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The Biovel Project: Robust phylogenetic workflows running on the GRID

The Biovel Project: Robust phylogenetic workflows running on the GRID. www.biovel.eu. Bachir Balech (IBBE-CNR). The Biovel Project.

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The Biovel Project: Robust phylogenetic workflows running on the GRID

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  1. The Biovel Project: Robustphylogeneticworkflowsrunning on the GRID www.biovel.eu Bachir Balech (IBBE-CNR)

  2. The Biovel Project • BioVeL is a virtual e-laboratory that supports research on Biodiversity issues using large amounts of data from cross-disciplinary sources. It is a consortium of 15 partners from 9 countries, as well as an outer circle of ‘Friends of BioVeL’ • Access a worldwide network of expert scientists • Sharing knowledge on Biodiversity research • BiodiversityIssues • Species identification, discovery and distributions • The changing nature of ecosystems altering organismal composition • The increased risks of species extinction Decisionmaking in biodiversity management at multiple scales (genomic, organismal, habitat, ecosystem, landscape, etc…)

  3. Biodiversity Solutions • Services: data processing techniques. Each technique is available as a single executable application which can be used either alone or within a workflow builder environment (e.g. Taverna) • Workflows: examples of services use that can be modified • Services and Workflows for Biodiversity Analysis: • Taxonomy • Phylogenetics • Metagenomics • Ecological Niche Modeling • Ecosystem Functioning and Valuation • Geospatial Visualization Services Sharing Workflows

  4. Example of Phylogenetic Services Job Submission Tool Alignment Phylogeny Inference

  5. Job Sumbission Tool: JST • Frontend: • Username • Task status • Dependencies of each task • Priority • Job provenance • Task description • Number of failures • Date and time of execution • Infrastructure information (grid, local farm, interactive server) • Backend: • Task submission at a given rate • Stops jobs submission when no more unassigned tasks are found in the TaskList

  6. Multiple Sequence Alignment Workflow

  7. Multiple Sequence Alignment Workflow Multiple Alignment of DNA coding File upload Translation • Higheralignmentprecisiongiven by: • HMM searchassigning a per site quality score (posteriorprobability) • Back-align (amino acid -> DNA) HMM search Pfam profile selection HMM align & Back-align In progress: Multiple Domain Coding sequences Alignment

  8. Example Phylogenetic Inference Workflow

  9. Example Phylogenetic Inference Workflow in Taverna MrBayes Web Interface • Peculiarity: • Partitionedmodels • Convergencecalculation • Short Computation time on the Grid (even for long jobs) Bayesian Phylogeny Computation & Output Retrieval GeoKS Execution Consensus Tree Calculation • OtheravailablePhylogenetic Services: • Maximum Likelihood (RaxML) • PhylogeneticDiversity (Phylocom) Tree Visualization

  10. Acknowlegments ICT specialists Dr. Giacinto DONVITO Dr. Pasquale NOTARANGELO Bioinformatic Scientists Prof. Graziano Pesole Dr. Saverio Vicario Funding: European Commission 7th Framework Programme (FP7), through the grant agreement: 283359

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