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

Codo, L.; Bayarri, G.; Alvarex-Cid-Fuentes, J.; Conejero, J.; Hospital, A.; Royo, R.; Repchevsky, D.; Pasi, M.; Meletiou, A.; McDowall, M. D.; Reham, F.; Alcantara, J. A.; Jimenez-Garcia, B.; Walther, J.; Illa, R.; Serra, F.; Goodstadt, M.; Castillo, D.; Sati, S.; Buitrago, D.; Brun-Heath, I.; Fernandez-Recio, J.; Cavalli, G.; Marti-Renom, M. A.; Yates, A.; Laughton, C. A.; Badia, R. M.; Orozco, M.; Gelpi, J. L.

doi:10.1101/602474

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bioRxiv · 10.1101/602474

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

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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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Codo, L., Bayarri, G., Alvarex-Cid-Fuentes, J., Conejero, J., Hospital, A., Royo, R., Repchevsky, D., Pasi, M., Meletiou, A., McDowall, M. D., Reham, F., Alcantara, J. A., Jimenez-Garcia, B., Walther, J., Illa, R., Serra, F., Goodstadt, M., Castillo, D., Sati, S., Buitrago, D., Brun-Heath, I., Fernandez-Recio, J., Cavalli, G., Marti-Renom, M. A., Yates, A., Laughton, C. A., Badia, R. M., Orozco, M., Gelpi, J. L.. 2019-04-09. MuGVRE. A virtual research environment for 3D/4D genomics. https://doi.org/10.1101/602474

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