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

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.

[1]  Arcadi Navarro,et al.  The European Genome-phenome Archive of human data consented for biomedical research , 2015, Nature Genetics.

[2]  Byungkyu Brian Park,et al.  DBBP: database of binding pairs in protein-nucleic acid interactions , 2014, BMC Bioinformatics.

[3]  M. Orozco,et al.  Triplex-forming oligonucleotide target sequences in the human genome. , 2004, Nucleic acids research.

[4]  Alexander S. Rose,et al.  NGL Viewer: a web application for molecular visualization , 2015, Nucleic Acids Res..

[5]  Heinz Sklenar,et al.  Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps. , 2004, Biophysical journal.

[6]  Modesto Orozco,et al.  Multiscale simulation of DNA. , 2016, Current opinion in structural biology.

[7]  Feng Ding,et al.  Multiscale modeling of nucleosome dynamics. , 2007, Biophysical journal.

[8]  Richard Lavery,et al.  Towards a molecular view of transcriptional control. , 2012, Current opinion in structural biology.

[9]  Sergei A. Spirin,et al.  NPIDB: nucleic acid—protein interaction database , 2012, Nucleic Acids Res..

[10]  Robert Petryszak,et al.  ArrayExpress update—simplifying data submissions , 2014, Nucleic Acids Res..

[11]  David A. Case,et al.  μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA , 2014, Nucleic acids research.

[12]  Modesto Orozco,et al.  Unravelling the hidden DNA structural/physical code provides novel insights on promoter location , 2013, Nucleic acids research.

[13]  John Chilton,et al.  The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update , 2016, Nucleic Acids Res..

[14]  Sergio Pantano,et al.  A Coarse Grained Model for Atomic-Detailed DNA Simulations with Explicit Electrostatics. , 2010, Journal of chemical theory and computation.

[15]  Modesto Orozco,et al.  Determining promoter location based on DNA structure first-principles calculations , 2007, Genome Biology.

[16]  Baris E. Suzek,et al.  The Universal Protein Resource (UniProt) in 2010 , 2009, Nucleic Acids Res..

[17]  Jordi Torres,et al.  PyCOMPSs: Parallel computational workflows in Python , 2016, Int. J. High Perform. Comput. Appl..

[18]  Marta Bleda,et al.  Genome Maps, a new generation genome browser , 2013, Nucleic Acids Res..

[19]  Carlos Prieto,et al.  D3GB: An Interactive Genome Browser for R, Python, and WordPress , 2017, J. Comput. Biol..

[20]  David Haussler,et al.  The UCSC Genome Browser database: 2018 update , 2017, Nucleic Acids Res..

[21]  Thomas Cremer,et al.  Multicolor 3D fluorescence in situ hybridization for imaging interphase chromosomes. , 2008, Methods in molecular biology.

[22]  Suzanna E Lewis,et al.  JBrowse: a dynamic web platform for genome visualization and analysis , 2016, Genome Biology.

[23]  Xiang-Jun Lu,et al.  3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures , 2008, Nature Protocols.

[24]  Guy Cochrane,et al.  The International Nucleotide Sequence Database Collaboration , 2011, Nucleic Acids Res..

[25]  A. Mortazavi,et al.  Genome-Wide Mapping of in Vivo Protein-DNA Interactions , 2007, Science.

[26]  J. Dekker,et al.  Capturing Chromosome Conformation , 2002, Science.

[27]  G. Cochrane,et al.  The International Nucleotide Sequence Database Collaboration , 2011, Nucleic Acids Res..

[28]  Michael Q. Zhang,et al.  NONCODEV5: a comprehensive annotation database for long non-coding RNAs , 2017, Nucleic Acids Res..

[29]  Byungwook Lee,et al.  3DIV: A 3D-genome Interaction Viewer and database , 2017, Nucleic Acids Res..

[30]  Srinivas Ramachandran,et al.  Precise genome-wide mapping of single nucleosomes and linkers in vivo , 2018, Genome Biology.

[31]  Modesto Orozco,et al.  Nucleosome architecture throughout the cell cycle , 2016, Scientific Reports.

[32]  Helmut Schiessel,et al.  Physics behind the mechanical nucleosome positioning code. , 2017, Physical review. E.

[33]  Zhihua Zhang,et al.  Delta: a new web-based 3D genome visualization and analysis platform , 2018, Bioinform..

[34]  Modesto Orozco,et al.  Exploring polymorphisms in B-DNA helical conformations , 2012, Nucleic acids research.

[35]  James T. Robinson,et al.  Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom. , 2016, Cell systems.

[36]  Jordi Torres,et al.  BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data , 2015, Nucleic Acids Res..

[37]  Marc A Marti-Renom,et al.  Challenges for visualizing three‐dimensional data in genomic browsers , 2017, FEBS letters.

[38]  Ting Wang,et al.  Exploring long-range genome interactions using the WashU Epigenome Browser , 2013, Nature Methods.

[39]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer , 2011, Nature Biotechnology.

[40]  Helga Thorvaldsdóttir,et al.  The GenePattern Notebook Environment. , 2017, Cell systems.

[41]  Modesto Orozco,et al.  Fuzziness and noise in nucleosomal architecture , 2014, Nucleic acids research.

[42]  Haruki Nakamura,et al.  The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data , 2006, Nucleic Acids Res..

[43]  Carlos González,et al.  NAFlex: a web server for the study of nucleic acid flexibility , 2013, Nucleic Acids Res..

[44]  María Martín,et al.  The Universal Protein Resource (UniProt) in 2010 , 2010 .

[45]  Domenico Talia,et al.  ServiceSs: An Interoperable Programming Framework for the Cloud , 2013, Journal of Grid Computing.

[46]  D. Case,et al.  A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA , 2009, Nucleic acids research.