Organic Data Science Framework - User contributions [en]

Hydrology

2014-06-09T18:51:51Z

Jordan: Added PropertyValue: Is a = Expertise

[[Category:Object]]


{{#set:|
Is a=Expertise}}

Hydrology

2014-06-09T18:51:36Z

Jordan: Creating new page with Category: Object

[[Category:Object]]

Hydrodynamic modeling

2014-06-09T18:50:18Z

Jordan:

[[Category:Object]]
Hydrodynamic modeling involves simulating the temporally-resolved mixing and fluxes of various scalars that are important to water researches or managers. These scalars include heat, dissolved constituents (including ions and dissolved organic carbon), particulate matter, and others. Hydrodynamic models can take the form of resolved layers, grids, cubes, etc in 0, 1, 2, or 3 dimensions (0D, 1D, 2D, or 3D). For example, most 1D models (e.g., [[GLM_Software|GLM]]) are built using a vertically resolved layer structure, while 0D models simulate a single water volume which evolves over time.

Hydrodynamic modeling

2014-06-09T18:49:57Z

Jordan:

[[Category:Model]]
Hydrodynamic modeling involves simulating the temporally-resolved mixing and fluxes of various scalars that are important to water researches or managers. These scalars include heat, dissolved constituents (including ions and dissolved organic carbon), particulate matter, and others. Hydrodynamic models can take the form of resolved layers, grids, cubes, etc in 0, 1, 2, or 3 dimensions (0D, 1D, 2D, or 3D). For example, most 1D models (e.g., [[GLM_Software|GLM]]) are built using a vertically resolved layer structure, while 0D models simulate a single water volume which evolves over time.

Hydrodynamic modeling

2014-06-09T18:48:35Z

Jordan: Creating new page with Category: Object

[[Category:Object]]

Matt Hipsey

2014-06-09T18:03:44Z

Jordan: Added PropertyValue: Expertise = Hydrodynamic modeling

[[Category:Person]]


{{#set:
Affilation=Aquatic_EcoDynamics_Group|
Affiliation=University_of_Western_Australia|
Expertise=Hydrodynamic_modeling|
Expertise=Ecosystem_modeling|
Is a=Researcher}}

Ecosystem modeling

2014-06-09T17:59:23Z

Jordan:

[[Category:Model]]
Ecosystem modeling involves simulating the temporally-resolved biogeochemical transformations that are relevant to ecosystem biota or processes. Physical transport or mixing can be simulated using a [[Hydrodynamic_modeling|Hydrodynamic model]], or these processes can be built into an ecosystem model.

Ecosystem modeling

2014-06-09T17:59:13Z

Jordan:

[[Category:Model]]
Ecosystem modeling involves simulating the temporally-resolved biogeochemical transformations that are relevant to ecosystem biota or processes. Physical transport or mixing can be simulated using a [[Hydrodynamic_modeling|Hydrodynamic model]]) , or these processes can be built into an ecosystem model.

Ecosystem modeling

2014-06-09T17:58:14Z

Jordan: Created page with "Category:Model Ecosystem modeling involves simulating the temporally-resolved biogeochemical transformations that are relevant to ecosystem biota or processes. Physical tr..."

[[Category:Model]]
Ecosystem modeling involves simulating the temporally-resolved biogeochemical transformations that are relevant to ecosystem biota or processes. Physical transport or mixing can be simulated using a Hydrodynamic model, or these processes can be built into an ecosystem model.

Hydrodynamic modeling

2014-06-09T17:55:48Z

Jordan:

Hydrodynamic modeling

2014-06-09T17:55:38Z

Jordan:

[[Category:Model]]

Hydrodynamic modeling involves simulating the temporally-resolved mixing and fluxes of various scalars that are important to water researches or managers. These scalars include heat, dissolved constituents (including ions and dissolved organic carbon), particulate matter, and others. Hydrodynamic models can take the form of resolved layers, grids, cubes, etc in 0, 1, 2, or 3 dimensions (0D, 1D, 2D, or 3D). For example, most 1D models (e.g., [[GLM_Software|GLM]]) are built using a vertically resolved layer structure, while 0D models simulate a single water volume which evolves over time.

Hydrodynamic modeling

2014-06-09T17:53:10Z

Jordan: Creating new page with Category: Model

[[Category:Model]]

Hydrodynamic modeling

2014-06-09T17:53:03Z

Jordan:

Hydrodynamic modeling involves simulating the temporally-resolved mixing and fluxes of various scalars that are important to water researches or managers. These scalars include heat, dissolved constituents (including ions and dissolved organic carbon), particulate matter, and others. Hydrodynamic models can take the form of resolved layers, grids, cubes, etc in 0, 1, 2, or 3 dimensions (0D, 1D, 2D, or 3D). For example, most 1D models (e.g., [[GLM_Software|GLM]]) are built using a vertically resolved layer structure, while 0D models simulate a single water volume which evolves over time.

Hydrodynamic modeling

2014-06-09T17:50:46Z

Jordan:

Hydrodynamic modeling involves simulating the temporally-resolved mixing and fluxes of various scalars that are important to water researches or managers. These scalars include heat, dissolved constituents (including ions and dissolved organic carbon), particulate matter, and others. Hydrodynamic models can take the form of resolved layers, grids, cubes, etc in 0, 1, 2, or 3 dimensions (0D, 1D, 2D, or 3D). For example, most 1D models (e.g., [[GLM_Software]]) are built using a vertically resolved layer structure, while 0D models simulate a single water volume which evolves over time.

Hydrodynamic modeling

2014-06-09T17:48:16Z

Jordan:

Hydrodynamic modeling involves simulating the temporally-resolved mixing and fluxes of various scalars that are important to water researches or managers. These scalars include heat, dissolved constituents (including ions and dissolved organic carbon), particulate matter, and others. Hydrodynamic models can take the form of resolved layers, grids, cubes, etc in 0, 1, 2, or 3 dimensions (0D, 1D, 2D, or 3D). For example, most 1D models (e.g., GLM) are built using a vertically resolved layer structure, while 0D models simulate a single water volume which evolves over time.

Hydrodynamic modeling

2014-06-09T17:46:58Z

Jordan: Created page with "Hydrodynamic modeling involves simulating the temporally-resolved mixing and fluxes of various scalars that are important to lake researches or managers. These scalars include..."

Hydrodynamic modeling involves simulating the temporally-resolved mixing and fluxes of various scalars that are important to lake researches or managers. These scalars include heat, dissolved constituents (including ions and dissolved organic carbon), and particulate matter. Hydrodynamic models can take the form of resolves layers, grids, cubes, etc in 0, 1, 2, or 3 dimensions (0D, 1D, 2D, or 3D). For example, most 1D models (e.g., GLM) are built using a vertically resolved layer structure, while 0D models simulate a single water volume which evolves over time.

U.S. Geological Survey

2014-05-05T17:52:00Z

Jordan: Added PropertyValue: Is a = Federal agency

{{#set:
Is a=Federal_agency|
Is a=Science_organization|
Web site=http://www.usgs.gov/}}

Main Page

2014-05-05T17:47:19Z

Jordan:

= What is Organic Data Science? =

We are investigating [[What_Is_Organic_Data_Science| Organic Data Science]], a new approach aimed to allow scientists to formulate and resolve science processes through an open framework that facilitates ad-hoc participation and entice collaborators based on attractive science goals. [[What_Is_Organic_Data_Science| Read more about Organic Data Science]].

= Contributing to Organic Data Science =

We are using a semantic wiki framework with significant extensions to structure collaboration processes.

[[Organic_Data_Science_through_a_Semantic_Wiki | Read more about how this framework works and how to participate and contribute]].

[[How_to_use_this_organic_data_science_wiki | Learn how to use this wiki]].

= Our Science Goal: The Age of Water =

We focus on long-standing problems of coupled water and carbon budgets through development of a new scientific paradigm, The Age of Water and Carbon, that melds theory and practice from limnology and hydrology within the new collaborative paradigm of [[Organic_Data_Science | Organic Data Science]]. We are integrating analytical frameworks from two communities – hydrology and isotope modeling in [http://criticalzone.org Critical Zone Observatories (CZOs)] and hydrodynamic water quality modeling from the [http://www.gleon.org Global Lake Ecological Observatory Network (GLEON)] – to quantify water and material fluxes from two research sites, the Shales Hills CZO and the GLEON member site, [http://www.lternet.edu/sites/ntl North Temperate Lakes LTER]. This foundation will serve as a nexus for participation by multiple communities and will seed the growth of additional science through shared ideas, knowledge, and data.

== Starting Points ==

* [[Changing_Connectivity_in_the_Hydroscape | Modeling connectivity in the hydroscape]].
* The [[Lake_Organic_Carbon_Models | lake organic carbon models]].
* [[Document_PIHM_Model | Documentation for the PIHM model]].
* [[Lake_Modeling_Support | Lake modeling support]].
* [[Framework Design]]

== Today's Highlights ==

We are starting to describe contributors to the project, help us fill in the blanks:

{{ #ask: [[Is a::researcher]]
| ?expertise
| ?affiliation
| default=No researchers are described in this site
}}

We are starting to describe models, help us fill in the blanks:

{{ #ask: [[Is a::model]]
| ?author
| ?software_license
| ?language
| default=No models are described in this site
}}

= Acknowledgements =

This work is supported by the National Science Foundation through the INSPIRE program with grant number IIS-1344272.

University of Western Australia

2014-05-05T17:43:48Z

Jordan: Created page with "   {{#set: Is a=University}}"

{{#set:
Is a=University}}

Universidade Federal do Rio Grande do Sul

2014-05-05T17:43:33Z

Jordan: Created page with "   {{#set: Is a=University}}"

{{#set:
Is a=University}}

University of Virginia

2014-05-05T17:43:15Z

Jordan: Added PropertyValue: Is a = University

{{#set:
Is a=University|
Web site=http://www.virginia.edu}}

David da Motta Marques

2014-05-05T17:42:40Z

Jordan: Added PropertyValue: Affiliation = Universidade Federal do Rio Grande do Sul

[[Category:Person]]


{{#set:
Affiliation=Universidade_Federal_do_Rio_Grande_do_Sul|
Expertise=Hydrology|
Expertise=Hydrodynamic_modeling|
Is a=Researcher|
ResearchGate=http://www.researchgate.net/profile/David_Da_Motta_Marques}}

David da Motta Marques

2014-05-05T17:42:15Z

Jordan: Added PropertyValue: Expertise = Hydrodynamic modeling

[[Category:Person]]


{{#set:
Expertise=Hydrodynamic_modeling|
Expertise=Hydrology|
Is a=Researcher|
ResearchGate=http://www.researchgate.net/profile/David_Da_Motta_Marques}}

David da Motta Marques

2014-05-05T17:41:59Z

Jordan: Added PropertyValue: Expertise = Hydrology

[[Category:Person]]


{{#set:
Expertise=Hydrology|
Is a=Researcher|
ResearchGate=http://www.researchgate.net/profile/David_Da_Motta_Marques}}

Property:ResearchGate

2014-05-05T17:41:16Z

Jordan: Creating new Property

Property type: [[has type::URL]]

David da Motta Marques

2014-05-05T17:41:16Z

Jordan: Added PropertyValue: ResearchGate = http://www.researchgate.net/profile/David_Da_Motta_Marques

[[Category:Person]]


{{#set:
Is a=Researcher|
ResearchGate=http://www.researchgate.net/profile/David_Da_Motta_Marques}}

David da Motta Marques

2014-05-05T17:40:40Z

Jordan: Created page with "Category:Person   {{#set: Is a=Researcher}}"

[[Category:Person]]


{{#set:
Is a=Researcher}}

Modeling support forum

2014-05-05T17:31:54Z

Jordan: Added PropertyValue: Web page = https://groups.google.com/forum/#!forum/aquaticmodelling

{{#set:|
Web page=https://groups.google.com/forum/#%21forum/aquaticmodelling}}

Main Page

2014-05-05T17:25:45Z

Jordan: /* Starting Points */

= What is Organic Data Science? =

We are investigating [[What_Is_Organic_Data_Science| Organic Data Science]], a new approach aimed to allow scientists to formulate and resolve science processes through an open framework that facilitates ad-hoc participation and entice collaborators based on attractive science goals. [[What_Is_Organic_Data_Science| Read more about Organic Data Science]].

= Contributing to Organic Data Science =

We are using a semantic wiki framework with significant extensions to structure collaboration processes.

[[Organic_Data_Science_through_a_Semantic_Wiki | Read more about how this framework works and how to participate and contribute]].

[[How_to_use_this_organic_data_science_wiki | Learn how to use this wiki]].

= Our Science Goal: The Age of Water =

We focus on long-standing problems of coupled water and carbon budgets through development of a new scientific paradigm, The Age of Water and Carbon, that melds theory and practice from limnology and hydrology within the new collaborative paradigm of [[Organic_Data_Science | Organic Data Science]]. We are integrating analytical frameworks from two communities – hydrology and isotope modeling in [http://criticalzone.org Critical Zone Observatories (CZOs)] and hydrodynamic water quality modeling from the [http://www.gleon.org Global Lake Ecological Observatory Network (GLEON)] – to quantify water and material fluxes from two research sites, the Shales Hills CZO and the GLEON member site, [http://www.lternet.edu/sites/ntl North Temperate Lakes LTER]. This foundation will serve as a nexus for participation by multiple communities and will seed the growth of additional science through shared ideas, knowledge, and data.

== Starting Points ==

* [[Changing_Connectivity_in_the_Hydroscape | Modeling connectivity in the hydroscape]].
* The [[Lake_Organic_Carbon_Models | lake organic carbon models]].
* [[Document_PIHM_Model | Documentation for the PIHM model]].
* [[Lake_Modeling_Tools | Lake modeling tools]].
* [[Framework Design]]

== Today's Highlights ==

We are starting to describe contributors to the project, help us fill in the blanks:

{{ #ask: [[Is a::researcher]]
| ?expertise
| ?affiliation
| default=No researchers are described in this site
}}

We are starting to describe models, help us fill in the blanks:

{{ #ask: [[Is a::model]]
| ?author
| ?software_license
| ?language
| default=No models are described in this site
}}

= Acknowledgements =

This work is supported by the National Science Foundation through the INSPIRE program with grant number IIS-1344272.

Paul Hanson

2014-05-05T17:23:40Z

Jordan: Added PropertyValue: Github = https://github.com/pchanson

[[Category:Person]]


{{#set:
Affiliation=Center_For_Limnology|
Affiliation=University_of_Wisconsin_-_Madison|
Expertise=Carbon_cycling|
Github=https://github.com/pchanson|
Has User ID=Paul|
Is a=Researcher|
Web site=http://hanson.limnology.wisc.edu}}

Jordan Read

2014-05-05T17:22:39Z

Jordan:

[[Category:Person]]


{{#set:
Affiliation=Center_for_Integrated_Data_Analytics |
Affiliation=U.S._Geological_Survey |
Expertise=Hydrodynamic_modeling |
Expertise=Physical_limnology |
Github=https:github.com/jread-usgs |
Has User ID=Jordan |
Is a=Researcher |
Web site=http://cida.usgs.gov/people/jread.html }}

Jordan Read

2014-05-05T17:22:13Z

Jordan: updated to new webpage

[[Category:Person]]


{{#set:
Affiliation=Center_for_Integrated_Data_Analytics |
Affiliation=U.S._Geological_Survey |
Expertise=Hydrodynamic_modeling |
Expertise=Physical_limnology |
Github=Https:github.com/jread-usgs |
Has User ID=Jordan |
Is a=Researcher |
Web site=http://cida.usgs.gov/people/jread.html }}

Center for Integrated Data Analytics

2014-05-05T17:21:03Z

Jordan:

The USGS Center for Integrated Data Analytics is committed to advancing USGS science and a broader understanding of our changing world by integrating disparate data across scales and domains, improving access to data and research, developing tools for analysis and visualization, and fostering collaboration in order to enable a new era of scientific investigation.



{{#set:|
Web site=http://cida.usgs.gov }}

Physical limnology

2014-05-05T17:19:48Z

Jordan: Created page with "Physical limnology is the study of physical processes within lakes. This study focuses on water circulation, mixing within lakes and the thermal structure of lakes, including ..."

Physical limnology is the study of physical processes within lakes. This study focuses on water circulation, mixing within lakes and the thermal structure of lakes, including ice formation, water temperature and stratification. These processes are, in turn, driven by atmospheric processes – heat fluxes, momentum transfer – at the surface of a lake, and constrained by the morphology – size, depth, shape, sediment – of a lake. River inflow/outflow also influences the physical processes of lakes, most noticeably the residence time of the water. Whilst of intrinsic interest to the lake physicist these processes are also of fundamental importance to the ecology and chemistry of lake systems.

Landscape limnology

2014-05-05T17:16:10Z

Jordan: Blanked the page

Landscape limnology

2014-05-05T17:15:47Z

Jordan: Creating new page with Category: Answer

[[Category:Answer]]

Patricia Soranno

2014-05-05T17:14:54Z

Jordan: Added PropertyValue: Expertise = Landscape limnology

[[Category:Person]]


{{#set:
Affiliation=Michigan_State_University|
Expertise=Landscape_limnology|
Is a=Researcher|
Web site=http://www.fw.msu.edu/~soranno}}

GLM Software

2014-05-05T17:11:16Z

Jordan:

[[Category:Component]]

= Overview =
:The General Lake Model (GLM) is a 1D lake water balance and vertical stratification model. GLM has been designed to be an open-source community model suited to environmental modeling studies where simulation of lakes or reservoirs is required. GLM was developed by the [http://aed.see.uwa.edu.au/research/models/GLM/ University of Western Australia's Aquatic Eco-Dynamics group] 

= Concept =

:[From AED website] GLM computes vertical profiles of temperature, salinity and density by accounting for the effect of inflows/outflows, mixing and surface heating and cooling, including the effect of ice cover on heating and mixing of the lake. Since the model is one-dimensional it assumes no horizontal variability so users must ensure the lake conditions match this one-dimensional assumption. The model is ideally suited to long-term investigations ranging from seasons to decades, and for coupling with biogeochemical models to explore the role that stratification and vertical mixing play on the dynamics of lake ecosystem.

:GLM incorporates a flexible Lagrangian layer structure similar to the approach of several 1-D lake model designs (Imberger and Patterson 1981; Hamilton and Schladow 1997). The Lagrangian approach was originally introduced in the model DYRESM developed by the Centre for Water Research and allows for layers to change thickness by contracting and expanding in response to inflows, outflows, mixing and surface mass fluxes. When sufficient energy becomes available to over come density gradients, two layers will merge thus accounting for the process of mixing. Layer thicknesses are adjusted by the model in order to sufficiently resolve the vertical density gradient. Unlike the fixed grid design where mixing algorithms are typically based on vertical velocities, numerical diffusion of the thermocline is limited, making the GLM approach particularly suited to long-term investigations.

:Although GLM is a new light-weight model code, many of the heating and mixing algorithms have been based on equations presented by Hamilton and Schladow (1997). GLM has been written with a modernized code structure and features a number of customizations to make the model easy and efficient to use. The model integrates with LakeAnalyser (LA) for derivation of numerous metrics of relevance to lake hydrodynamics and may also be integrated within a Markov Chain Monte Carlo (MCMC) algorithm.


{{#set:
Author=Casper_Boon |
Author=Louise_Bruce |
Author=Matt_Hipsey |
Is a=Model |
Language=C |
Web site=http://aed.see.uwa.edu.au/research/models/GLM }}

GLM Software

2014-05-05T17:10:23Z

Jordan: Adding GLM structure to match PIHM documentation

[[Category:Component]]

= Overview =
:The General Lake Model (GLM) is a 1D lake water balance and vertical stratification model. GLM has been designed
to be an open-source community model suited to environmental modeling studies where
simulation of lakes or reservoirs is required. GLM was developed by the [http://aed.see.uwa.edu.au/research/models/GLM/ University of Western Australia's Aquatic Eco-Dynamics group] 

= Concept =

:[From AED website] GLM computes vertical profiles of temperature, salinity and density by accounting for the effect of inflows/outflows, mixing and surface heating and cooling, including the effect of ice cover on heating and mixing of the lake. Since the model is one-dimensional it assumes no horizontal variability so users must ensure the lake conditions match this one-dimensional assumption. The model is ideally suited to long-term investigations ranging from seasons to decades, and for coupling with biogeochemical models to explore the role that stratification and vertical mixing play on the dynamics of lake ecosystem.

GLM incorporates a flexible Lagrangian layer structure similar to the approach of several 1-D lake model designs (Imberger and Patterson 1981; Hamilton and Schladow 1997). The Lagrangian approach was originally introduced in the model DYRESM developed by the Centre for Water Research and allows for layers to change thickness by contracting and expanding in response to inflows, outflows, mixing and surface mass fluxes. When sufficient energy becomes available to over come density gradients, two layers will merge thus accounting for the process of mixing. Layer thicknesses are adjusted by the model in order to sufficiently resolve the vertical density gradient. Unlike the fixed grid design where mixing algorithms are typically based on vertical velocities, numerical diffusion of the thermocline is limited, making the GLM approach particularly suited to long-term investigations.

Although GLM is a new light-weight model code, many of the heating and mixing algorithms have been based on equations presented by Hamilton and Schladow (1997). GLM has been written with a modernised code structure and features a number of customisations to make the model easy and efficient to use. The model integrates with LakeAnalyser (LA) for derivation of numerous metrics of relevance to lake hydrodynamics and may also be integrated within a Markov Chain Monte Carlo (MCMC) algorithm..


{{#set:
Author=Casper_Boon |
Author=Louise_Bruce |
Author=Matt_Hipsey |
Is a=Model |
Language=C |
Web site=http://aed.see.uwa.edu.au/research/models/GLM }}

Xuan Yu

2014-04-07T19:42:07Z

Jordan:

[[Category:Person]]


{{#set:
Affiliation=Pennsylvania State University |
Is a=Researcher }}

Louise Bruce

2014-01-16T09:26:24Z

Jordan: Added PropertyValue: Affiliation = Aquatic EcoDynamics Group

{{#set:
Affiliation=Aquatic_EcoDynamics_Group |
Affliation=University_of_Western_Australia |
Is a=Postdoctoral_Fellow }}

Casper Boon

2014-01-16T09:25:24Z

Jordan: Added PropertyValue: Affiliation = School of Earth and Environmen

[[Category:People]]


{{#set:
Affiliation=School_of_Earth_and_Environmen |
Affiliation=University_of_Western_Australia |
Is a=Model_Developer }}

Casper Boon

2014-01-16T09:25:07Z

Jordan: Deleted PropertyValue: Affiliation = Centre_for_Water_Research

[[Category:People]]


{{#set:
Affiliation=University_of_Western_Australia |
Is a=Model_Developer }}

Casper Boon

2014-01-16T09:25:05Z

Jordan: Added PropertyValue: Affiliation = University of Western Australia

[[Category:People]]


{{#set:
Affiliation=University_of_Western_Australia |
Affiliation=Centre_for_Water_Research |
Is a=Model_Developer }}

Louise Bruce

2014-01-16T09:24:31Z

Jordan: Deleted PropertyValue: Affiliation = Centre_for_Water_Research

{{#set:
Affliation=University_of_Western_Australia |
Is a=Postdoctoral_Fellow }}

Louise Bruce

2014-01-16T09:24:27Z

Jordan: Added PropertyValue: Affliation = University of Western Australia

{{#set:
Affiliation=Centre_for_Water_Research |
Affliation=University_of_Western_Australia |
Is a=Postdoctoral_Fellow }}

Louise Bruce

2014-01-16T09:23:56Z

Jordan: Deleted PropertyValue: Afflication = University_of_Western_Australia

{{#set:
Affiliation=Centre_for_Water_Research |
Is a=Postdoctoral_Fellow }}

Louise Bruce

2014-01-16T09:23:48Z

Jordan: Added PropertyValue: Afflication = University of Western Australia

{{#set:
Affiliation=Centre_for_Water_Research |
Afflication=University_of_Western_Australia |
Is a=Postdoctoral_Fellow }}

Property:Afflication

2014-01-16T09:23:47Z

Jordan: Creating new Property

Property type: [[has type::Page]]

GLM Software

2013-12-17T20:48:08Z

Jordan: Deleted PropertyValue: Language = FORTRAN

[[Category:Component]]


{{#set:
Author=Casper_Boon |
Author=Louise_Bruce |
Author=Matt_Hipsey |
Is a=Model |
Language=C |
Web site=http://aed.see.uwa.edu.au/research/models/GLM }}

Delft3d

2013-11-25T13:27:38Z

Jordan: Added PropertyValue: Author = Deltares systems

[[Category:Model]]


{{#set:
Author=Deltares_systems |
Is a=Model |
Web site=http://www.deltaressystems.com/hydro/product/621497/delft3d-suite }}