EcoPath with EcoSim repository

229 EwE models available for download
496 EwE models with metadata
0 EwE pending model(s)

What is EcoBase?

EcoBase is an open-access database of Ecopath with Ecosim (EwE) models published worldwide in the scientific literature. More precisely, EcoBase is an information repository of EwE models freely accessible online here or via the free EwE software - version 6.5.

Who manages EcoBase?

EcoBase was created in 2015 by a group of scientists interested in conducting global meta-analyses based on existing EwE models . Since 2014, EcoBase is managed and supported by the members of the Model repository working group of the Ecopath Research and Development Consortium (ERDC) . The ERDC is a global, cooperative network focused on the research, development and sustainability of the EwE approach and software, its information basis, and complementary activities and capabilities.

What is EcoBase for?

EcoBase was created with the intention of making EwE models discoverable, accessible, and reusable to the scientific community, as soon as they are published. Only the Ecopath models are freely accessible at this stage (Ecosim and Ecospace parameters are not available). The main goals of EcoBase are to:

1. Provide a comprehensive and up-to-date list of EwE models and EwE-based publications;
2. Gather information from the referenced models and publications, and notably critical metadata ;
3. Facilitate the search, sharing and reuse of published EwE models for future studies;
4. Enhance interactions and collaborations within the scientific community, and particularly the EwE community.

Why using EcoBase?

If you are not yet an EwE user… then let’s briefly introduce EwE: EwE is a modeling software offering a wide range of different tools and allowing analyses of various ecological phenomena, which is why it has been applied to hundreds of ecosystems worldwide. Building EwE models require the collection, compilation and harmonization of various types of information on these ecosystems. Thus, a large amount of data has been gathered in EwE-based studies.
If you already are an EwE user… then you know that: Building EwE models help summarizing available knowledge on the ecosystems of interest and deriving various ecosystem properties, so that EwE applications may be seen as an important source of data.

EcoBase offers a framework where these data may be properly stored, so that they can be properly reused for future applications, such as models comparisons, meta-analyses, etc.

How to use EcoBase?

You may use EcoBase by following these 5 simple steps:

1. Go to Discovery tools
2. Read and agree with the EcoBase data access agreement
3. Look for your models of interest, either by scrolling and zooming in on the interactive map, or by searching for keywords in the metadata and references tables
4. Click on the name of the models to access to the their reference cards, which provide associated metadata (including references and maps) and available data
5. Within EwE click File ---> import models ---> import from Ecobase and pick the model you want to use

How to contribute to EcoBase?

If you are willing to share an EwE model you recently developed and published, please use the EcoBase export plug-in available in the new version of the EwE software (v6.5). If you encounter any problem, please contact the EcoBase administrator at jerome.guitton@agrocampus-ouest.fr so that your model may be added to the more than 500 models currently referenced in EcoBase.

Documentation and dataset

script to play with EcoBase

#To get the list of available Ewe models

library(RCurl)
library(XML)
library(plyr)
library(dplyr)


#To obtain the list of available model
h=basicTextGatherer()
curlPerform(url = 'http://sirs.agrocampus-ouest.fr/EcoBase/php/webser/soap-client_3.php',writefunction=h$update)

data<-xmlTreeParse(h$value(),useInternalNodes=TRUE)
liste_mod<-ldply(xmlToList(data),data.frame)%>% filter(model.dissemination_allow =='true')
        
#liste_mod contains a list and decription of available models in EcoBase

#To get the input values for model mymodel - 403 

library(RCurl)
library(XML)
library(plyr)


h=basicTextGatherer()
mymodel<-403
curlPerform(url = paste('http://sirs.agrocampus-ouest.fr/EcoBase/php/webser/soap-client.php?no_model=',mymodel,sep=''),writefunction=h$update,verbose=TRUE)


data<-xmlTreeParse(h$value(),useInternalNodes=TRUE)

input1<-xpathSApply(data,'//group',function(x) xmlToList(x))

#To get the ouptput values for model mymodel - 403 

library(RCurl)
library(XML)
library(plyr)

#To Obtain a model - output
h=basicTextGatherer()
mymodel<-403

curlPerform(url = paste('http://sirs.agrocampus-ouest.fr/EcoBase/php/webser/soap-client_output.php?no_model=',mymodel,sep=''),writefunction=h$update,verbose=TRUE)


data<-xmlTreeParse(h$value(),useInternalNodes=TRUE)

output1<-xpathSApply(data,'//group',function(x) xmlToList(x))

Publications about EcoBase and associated supplementary material

COLLETER, M. VALLS, A. GUITTON, J. MORISSETTE, L. ARREGUIN-SANCHEZ, F. CHRISTENSEN, V. GASCUEL, D. PAULY, D., 2013. EcoBase: a repository solution to gather and communicate information from EwE models. Fisheries Centre Research Report (FCRR), 21(1)
COLLETER, M. VALLS, A. GUITTON, J. GASCUEL, D. PAULY, D. CHRISTENSEN, V., 2015. Global overview of the applications of the Ecopath with Ecosim modeling approach using the EcoBase models repository. Ecological Modelling, 302: 42-53

You will be able to find here the datasets used in the article "Global overview of the applications of the Ecopath with Ecosim modeling approach using the EcoBase model repository" submitted for publication in Ecological Modelling:

229 EwE models available for download 496 EwE models with metadata 0 EwE pending model(s)