FedCloudOPENMODELLER

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General Information

Short Description

BioVeL is a virtual e-laboratory that supports research on biodiversity issues using large amounts of data from cross-disciplinary sources. BioVeL offers the possibility to use computerised "workflows" (series of data analysis steps) to process data, be that from one's own research and/or from existing sources. BioVeL is funded through the European Community 7th Framework Programme and is free and available to use via the Internet.

OpenModeller (oM) is a generic framework that includes various modelling algorithms and which is compatible with different data formats. Its functionality is available through command line, desktop and web services interfaces, allowing integration with other specialized services that could help for example finding input data for the modelling process. The CRIA institute in Brazil operates an oM server. The server implements the oM web service API and runs as a CGI application. This use case aims to setup and operate an instance of the web service in Europe using resources from the EGI Federated Cloud and from the EGI Service Availability Monitoring infrastructure. The instance would serve the Biodiversity Virtual e-Laboratory (BioVel) that supports research on biodiversity issues using large amounts of data from cross-disciplinary sources. EUBrazilOpenBio is a project aiming to deploy an open-access platform from the federation and integration of existing European and Brazilian infrastructures and resources. The cloud-enabled ENM Service developed in EU-BrazilOpenBio, allows the execution of ENM workflows through the EU-BrazilOpenBio Gateway and through the Workflow Management System available in the BioVeL project. A new application, developed as part of EU-BrazilOpenBio, allows scientists to carry out complex experiments leveraging the openModeller environment and generating models for a large number of species, using complex modelling strategies and involving several algorithms and high-resolution environmental data. The application exploits the interoperability features of the COMPSs middleware aggregating computational resources available to the projects through the EGI Cloud Federation.

http://openmodeller.sourceforge.net/

Use Case

Requirements

Tasks:

  1. Assess BioVeL requirements (complete)
  2. Initial setup of an oM instance in one FedCloud RP (complete; not using FedCloud standards though)
  3. Adopt FedCloud standards
    • provide oM SOAP service end-point (done by EUBrazilOpenBio)
    • test service endpoint (complete)
    • provide OCCI connector to EGI FedCloud (complete)
  4. Optimize the resource allocation in order to reduce the overhead of VMs creation (COMPSs level)
    • deploy the application as a service (testing)
    • static pool of initial VMs to execute oM requests and dynamically create new VMs if overloaded

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