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MuGVRE. A virtual research environment for 3D/4D genomics

Laia Codó, Genís Bayarri, Javier Alvarez Cid-Fuentes, Javier Conejero, Adam Hospital, Romina Royo, Dmitry Repchevsky, Marco Pasi, Athina Meletiou, Mark D. McDowall, Fatima Reham, José A. Alcantara, Brian Jimenez-Garcia, Jürgen Walther, Ricard Illa, François Serra, Michael Goodstadt, David Castillo, Satish Sati, Diana Buitrago, Isabelle Brun-Heath, Juan Fernandez-Recio, Giacomo Cavalli, Marc Marti-Renom, Andrew Yates, Charles A. Laughton, Rosa M. Badia, Modesto Orozco, Josep Ll. Gelpí
doi: https://doi.org/10.1101/602474
Laia Codó
1Barcelona Supercomputing Center, Barcelonar, Spain
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Genís Bayarri
2Institute for Research in Biomedicine, the Barcelona Institute of Science and Technology. Barcelona, Spain
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Javier Alvarez Cid-Fuentes
1Barcelona Supercomputing Center, Barcelonar, Spain
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Javier Conejero
1Barcelona Supercomputing Center, Barcelonar, Spain
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2Institute for Research in Biomedicine, the Barcelona Institute of Science and Technology. Barcelona, Spain
Romina Royo
1Barcelona Supercomputing Center, Barcelonar, Spain
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Dmitry Repchevsky
1Barcelona Supercomputing Center, Barcelonar, Spain
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Marco Pasi
3Sch. of Pharmacy and Centre for Biomolecular Sciences, Nottingham, UK
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Athina Meletiou
3Sch. of Pharmacy and Centre for Biomolecular Sciences, Nottingham, UK
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Mark D. McDowall
4European Molecular Biological Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
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Fatima Reham
4European Molecular Biological Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
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José A. Alcantara
2Institute for Research in Biomedicine, the Barcelona Institute of Science and Technology. Barcelona, Spain
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Brian Jimenez-Garcia
1Barcelona Supercomputing Center, Barcelonar, Spain
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Jürgen Walther
2Institute for Research in Biomedicine, the Barcelona Institute of Science and Technology. Barcelona, Spain
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Ricard Illa
2Institute for Research in Biomedicine, the Barcelona Institute of Science and Technology. Barcelona, Spain
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François Serra
5CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain. Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain. Universitat Pompeu Fabra (UPF), Barcelona, Spain
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Michael Goodstadt
5CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain. Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain. Universitat Pompeu Fabra (UPF), Barcelona, Spain
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David Castillo
5CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain. Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain. Universitat Pompeu Fabra (UPF), Barcelona, Spain
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Satish Sati
6Institute of Human Genetics, CNRS, Univ. Montpellier, Montpellier, France
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Diana Buitrago
2Institute for Research in Biomedicine, the Barcelona Institute of Science and Technology. Barcelona, Spain
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Isabelle Brun-Heath
2Institute for Research in Biomedicine, the Barcelona Institute of Science and Technology. Barcelona, Spain
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Juan Fernandez-Recio
1Barcelona Supercomputing Center, Barcelonar, Spain
7ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
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Giacomo Cavalli
6Institute of Human Genetics, CNRS, Univ. Montpellier, Montpellier, France
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Marc Marti-Renom
5CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain. Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain. Universitat Pompeu Fabra (UPF), Barcelona, Spain
8Dept. of Biochemistry and Molecular Biomedicine, University of Barcelona, Barcelona, Spain
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Andrew Yates
4European Molecular Biological Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
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Charles A. Laughton
3Sch. of Pharmacy and Centre for Biomolecular Sciences, Nottingham, UK
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Rosa M. Badia
1Barcelona Supercomputing Center, Barcelonar, Spain
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Modesto Orozco
2Institute for Research in Biomedicine, the Barcelona Institute of Science and Technology. Barcelona, Spain
8Dept. of Biochemistry and Molecular Biomedicine, University of Barcelona, Barcelona, Spain
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Josep Ll. Gelpí
1Barcelona Supercomputing Center, Barcelonar, Spain
8Dept. of Biochemistry and Molecular Biomedicine, University of Barcelona, Barcelona, Spain
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  • For correspondence: gelpi@ub.edu
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ABSTRACT

Multiscale Genomics (MuG) Virtual Research Environment (MuGVRE) is a cloud-based computational infrastructure created to support the deployment of software tools addressing the various levels of analysis in 3D/4D genomics. Integrated tools tackle needs ranging from high computationally demanding applications (e.g. molecular dynamics simulations) to high-throughput data analysis applications (like the processing of next generation sequencing). The MuG Infrastructure is based on openNebula cloud systems implemented at the Institute for research in Biomedicine, and the Barcelona Supercomputing Center, and has specific interfaces for users and developers. Interoperability of the tools included in MuGVRE is maintained through a rich set of metadata allowing the system to associate tools and data in a transparent manner. Execution scheduling is based in a traditional queueing system to handle demand peaks in applications of fixed needs, and an elastic and multi-scale programming model (pyCOMPSs, controlled by the PMES scheduler), for complex workflows requiring distributed or multi-scale executions schemes. MuGVRE is available at https://vre.multiscalegenomics.eu and documentation and general information at https://www.multiscalegenomics.eu. The infrastructure is open and freely accessible.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted April 09, 2019.
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MuGVRE. A virtual research environment for 3D/4D genomics
Laia Codó, Genís Bayarri, Javier Alvarez Cid-Fuentes, Javier Conejero, Adam Hospital, Romina Royo, Dmitry Repchevsky, Marco Pasi, Athina Meletiou, Mark D. McDowall, Fatima Reham, José A. Alcantara, Brian Jimenez-Garcia, Jürgen Walther, Ricard Illa, François Serra, Michael Goodstadt, David Castillo, Satish Sati, Diana Buitrago, Isabelle Brun-Heath, Juan Fernandez-Recio, Giacomo Cavalli, Marc Marti-Renom, Andrew Yates, Charles A. Laughton, Rosa M. Badia, Modesto Orozco, Josep Ll. Gelpí
bioRxiv 602474; doi: https://doi.org/10.1101/602474
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MuGVRE. A virtual research environment for 3D/4D genomics
Laia Codó, Genís Bayarri, Javier Alvarez Cid-Fuentes, Javier Conejero, Adam Hospital, Romina Royo, Dmitry Repchevsky, Marco Pasi, Athina Meletiou, Mark D. McDowall, Fatima Reham, José A. Alcantara, Brian Jimenez-Garcia, Jürgen Walther, Ricard Illa, François Serra, Michael Goodstadt, David Castillo, Satish Sati, Diana Buitrago, Isabelle Brun-Heath, Juan Fernandez-Recio, Giacomo Cavalli, Marc Marti-Renom, Andrew Yates, Charles A. Laughton, Rosa M. Badia, Modesto Orozco, Josep Ll. Gelpí
bioRxiv 602474; doi: https://doi.org/10.1101/602474

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