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Files (15)
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3194?size=60x60 Hu Ferenc HORVATH
Project Biovel
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Blob Thornton (2000) User's Guide for Biome-BGC, version ...

Created: 2014-05-21 04:54:33

Credits: User Ferenc HORVATH

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This User's Guide give a detailed reference to setting Biome-BGC model.

File type: Adobe PDF

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3194?size=60x60 Hu Ferenc HORVATH
Project Biovel
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Blob Trusilova et al. (2009) Parameter estimation and val...

Created: 2014-05-21 04:56:56 | Last updated: 2014-05-21 05:15:32

Credits: User Ferenc HORVATH

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Trusilova, K., Trembath, J., Churkina, G. (2009) Parameter estimation and validation of the terrestrial ecosystem model Biome-BGC using eddy-covariance flux measurements. Max-Planck-Institut für Biogeochemie, Technical Reports 16, 1-60.      

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3194?size=60x60 Hu Ferenc HORVATH
Project Biovel
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Blob Biome-BGC 4.1.1 executable for Windows

Created: 2014-05-21 05:01:21

Credits: User Ferenc HORVATH

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Compressed directory contains all necessary subdirectories and files for running the Biome-BGC model, version 4.1.1 MPI.

File type: Trident (Package)

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3194?size=60x60 Hu Ferenc HORVATH
Project Biovel
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Blob TEST DEMO EPC GRASSLAND MuSo v2.2 NITROGEN

Created: 2014-05-26 05:57:25

Credits: User Ferenc HORVATH

License: Creative Commons Attribution-Share Alike 3.0 Unported License

TEST DEMO EPC file 'NITROGEN' for Biome-BGC MuSo v2.2 simulation runs

File type: Trident (Package)

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3194?size=60x60 Hu Ferenc HORVATH
Project Biovel
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Blob TEST DEMO EPC GRASSLAND MuSo v2.2 LEAFAREA

Created: 2014-05-26 05:58:54

Credits: User Ferenc HORVATH

License: Creative Commons Attribution-Share Alike 3.0 Unported License

TEST DEMO EPC file 'LEAFAREA' for Biome-BGC MuSo v2.2 simulation runs

File type: Trident (Package)

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3194?size=60x60 Hu Ferenc HORVATH
Project Biovel
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Blob TEST DEMO METDATA FOR Biome-BGC, HHS, 1901-2000

Created: 2014-05-26 06:01:41

Credits: User Ferenc HORVATH

License: Creative Commons Attribution-Share Alike 3.0 Unported License

TEST DEMO METDATA (daily meteorology data) file for Biome-BGC simulation runs

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3194?size=60x60 Hu Ferenc HORVATH
Project Biovel
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Blob TEST DEMO Daily Observation Data 2001-2002 - AIR

Created: 2014-05-26 06:39:44

Credits: User Ferenc HORVATH

License: Creative Commons Attribution-Share Alike 3.0 Unported License

TEST DEMO Daily Observation Data 2001-2002 - AIR for GLUE analysis

File type: text/csv

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3194?size=60x60 Hu Ferenc HORVATH
Project Biovel
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Blob TEST DEMO Daily Observation Data 2001-2002 - HUMUS

Created: 2014-05-26 06:40:56

Credits: User Ferenc HORVATH

License: Creative Commons Attribution-Share Alike 3.0 Unported License

TEST DEMO Daily Observation Data 2001-2002 - HUMUS for GLUE analysis

File type: text/csv

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3194?size=60x60 Hu Ferenc HORVATH
Project Biovel
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Blob TEST DEMO Daily Observation Data 2001-2002 - NINE

Created: 2014-05-26 06:42:09 | Last updated: 2014-05-26 09:40:45

Credits: User Ferenc HORVATH

License: Creative Commons Attribution-Share Alike 3.0 Unported License

TEST DEMO Daily Observation Data 2001-2002 - NINE for GLUE analysis

File type: text/csv

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3194?size=60x60 Hu Ferenc HORVATH
Project Biovel
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Blob TEST DEMO Daily Observation Data 2001-2002 - AIR

Created: 2014-05-26 09:43:22

Credits: User Ferenc HORVATH

License: Creative Commons Attribution-Share Alike 3.0 Unported License

TEST DEMO Daily Observation Data 2001-2002 - AIR for GLUE analysis

File type: text/csv

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3194?size=60x60 Hu Ferenc HORVATH
Project Biovel
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Blob TEST DEMO Daily Observation Data 2001-2002 - HUMUS

Created: 2014-05-26 09:44:56

Credits: User Ferenc HORVATH

License: Creative Commons Attribution-Share Alike 3.0 Unported License

TEST DEMO Daily Observation Data 2001-2002 - HUMUS for GLUE analysis

File type: text/csv

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3194?size=60x60 Hu Ferenc HORVATH
Project Biovel
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Blob TEST DEMO Daily Observation Data 2001-2002 - AIR

Created: 2014-05-27 15:18:56

Credits: User Ferenc HORVATH

License: Creative Commons Attribution-Share Alike 3.0 Unported License

TEST DEMO Daily Observation Data 2001-2002 - AIR

File type: text/csv

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3194?size=60x60 Hu Ferenc HORVATH
Project Biovel
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Blob TEST DEMO Daily Observation Data 2001-2002 - HUMUS

Created: 2014-05-27 15:20:38

Credits: User Ferenc HORVATH

License: Creative Commons Attribution-Share Alike 3.0 Unported License

TEST DEMO Daily Observation Data 2001-2002 - HUMUS

File type: text/csv

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Parametric Bootstrap or Resample a projection matrix...

Created: 2014-07-25 09:41:10

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Gerard Oostermeijer

Attributions: Workflow Parametric Bootstrap or Resample a projection matrix Workflow

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.The Parametric Bootstrap or Resample a projection matrix Workflow provides an environment to resample a projection matrix using a multinomial distribution for transitions and a log normal distribution for fertilities (Stubben, Milligan, and Nantel. 2011). The resample is based on number of plants surveyed. The projection matrix A is first split into separate transition and ...

File type: Adobe PDF

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Bootstrap of observed census transitions documentation

Created: 2014-07-25 10:37:03

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Gerard Oostermeijer

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.The Bootstrap of observed census transitions (confidence intervals of λ) workflow for local execution calculates bootstrap distributions of population growth rates (λ), stage vectors, and projection matrix elements by randomly sampling with replacement from a stage-fate data frame of observed transitions. The goal of a demographic analysis is very often to est...

File type: Adobe PDF

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Groups (2)
Owner
Avatar Gb Robert Muetzelfeldt
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Network-member Plasmo: Plant Systems Biology Modelling

Unique name: Plasmo
Created: Friday 27 March 2009 01:19:04 (UTC)

The Plasmo project aims to create a web-based repository and portal for plant models represented in Simile XML.    Simile models are based on the System Dynamics (stock-and-flow) notation, with an object-oriented flavour.  

1 shared item   |   0 announcements

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2577?size=80x80 Ie David PS
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Network-member IMPEx

Unique name: IMPEx
Created: Tuesday 10 September 2013 08:20:32 (UTC)

IMPEx is aimed at the creation of an integrated interactive computational framework where data from planetary missions will be interconnected with numerical models providing a possibility......to simulate planetary phenomena and interpret space missions measurements;...to test models versus experimental data and perform further improvements of models;...to fill gaps in the measurements by appro...

23 shared items   |   0 announcements

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Packs (6)
Creator
3194?size=60x60 Hu Ferenc HORVATH
Project Biovel
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Pack Understanding Basics of a Biome-BGC simulation run


Created: 2014-05-21 04:31:40 | Last updated: 2014-05-21 05:03:34

Biome-BGC is a biogeochemical model that simulates the storage and flux of water, carbon, and nitrogen between the ecosystem and the atmosphere, and within the components of the terrestrial ecosystems (Thornton, 2000). The Biome-BGC was developed by the Numerical Terradynamic Simulation Group (NTSG), University of Montana.The executable code of Biome-BGC are embedded in web services and workflows, while input and parameter files or datasets are managed with Biome-BGC Projects d...

3 items in this pack

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3194?size=60x60 Hu Ferenc HORVATH
Project Biovel
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Pack Preparatory working with Biome-BGC Projects database...


Created: 2014-05-26 06:10:06 | Last updated: 2014-05-27 15:23:06

Various meteorology, EPC (ecophysiology parameter) and observation files for Biome-BGC simulation runs.

9 items in this pack

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Creator
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Pack Matrix Population Model construction pack


Created: 2014-06-19 11:23:27 | Last updated: 2014-07-25 12:48:25

This pack contains a workflow, a file and documentation (tutorial to run the workflow).Creation of a stage matrix model from demographic monitoring of individuals in an animal or plant population Workflow for local executionThe Creation of a stage matrix model Workflow allows us to construct a stage o several stage matrices. This workflow create a stage matrix based on two years census data that contains transitions probabilities from each stage to the next, of tagged or mapped individuals of...

4 items in this pack

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Pack Damping ratio pack


Created: 2014-07-02 13:32:31 | Last updated: 2014-07-25 11:07:16

This pack contains a workflow, a file and documentation (tutorial to run the workflow).The Damping ratio pack contains a workflow that provides an environment to calculate the damping ratio of several matrices and plot them.The damping ratio can be considered as a measure of the intrinsic resilience of the population, describing how quickly transient dynamics decay following disturbance or perturbation regardless of population structure, the larger the p, the quicker the population converges ...

8 items in this pack

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Creator
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Pack Bootstrap of observed census transitions pack


Created: 2014-07-09 12:56:51 | Last updated: 2014-07-25 10:37:19

This pack contains a workflow, a file and documentation (tutorial to run the workflow).The Bootstrap of observed census transitions (confidence intervals of λ) workflow for local execution calculates bootstrap distributions of population growth rates (λ), stage vectors, and projection matrix elements by randomly sampling with replacement from a stage-fate data frame of observed transitions. The goal of a demographic analysis is very often to estimate lambda, because lambda is es...

4 items in this pack

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Creator
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Pack Simulate stochastic growth from a sequence of matric...


Created: 2014-07-10 12:05:44 | Last updated: 2014-07-30 13:48:06

This pack contains a workflow, a file and documentation (tutorial to run the workflow).The Simulate stochastic growth from a sequence of matrices Workflow provides an environment to simulate stochastic growth by projection using whole matrix selection techniques in an independently and identically distributed (iid) environment from a set of 2 or more projection matrices.Outputs:Equal selection dataStochastic projectionUnequal selection dataTo know more details about the analysis, Morris and D...

8 items in this pack

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Workflows (27)
SimileXMLv3
Uploader
Avatar Gb Robert Muetzelfeldt

Workflow MiscanMod (1)

This is the MiscanMod model. To explore the model, go here.

Created: 2009-03-27 | Last updated: 2009-04-23

Credits: User Robert Muetzelfeldt

SimileXMLv3
Uploader
Avatar Gb Robert Muetzelfeldt

Workflow LINTUL crop model (1)

LINTUL is a simple, generic crop model.

Created: 2009-04-01

Credits: User Robert Muetzelfeldt

Taverna 2
Uploader
254?size=60x60 Cn Peter Li

Workflow Construction of skeleton SBML model using ... (1)

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This workflow generates a skeleton SBML model consisting of the metabolic reactions for a given list of yeast enzymes ORF numbers

Created: 2010-03-26 | Last updated: 2010-03-26

Credits: User Peter Li

Taverna 2
Uploader
254?size=60x60 Cn Peter Li

Workflow Construction of skeleton SBML model using ... (1)

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This workflow generates a skeleton SBML model consisting of the metabolic reactions for a given subsystem term.

Created: 2010-03-26 | Last updated: 2010-03-26

Credits: User Peter Li

Taverna 2
Uploader
254?size=60x60 Cn Peter Li

Workflow SBML model parameterisation (1)

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This workflow parameterises an SBML model generated by the qualitative SBML model construction workflow

Created: 2010-03-26

Credits: User Peter Li

Taverna 2
Uploader
254?size=60x60 Cn Peter Li

Workflow SBML model optimisation (1)

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This workflow modifies reaction kinetic parameters against experimental data stored in the MCISB key results database

Created: 2010-03-26

Credits: User Peter Li

Taverna 2
Uploader
254?size=60x60 Cn Peter Li

Workflow Copasi time simulation of SBML model (1)

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Uses the synchronous Copasi time simulation web service to predict the concentrations of species over a time period. The results from Copasi are provided in SBRML format which is visualised as a graph using an R script.

Created: 2010-03-26

Credits: User Peter Li

Bioclipse Scripting Language
Uploader
4506?size=60x60 Nl Egon Willighagen

Workflow Run OpenTox models on local data. (1)

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 Runs a remote OpenTox model to predict properties for local data which is uploaded on the fly.

Created: 2010-11-13 | Last updated: 2010-11-13

Credits: User Egon Willighagen

RapidMiner
Uploader
Avatar Sebastian Loh

Workflow 2. Getting Started: Retrieve and Apply a M... (1)

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This getting started process demonstrates how to load (retrieve) a model from the repository and apply it to a data set. The result is a data set (at the lab output for "labeled data" ) with has a new "prediction" attribute which indicated the prediction for each example (ie. row/record). You will need to adjust the path of the retrieve data operator to the actual location where the model is stored by a previews execution of the "1. Getting Started: Learn and Store a...

Created: 2011-01-17 | Last updated: 2011-01-19

RapidMiner
Uploader
Avatar Sebastian Loh

Workflow 1. Getting Started: Learn and Store a Model (1)

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This getting started process shows the first step of learning and storing a model. After a model is learned, you can load (Retrieve operator) the model and apply it to a test data set (see 2. Getting Started: Retrieve and Apply Model). The process is NOT concerned with evaluation of the model. This process will not immediately run in RapidMiner because you have to adjust the repository path in the Retrieve operator. Tags: Rapidminer, model, learn, learning, training, train, store, first step

Created: 2011-01-17 | Last updated: 2011-01-17

Taverna 2
Uploader
2472?size=60x60 Pl trybik

Workflow Multi-parameter sensitivity analysis (MPSA... (2)

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Exemplary multi-parameter sensitivity analysis (MPSA) experiment using Tav4SB (http://bioputer.mimuw.edu.pl/tav4sb/) WS operations. In this version of MPSA PRISM probabilistic model checking is basis of analysis of SBML model parameters space.

Created: 2011-07-14 | Last updated: 2011-07-21

Credits: User trybik

Taverna 2
Uploader
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel

Workflow Eigen analysis (3)

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The Eigen analysis results are a set of demographic statistics: 1) Lambda or dominant eigenvalue: The population will be stable, grow or decrease at a rate given by lambda: eg: ? = 1 (population is stable), ? > 1 (population is growing) and finally ? < 1 (populatiopn is decreasing) . 2) The stable stage distribution: It is the proportion of the number of individuals per stage and it is given by (w). Elasticity and Sensitivity: Sensitivity and elasticity analyses are prospective analyses....

Created: 2012-11-02 | Last updated: 2014-07-25

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Gerard Oostermeijer

Attributions: Workflow Matrix Population Model construction and analysis v20 Workflow Matrix Population Model analysis v12 Blob Stage Matrix of Gentiana pneumonanthe 1987-88

Taverna 2
Uploader
2577?size=60x60 Ie David PS

Workflow Venus: Compare VEX data with HYB model (1)

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It compares data from VEX from a certain date range with what HYB has modeled in the coordinates where VEX spacecraft is at that moment.

Created: 2013-04-07

Credits: User David PS User Natasha

Taverna 2
Uploader
3194?size=60x60 Hu Ferenc HORVATH
Project Biovel

Workflow Biome-BGC MCE 1.4.1 (4)

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Biome-BGC is a process-based biogeochemical model that can be used to simulate carbon, nitrogen and water fluxes of different terrestrial ecosystems. Two models were implemented: Biome-BGC 4.1.1 MPI (Trusilova et al. 2009) and Biome-BGC MuSo 3.0 (Hidy & Barcza 2014). Its has about 40 and 60 various parameters. The only way to estimate or set these parameters is "calibration" (data-model-harmonization or model-data-fusion), which demands a hugh amount of computational capacity. Monte Carlo Exp...

Created: 2013-06-04 | Last updated: 2014-10-04

Credits: User Ferenc HORVATH User Zoltan BARCZA User Dora Krasser User Peter Ittzes Network-member BioVeL

Taverna 2
Uploader
3194?size=60x60 Hu Ferenc HORVATH
Project Biovel

Workflow Biome-BGC ESI version 1.4.1 (3)

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Biome-BGC is a process-based biogeochemical model that can be used to simulate carbon, nitrogen and water fluxes of different terrestrial ecosystems. The model can help us to quantify a broad range of ecosystem service indicators. These newly developed measures include: annual wood increment, yearly production of grasslands or croplands, total average carbon stock, annual evapotranspiration, damping of ecosystem daily water outflow, living and dead biomass protecting the soil against erosion,...

Created: 2013-08-12 | Last updated: 2014-10-04

Credits: User Ferenc HORVATH User Dora Krasser User Peter Ittzes Network-member BioVeL

Taverna 2
Uploader
2577?size=60x60 Ie David PS

Workflow Interpolate values on planetary models pro... (1)

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This is a simple workflow using one of the webservice provided by IMPEx. It calculates the value of different variables, at the cordinates provided, for a particular planetary model.

Created: 2013-09-10

Credits: User David PS

Taverna 2
Uploader
2577?size=60x60 Ie David PS

Workflow Interpolate values on planetary models pro... (2)

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This is a simple workflow using one of the webservice provided by IMPEx. It calculates the value of different variables, at the cordinates that a spacecraft pass through for the time range provided, for a particular planetary model. The orbital values of the spacecraft are obtained by AMDA.

Created: 2013-09-10 | Last updated: 2013-09-10

Credits: User David PS

Taverna 2
Uploader
2577?size=60x60 Ie David PS

Workflow Particle trajectories in the planetary mod... (1)

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This is a simple workflow using one of the webservice provided by IMPEx. It calculates the particle trajectories for the defined particle (initial position, velocity, mass and charge) for a particular planetary model.

Created: 2013-09-10

Credits: User David PS

Taverna 2
Uploader
2577?size=60x60 Ie David PS

Workflow Vector field lines in the planetary models... (1)

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This is a simple workflow using one of the webservice provided by IMPEx. It calculates the field lines for the vector field requested for the starting points provided for a particular planetary model.

Created: 2013-09-10

Credits: User David PS

Taverna 2
Uploader
2577?size=60x60 Ie David PS

Workflow Interpolate n-randon points in a sphere on... (1)

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This is a workflow that uses 2 different services from IMPEx to calculate different variables at a certain radius for a particular planetary model.

Created: 2013-09-10

Credits: User David PS

Attributions: Workflow Interpolate values on planetary models provided under IMPEx Workflow VOTable on the net maker for IMPEx Workflow Sphere lan-lot random points

Taverna 2
Uploader
2577?size=60x60 Ie David PS

Workflow Get Particle trajectories from starting po... (1)

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This is a workflow that uses 2 different services from IMPEx to calculate different variables at a certain radius for a particular planetary model.

Created: 2013-09-10

Credits: User David PS

Attributions: Workflow Sphere lan-lot random points Workflow Particle trajectories in the planetary models provided under IMPEx Workflow VOTable on the net maker for IMPEx Workflow Interpolate n-randon points in a sphere on a planetary models provided under IMPEx

Taverna 2
Uploader
Avatar Ie Eoincar

Workflow CME froward propagation (1)

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Ballistic propagation of CME is the SHEBA propagation model. CME speed and speed error produces an estimated time of arrival at desired location.Constructed by David Perez Suarez.

Created: 2014-01-13

Credits: User Eoincar

Taverna 2
Uploader
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel

Workflow Parametric Bootstrap or Resample a project... (3)

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The Parametric Bootstrap or Resample a projection matrix Workflow provides an environment to resample a projection matrix using a multinomial distribution for transitions and a log normal distribution for fertilities (Stubben, Milligan, and Nantel. 2011). The resample is based on number of plants surveyed. The projection matrix A is first split into separate transition and fertility matrices. Dead fates are added to the transition matrix and the columns are then sampled from a Multinomial dis...

Created: 2014-06-18 | Last updated: 2014-07-25

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Gerard Oostermeijer

Attributions: Workflow Matrix Population Model analysis v12

Taverna 2
Uploader
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel

Workflow Damping ratio (2)

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The Damping ratio Workflow provides an environment to calculate the damping ratio of several matrices and plot them. The damping ratio can be considered as a measure of the intrinsic resilience of the population, describing how quickly transient dynamics decay following disturbance or perturbation regardless of population structure, the larger the p, the quicker the population converges. ============================================================= This workflow requires an instance of Rse...

Created: 2014-06-25 | Last updated: 2014-07-25

Credits: User Maria Paula Balcazar-Vargas User Mikolaj Krzyzanowski User Jon Giddy User Gerard Oostermeijer

Taverna 2
Uploader
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel

Workflow Simulate stochastic growth from a sequence... (1)

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The Simulate stochastic growth from a sequence of matrices Workflow provides an environment to simulate stochastic growth by projection using whole matrix selection techniques in an independently and identically distributed (iid) environment from a set of 2 or more projection matrices. This workflow is based on the popbio package (script: stoch.projection - Simulate stochastic growth from a sequence of matrices, Stubben, Milligan and Nantel, 2013) based on the The MATLAB code in Box 7.3 (Mo...

Created: 2014-07-30 | Last updated: 2014-08-14

Credits: User Maria Paula Balcazar-Vargas User Mikolaj Krzyzanowski User Jon Giddy User Francisco Quevedo User Gerard Oostermeijer

Taverna 2
Uploader
3194?size=60x60 Hu Ferenc HORVATH
Project Biovel

Workflow Biome-BGC CARBON 1.2 (4)

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Biome-BGC is a process-based biogeochemical model that can be used to simulate carbon, nitrogen and water fluxes of different terrestrial ecosystems. A new version of the model, called Biome-BGC MuSo was developed to perform more realistic simulations in terms of soil hydrology, and improved ecosystem management options essentially (Hidy et al. 2012; Hidy & Barcza 2014). The Biome-BGC CARBON service executes a single simulation run at a given geographic location under that distinctive environ...

Created: 2013-06-04 | Last updated: 2015-06-12

Credits: User Ferenc HORVATH User Dora Krasser User Peter Ittzes User Zoltan BARCZA Network-member BioVeL

Attributions:

KNIME
Uploader
4528?size=60x60 In Insilic...

Workflow Antiviral activity multiclass Predictor (1)

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A simple multi-class antiviral activity predictor based on expanded Pubchem fingerprints and random forest algorithm. Seems to work well to perform quick screens for antiviral molecules.Download training data from CTD (http://ctdbase.org/downloads/) or  use this preprocessed version https://www.myexperiment.org/files/2285.html. Write to me at rajeev.gangal@gmail.com regarding any queries.I make no claim that the predictive model is accurate for clinical hypotheses or that it will find mo...

Created: 2020-03-23 | Last updated: 2020-03-25

Credits: User Insilicoconsulting

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Linked Data

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