Internet Archive Scholar

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

Laia Codo, Genis Bayarri, Javier Alvarex-Cid-Fuentes, Javier Conejero, Adam Hospital, Romina Royo, Dmitry Repchevsky, Marco Pasi, Athina Meletiou, Mark D. McDowall, Fatima Reham, Jose A. Alcantara (+17 others)
2019 bioRxiv   pre-print

Preserved Fulltext

fulltext thumbnail
Web Archive Capture PDF (1.9 MB)
https://web.archive.org/web/20190502013408/https://www.biorxiv.org/content/biorxiv/early/2019/04/09/602474.full.pdf

A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL. The file type is application/pdf.

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
more » ... ystems 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/MuGVRE/. The infrastructure is open and freely accessible.
doi:10.1101/602474 fatcat:ikxzgfug55dlznv6lxd5fqb3ae
Citation

Laia Codo, Genis Bayarri, Javier Alvarex-Cid-Fuentes, Javier Conejero, Adam Hospital, Romina Royo, Dmitry Repchevsky, Marco Pasi, Athina Meletiou, Mark D. McDowall, Fatima Reham, Jose A. Alcantara, Brian Jimenez-Garcia, Jurghen Walther, Ricard Illa, Francois Serra, Michael Goodstadt, David Castillo, Satish Sati, Diana Buitrago, Isabelle Brun-Heath, Juan Fernandez-Recio, Giacomo Cavalli, Marc A. Marti-Renom, Andrew Yates, Charles A Laughton, Rosa M. Badia, Modesto Orozco, Josep Ll. Gelpi. "MuGVRE. A virtual research environment for 3D/4D genomics." bioRxiv (2019)