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EcosystModelSchemeIntroduction to using BioVeL workflows and Biome-BGC Project database for terrestrial ecosystem modelling, carbon sequestration and ecosystem service quantification studies



29-30 May 2014, Budapest, Hungary
The workshop will take place on 29-30 of May, 2014 in the heart of Budapest (venue and accomodation will be defined later). The number of participants is limited in 12-15 persons. The training registration/participation is free of charge, but attendees have to cover travel and accomodation costs.

Biogeochemical models are widely used to simulate functioning of terrestrial ecosystems. These process-based models are well representing the key ecophysiological and biogeochemical processes (e.g. photosynthesis; autotrophic respiration; soil organic matter decomposition; environmental stress limitation, etc.); the most important ecosystem pools (e.g. foliage; aboveground and belowground biomass compartments; soil water content, etc.); and a number of energy, water and carbon fluxes in details. Ecophysiological parameters specific to plant functional types (e.g. broadleaved trees) are used to tune appropriately these models, while forest monitoring or ecosystem scale flux measurements can provide independent datasets for calibration and validation. However model–data–fusion and application of these models are still difficult to achieve as it requires ecologists and environmental scientists to integrate their expertise, data, and methodologies across the traditional biological disciplines.

The Biodiversity Virtual e-Laboratory, BioVeL, addresses this challenge by having scientists and computer engineers working together to develop tools for pipelining data and analysis into efficient analytical pipelines, called "workflows." Workflows are complex digital data manipulations and modelling tasks that execute sequences of web services. BioVeL designs and deploys such workflows for a selected number of important areas in biodiversity and ecological research, e.g. for the analysis of data sets with ecological, taxonomic, phylogenetic, and environmental information.

BioVeL ecosystem modelling, carbon sequestration and ecosystem service indicator workflows and Biome-BGC Projects database allow researchers to:

(i) manage Biome-BGC investigations, and all related parameter, input and output datasets;
(ii) run two different versions of the Biome-BGC model; and
(iii) run complex and computationally intense analytical cycles; and
(iv) generate quantitative ecosystem service indicators of different biomes under various environmental conditions.


Workshop Objective
The training workshop will teach the attendees in using the informatic tools and services developed by the BioVeL project to address various analysis schemes of model–data–fusion framework or model applications for carbon sequestration or quantification of ecosystem service indicators. In particular, there will be introductions to the BioVeL e-infrastructure, model characterization by Sensitivity Analysis through Monte-Carlo Experiment, parameter estimation by GLUE method, and applying different management options.


After completion of course the participants are expected to be able to:

  • Understand the main processes and model representation of various terrestrial ecosystems
  • Carry out ecosystem modelling simulations depending on site options, environmental and climatic changes, under various management options according to different climate scenarios

Required preparation

  • Participants need to bring their own laptops. All workflows offered will be browser-based and don’t need any desktop installations. However it is optional to install and use also the Taverna Workbench for manage and develop scientific workflows from your personal computer.
  • Scientists should/may bring their own data and/or should/may have identified accessible data sources (site, meteorology – consult it with the organizers), but sample data sets will be provided with each workflow.

Target community & qualifications
This workshop is designed for scientists with a solid background in any of the relevant areas in global or regional ecology, landscape ecology, ecosystem research, forest or grassland monitoring, environmental sciences or vegetation aspects of climatology. It is desirable that the attendees are working or planning to work with climate change-related ecosystem impact studies, quantifying ecosystem services, analysis of various aspects of primary productions.




Contact Ferenc Horváth,




19 February 2015

At the final review of the project by the EC, one of the reviewers said: “Incredible work done with a community that is not unified. Remarkable work. It opens for new development in a near future. Hope for success. Good project. Happy that you have been financed three plus years ago.”

Read all about the project and its results in the Project Final Report or read the Executive Summary only.