into machine-readable form. +
Are you tired of hearing about the FAIR Principles? This clinic is for you then, because after you participate you’ll never need to attend another one!*
Good science depends on the careful and meticulous management and documentation of our research process. This includes our computational models, the datasets we use, the data transformation, analysis, and visualization scripts and workflows we build to evaluate and assess our models, and the assumptions and design decisions we make while writing our software.
Join us for a Carpentries-style interactive clinic with hands-on exercises where we will provide concrete guidance and examples for how to approach, conceptualize, and transform your computational models of earth systems into FAIR contributions to the scientific record whether they are greenfield projects or legacy code with a focus on existing, open infrastructure (GitHub / GitLab / Zenodo). We’ll also cover containerization (Docker, Apptainer) as a way to transparently document system and software dependencies for your models, and how it can be used to support execution on the Open Science Grid Consortium’s Open Science Pool fair-share access compute resources. Big parallel fun! https://osg-htc.org
∗ individual results may vary, this statement is provably false +
As agreed at earlier CSDMS forums, the major
impediment in using AI for modeling the deep-ocean
seafloor is a lack of training data, the data which guides the AI -
whichever set of algorithms is chosen. This clinic will expose participants to
globally-extensive datasets which are available through CSDMS.
It will debate the scientific questions of why certain data work well,
are appropriate to the processes, and are properly scaled.
Participants are encouraged to bring their own AI challenges to the clinic. +
As global population grows and infrastructure expands, the need to understand and predict processes
at and near the Earth’s surface—including water cycling, soil erosion, landsliding, flood
hazards, permafrost thaw, and coastal change—becomes increasingly acute. Progress in understanding
and predicting these systems requires an ongoing integration of data and numerical
models. Advances are currently hampered by technical barriers that inhibit finding, accessing,
and operating modeling software and related tools and data sets. To address these challenges, we present the CSDMS@HydroShare, a cloud-based platform for accessing and running models, developing model-data workflows, and sharing reproducible results.
CSDMS@HydroShare brings together cyberinfrastructure developed by two important community facilities: HydroShare (https://www.hydroshare.org/), which is an online collaboration environment for sharing data, models, and tools, and CSDMS Workbench (https://csdms.colorado.edu/wiki/Workbench), which is the integrated system of software tools, technologies, and standards for building, interfacing, and coupling models.
This workshop presents how to use CSDMS@HydroShare to discover, access, and operate the Python Modeling Tool (PyMT). PyMT is one of the tools from the CSDMS Workbench, which allows users to interactively run and couple numerical models contributed by the community. In PyMT, there are already model components for coastal & permafrost modeling, stratigraphic and subsidence modeling, and terrestrial landscape evolution modeling. It also includes data components to access and download hydrologic and soil datasets from remote servers to feed the model components as inputs.
This workshop aims to encourage the community to use existing or develop new model or data components under the PyMT modeling framework and share them through CSDMS@HydroShare to support reproducible research. This workshop includes hands-on exercises using tutorial Jupyter Notebooks and provides general steps for how to develop new components.
At a global scale, deltas significantly concentrate people by providing diverse ecosystem services and benefits for their populations. At the same time, deltas are also recognized as one of the most vulnerable coastal environments, due to a range of adverse drivers operating at multiple scales. These include global climate change and sea-level rise, catchment changes, deltaic-scale subsidence and land cover changes, such as rice to aquaculture. These drivers threaten deltas and their ecosystem services, which often provide livelihoods for the poorest communities in these regions. Responding to these issues presents a development challenge: how to develop deltaic areas in ways that are sustainable, and benefit all residents? In response to this broad question we have developed an integrated framework to analyze ecosystem services in deltas and their linkages to human well-being. The main study area is part of the world’s most populated delta, the Ganges-Brahmaputra-Meghna Delta within Bangladesh. The framework adopts a systemic perspective to represent the principal biophysical and socio-ecological components and their interaction. A range of methods are integrated within a quantitative framework, including biophysical and socio-economic modelling, as well as analysis of governance through scenario development. The approach is iterative, with learning both within the project team and with national policy-making stakeholders. The analysis allows the exploration of biophysical and social outcomes for the delta under different scenarios and policy choices. Some example results will be presented as well as some thoughts on the next steps. +
Bed material abrasion is a key control on the partitioning of basin scale sediment fluxes between coarse and fine material. While abrasion is traditionally treated as a simple exponential function of transport distance and a rock-specific abrasion coefficient, experimental studies have demonstrated greater complexity in the abrasion process: the rate of abrasion varies with clast angularity, transport rate, and grain size. Yet, few studies have attempted to assess the importance of these complexities in the field setting. Furthermore, existing approaches generally neglect the heterogeneity in size, abrasion potential, and clast density of the source sediment.
Combining detailed field measurements and new modeling approaches, we quantify abrasion in the Suiattle River, a basin in the North Cascades of Washington State dominated by a single coarse sediment source: large, recurrent debris flows from a tributary draining Glacier Peak stratovolcano. Rapid downstream strengthening of river bar sediment and a preferential loss of weak, low-density vesicular volcanic clasts relative to non-vesicular ones suggest that abrasion is extremely effective in this system. The standard exponential model for downstream abrasion fails to reproduce observed downstream patterns in lithology and clast strength in the Suiattle, even when accounting for the heterogeneity of source material strength and the underestimate of abrasion rates by tumbler experiments. Incorporating transport-dependent abrasion into our model largely resolves this failure. These findings hint at the importance of abrasion and sediment heterogeneity in the morphodynamics of sediment pulse transport in river networks. A new modeling tool will allow us to tackle these questions: the NetworkSedimentTransporter, a Landlab component to model Lagrangian bed material transport and channel bed evolution. This tool will allow for future work on the interplay of bed material abrasion and size selective transport at the basin scale.
While a simplified approach to characterizing abrasion is tempting, our work demonstrates that sediment heterogeneity and transport-dependent abrasion are important controls on the downstream fate of coarse sediment in fluvial systems.
Biostabilizing organisms, such as saltmarsh and microphytobenthos, can play a crucial role in shaping the morphology of estuaries and coasts by locally stabilizing the sediment. However, their impact on large-scale morphology, which highly depends on the feedback between spatio-temporal changes in their abundance and physical forcing, remains highly uncertain.
We studied the effect of seasonal growth and decay of biostabilizing organisms, in response to field calibrated physical forcings, on estuarine morphology over decadal timescales using a novel eco-morphodynamic model. The code includes temporal saltmarsh an microphytobenthos growth and aging as well as spatially varying vegetation fractions determined by mortality pressures. Growth representations are empirical and literature-based to avoid prior calibration.
Novel natural patterns emerged in this model revealing that observed density gradients in vegetation are defined by the life-stages that increase vegetation resilience with age. The model revealed that the formation of seasonal and long term mud layering is governed by a ratio of flow velocity and hydroperiod altered by saltmarsh and microphytobenthos differently, showing that the type of biostabilizer determines the conditions under which mud can settle and be preserved. The results show that eco-engineering effects define emerging saltmarsh patterns from a combination of a positive effect reducing flow velocities and a negative effect enhancing hydroperiod. Consequently, saltmarsh and mud patterns emerge from their bilateral interactions that hence strongly define morphological development. +
CSDMS 3.0 updates +
CSDMS Basic Model Interface (BMI) - When equipped with a Basic Model Interface, a model is given a common set of functions for configuring and running the model (as well as getting and setting its state). Models with BMIs can communicate with each other and be coupled in a modeling framework. The coupling of models from different authors in different disciplines may open new paths to scientific discovery. In this first of a set of webinars on the CSDMS BMI, we'll provide an overview of BMI and the functions that define it. This webinar is appropriate for new users of BMI, although experienced users may also find it useful.
'''Instructor:''' Mark Piper, Research Software Engineer, University of Colorado, Boulder
'''When:''' November 13th, 12PM Eastern Time +
CSDMS develops and maintains a suite of products and services with the goal of supporting research in the Earth and planetary surface processes community. This includes products such as Landlab, the Basic Model Interface, Data Components, the Model Repository, EKT Labs, and ESPIn. Examples of services include the Help Desk, Office Hours, Roadshows, RSEaaS, and EarthscapeHub. One problem, though, is that if the community doesn't know about these products and services, then they don't get used—and, like the Old Gods in Neil Gaiman's American Gods, they fade into obscurity. Let's break the cycle! Please join us for this webinar where we will present information about all of the products and services offered by CSDMS, and explain how they can help you accelerate your research. Attendees will leave with knowledge of what CSDMS can do for them, which they can bring back to their home institutions and apply to their research and share with their colleagues.
<br> +
CSDMS has developed a Web-based Modeling Tool – the WMT. WMT allows users to select models, to edit model parameters, and run the model on the CSDMS High-Performance Computing System. The web interface makes it straightforward to configure different model components and run a coupled model simulation. Users can monitor progress of simulations and download model output.<br><br> CSDMS has developed educational labs that use the WMT to teach quantitative concepts in geomorphology, hydrology, coastal evolution. These labs are intended to be used by Teaching assistants and Faculty alike. Descriptions of 4-hr hands-on labs have been developed for HydroTrend, Plume, Sedflux, CHILD, ERODE and ROMS-Lite. These labs include instructions for students to run the models and explore dominant parameters in sets of simulations. Learning objectives are split between topical concepts, on climate change and sediment transport amongst many others, and modeling strategies, modeling philosophy and critical assessment of model results.<br><br>In this clinic, we will provide an overview of the available models and labs, and their themes and active learning objectives. We will discuss the requirements and logistics of using the WMT in your classroom. We will run some simulations hands-on, and walk through one lab in more detail as a demonstration. Finally, the workshop intends to discuss future developments for undergraduate course use with the participants. +
CSDMS has developed a Web-based Modeling Tool – the WMT. WMT allows users to select models, to edit model parameters, and run the model on the CSDMS High-Performance Computing System. The web tool makes it straightforward to configure different model components and run a coupled model simulation. Users can monitor progress of simulations and download model output.<br><br>CSDMS has designed educational labs that use the WMT to teach quantitative concepts in geomorphology, hydrology, coastal evolution and coastal sediment transport. These labs are intended for use by Teaching assistants and Faculty alike. Descriptions of 2 to 4-hr hands-on labs have been developed for HydroTrend, Plume, Sedflux, CHILD, TOPOFLOW and ROMS-Lite. These labs include instructions for students to run the models and explore dominant parameters in sets of simulations. Learning objectives are split between topical concepts, on climate change and sediment transport amongst many others, and modeling strategies, modeling philosophy and critical assessment of model results.<br><br>In this clinic, we will provide an overview of the available models and labs, and their themes and active learning objectives. We will discuss the requirements and logistics of using the WMT in your classroom. We will run some simulations hands-on, and walk through one lab in more detail as a demonstration. Finally, the workshop intends to discuss future developments for earning assessment tools with the participants. +
CSDMS has developed the Basic Model Interface (BMI) to simplify the conversion of an existing model in C, C++, Fortran, Java, or Python into a reusable, plug-and-play component. By design, the BMI functions are straightforward to implement. However, in practice, the devil is in the details.<br><br>In this hands-on clinic, we will take a model -- in this case, an implementation of the two-dimensional heat equation in Python -- and together, we will write the BMI functions to transform it into a component. As we develop, we’ll unit test our component with nose, and we’ll explore how to use the component with a Jupyter Notebook. Optionally, we can set up a GitHub repository to store and to track changes to the code we write.<br><br>To get the most out of this clinic, come prepared to code! We have a lot to write in the time allotted. We recommend that clinic attendees have a laptop with the Anaconda Python distribution installed. We also request that you skim:<br><br>⤅ BMI description (https://csdms.colorado.edu/wiki/BMI_Description)<br>⤅ BMI documentation (http://bmi-forum.readthedocs.io/en/latest)<br>⤅ BMI GitHub repo(https://github.com/csdms/bmi-live)<br><br>before participating in the clinic. +
CSDMS’s newly released Python Modeling Tool (PyMT) is an open source python package that provides convenient tools for coupling of models that use the Basic Model Interface. Historically, earth-surface process models have often been complex and difficult to work with. To help improve this situation and make the discovery process more efficient, the CSDMS Python Modeling Tool (PyMT) provides an environment in which community-built numerical models and tools can be initialized and run directly from a Python command line or Jupyter notebook. To illustrate how PyMT works and the advantages it provides, we will present a demonstration of two coupled models. By simplifying the process of learning, operating, and coupling models, PyMT frees researchers to focus on exploring ideas, testing hypotheses, and comparing models with data. +
CSDMS’s newly released Python Modeling Tool (PyMT) is an open source Python package that provides convenient tools for coupling models that use the Basic Model Interface. Historically, earth-surface process models have often been complex and difficult to work with. To help improve this situation and make the discovery process more efficient, PyMT provides an environment in which community-built numerical models and tools can be initialized and run directly from a Python command line or a Jupyter Notebook. To illustrate how PyMT works and the advantages it provides, we will present a demonstration of two coupled models. By simplifying the process of learning, operating, and coupling models, PyMT frees researchers to focus on exploring ideas, testing hypotheses, and comparing models with data. Pre-registration required.<br><br>''See also: https://pymt.readthedocs.io/en/latest/'' +
Changing depth to water table and the associated stored water volume is a crucial component of the global hydrological cycle, with impacts on climate and sea level. However, long-term changes in global water-table distribution are not well understood. Coupled ground- and surface-water models are key to understanding the hydrologic evolution of post-glacial landscapes, the significance of terrestrial water storage, and the interrelationships between freshwater and climate. Here, I present the Water Table Model (WTM), which is capable of computing changes in water table elevation at large spatial scales and over long temporal scales. The WTM comprises groundwater and dynamic lake components to incorporate lakes into water-table elevation estimates. Sample results on both artificial and real-world topographies demonstrate the two-way coupling between dynamic surface-water and groundwater levels and flow. +
Cheniers are ridges consisting of coarse-grained sediments, resting on top of muddy sediment. Along these muddy coastlines, cheniers provide shelter against wave attack, mitigating erosion or even enhancing accretion. As such, cheniers play an important role in the dynamics of the entire coastal landscape. This research focused on cheniers along mangrove-mud coasts. Therefore, chenier dynamics needed to be understood at the temporal and spatial scales of the mangrove vegetation as well. We developed a hybrid modelling approach, combining the strengths of complex process-based modelling (Delft3D), which allowed us to model the mixed-sediment dynamics at small temporal and spatial scales, with the strengths of a highly idealized profile model, providing low computational efforts for larger temporal and spatial scales. +
Climate and tectonics ultimately drive the physical and chemical surface processes that evolve landscape structure, including the connectivity of landscape portions that facilitate or impede movement of organismal populations. Connectivity controls population spatial distribution, drives speciation where populations spatially fragment, and increases extinction susceptibility of species where its habitat shrinks. Here I demonstrate the role that landscape evolution models can have in exploring these process linkages in investigations of species diversification driven by climatic and tectonic forcings. The models were built with the tool, SpeciesEvolver that constructs lineages in response to environmental change at geologic, macroevolutionary, and landscape scales. I will also suggest how future studies can use landscape evolution models and tools such as SpeciesEvolver to pursue questions regarding the mechanisms by which lineages respond to the drivers and details of landscape evolution, and taxon-specific and region-specific interactions between biotas and their environments. +
Climate-induced disturbances are expected to increase in frequency and intensity and affect coastal wetland ecosystem mainly through altering its hydrology. Investigating how wetland hydrology responds to climate disturbances is an important first step to understand the ecological response of coastal wetlands to these disturbances. In this talk, I am going to introduce my research work on improving the understanding of how the water storage of coastal wetlands at North Carolina, Delaware Bay, and the entire southeast U.S. changes under climatic disturbances. In particular, I will address the uncertainties in estimating water flow through coastal wetlands by considering 1) the regional-scale hydrologic interaction between uplands, coastal wetlands, and the ocean and 2) the impact of coastal eco-geomorphologic change on the freshwater and saltwater interaction on coastal marshlands. +
