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MuG
Multi-Scale Complex Genomics
Total Cost €
0EC-Contrib. €
0Partnership
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0MuG project word cloud
Explore the words cloud of the MuG project. It provides you a very rough idea of what is the project "MuG" about.
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Project "MuG" data sheet
The following table provides information about the project.
| Coordinator |
FUNDACIO INSTITUT DE RECERCA BIOMEDICA (IRB BARCELONA)
Organization address contact info |
| Coordinator Country | Spain [ES] |
| Project website | http://www.multiscalegenomics.eu |
| Total cost | 2˙961˙163 € |
| EC max contribution | 2˙961˙163 € (100%) |
| Programme |
1. H2020-EU.1.4.1.3. (Development, deployment and operation of ICT-based e-infrastructures) |
| Code Call | H2020-EINFRA-2015-1 |
| Funding Scheme | RIA |
| Starting year | 2015 |
| Duration (year-month-day) | from 2015-11-01 to 2018-10-31 |
Partnership
Take a look of project's partnership.
| # | ||||
|---|---|---|---|---|
| 1 | FUNDACIO INSTITUT DE RECERCA BIOMEDICA (IRB BARCELONA) | ES (BARCELONA) | coordinator | 668˙625.00 |
| 2 | EUROPEAN MOLECULAR BIOLOGY LABORATORY | DE (HEIDELBERG) | participant | 567˙955.00 |
| 3 | FUNDACIO CENTRE DE REGULACIO GENOMICA | ES (BARCELONA) | participant | 510˙695.00 |
| 4 | BARCELONA SUPERCOMPUTING CENTER - CENTRO NACIONAL DE SUPERCOMPUTACION | ES (BARCELONA) | participant | 470˙250.00 |
| 5 | CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS | FR (PARIS) | participant | 408˙091.00 |
| 6 | THE UNIVERSITY OF NOTTINGHAM | UK (NOTTINGHAM) | participant | 335˙547.00 |
Map
Project objective
Genomics is probably the fastest evolving field in current science. A decade ago our main concern was to obtain the sequence (the 1D code) of the genome; but today the big challenges are to determine how genotype information is transferred into phenotype, and how pathological phenotypic changes can be predicted from genome alterations. While investigating these points, we have realized that a part of the regulation of gene expression is implicitly coded in the way in which chromatin is folded. As technology has advanced and information of the folded state of chromatin has emerged, a new branch of genomics (3D/4D genomics) has emerged. Hundreds of laboratories are now defining a young and active community that, though in the end concerned with the same scientific problem, uses many different approaches to study it that individually target radically different length and timescales. The community faces severe practical problems related to: i) how huge, noisy, and diverse data related to widely different size and time scales can be integrated, ii) the lack of standardized analysis and simulation tools, iii) the complete disconnection of associated informatics databases, and iv) the lack of validated and flexible visualization engines. MuG is born at the critical point in the evolution of the field, in a bottom-up approach from the biologist who are suffering severe IT problemes. MuG, supported by European leaders in the field, join three different expertise: biologist with interest in chromatin structure, methods developers and HPC facilities with strong history of supporting Bio-computational problems. We believe that MuG will be a steep-forward in approaching the potential of High Performance Computing to the development of 3D/4D genomics, and will contribute to give a structure to this new and exciting field.
Deliverables
| Project Handbook | Documents, reports | 2019-06-29 10:36:49 |
| A critical evaluation of the problems on data structure the browser has to solve | Demonstrators, pilots, prototypes | 2019-06-29 10:36:48 |
| Software tools of Protein-DNA interactions | Other | 2019-06-29 10:36:49 |
| A browser-track that implements and connects all the 2D data from a genome or a genomic domain | Demonstrators, pilots, prototypes | 2019-06-29 10:36:49 |
| Pipelines design & implementation | Documents, reports | 2019-06-29 10:36:48 |
| Plan for Dissemination and Use of Knowledge | Documents, reports | 2019-06-29 10:36:48 |
| Data Management Plan | Documents, reports | 2019-06-29 10:36:48 |
| Project Fact Sheet | Websites, patent fillings, videos etc. | 2019-06-29 10:36:48 |
| Database and ETL design & implementation | Documents, reports | 2019-06-29 10:36:48 |
| Initial Exploitation plan based on market knowledge | Documents, reports | 2019-06-29 10:36:49 |
| A requirement specification document with the data types, processing and data models needed | Documents, reports | 2019-06-29 10:36:48 |
| Preliminary browser-track that implements and connects all the 3D data from a genome or a genomic domain | Demonstrators, pilots, prototypes | 2019-06-29 10:36:48 |
| Monitoring of the Plan for Dissemination and Use of Knowledge | Documents, reports | 2019-06-29 10:36:49 |
| Computational infrastructure set-up z | Documents, reports | 2019-06-29 10:36:49 |
| A browser-track that implements and connects all the 1D data from a genome or a genomic domain | Demonstrators, pilots, prototypes | 2019-06-29 10:36:48 |
| Quality Plan | Documents, reports | 2019-06-29 10:36:48 |
| Project Website | Websites, patent fillings, videos etc. | 2019-06-29 10:36:49 |
| Design of computational architecture of software modules | Documents, reports | 2019-06-29 10:36:48 |
| Final Exploitation plan based on market knowledge | Documents, reports | 2019-06-29 10:36:47 |
| Final computational infrastructure and its components | Demonstrators, pilots, prototypes | 2019-06-29 10:36:47 |
| Report on the use of MuG VRE on the senescence project | Documents, reports | 2019-06-29 10:36:47 |
| Project’s outputs | Documents, reports | 2019-06-29 10:36:47 |
| Benchmarks & documentation | Documents, reports | 2019-06-29 10:36:47 |
| A first prototype of analysis tools for mining of the data provided by the browser | Demonstrators, pilots, prototypes | 2019-06-29 10:36:47 |
| Report on the MuG training programme | Documents, reports | 2019-06-29 10:36:47 |
| Report on the use of MuG VRE on the integration of DNA simulation data | Documents, reports | 2019-06-29 10:36:47 |
| Data access API specification & implementation | Documents, reports | 2019-06-29 10:36:47 |
| Software tools linking multiresolution structural and simulation data | Other | 2019-06-29 10:36:47 |
| A 3D genome browser connecting all the 1D-2D-3D tracks. The browser will allow different renderings of the upload coordinates | Demonstrators, pilots, prototypes | 2019-06-29 10:36:47 |
| Report on the use of MuG VRE on integration of whole yeast genome data | Documents, reports | 2019-06-29 10:36:47 |
| Tailored Implementation of browser to support pilot projects in WP7, including the interface with the Yeast Genome viewer | Demonstrators, pilots, prototypes | 2019-06-29 10:36:47 |
| Software tools linking multiresolution structural & simulation data | Other | 2019-06-29 10:36:47 |
| Computational infrastructure components implementation | Documents, reports | 2019-06-29 10:36:47 |
| Software tools on 3C interaction data | Other | 2019-06-29 10:36:47 |
Take a look to the deliverables list in detail: detailed list of MuG deliverables.
Publications
| year | authors and title | journal | last update |
|---|---|---|---|
| 2016 |
Pablo D Dans, Jürgen Walther, Hansel Gómez, Modesto Orozco Multiscale simulation of DNA published pages: 29-45, ISSN: 0959-440X, DOI: 10.1016/j.sbi.2015.11.011 |
Current Opinion in Structural Biology 37 | 2019-07-08 |
| 2016 |
Darré, Leonardo; Ivani, Ivan; Dans, Pablo D.; Gómez, Hansel; Hospital, Adam; Orozco, Modesto Small Details Matter: The 2\'-Hydroxyl as a Conformational Switch in RNA published pages: , ISSN: 0002-7863, DOI: 10.1021/jacs.6b09471 |
Journal of the American Chemical Society 4 | 2019-07-08 |
| 2017 |
Yuri B. Schwartz, Giacomo Cavalli Three-Dimensional Genome Organization and Function in Drosophila published pages: 5-24, ISSN: 0016-6731, DOI: 10.1534/genetics.115.185132 |
Genetics 205/1 | 2019-07-08 |
| 2017 |
Filippo Ciabrelli, Federico Comoglio, Simon Fellous, Boyan Bonev, Maria Ninova, Quentin Szabo, Anne Xuéreb, Christophe Klopp, Alexei Aravin, Renato Paro, Frédéric Bantignies, Giacomo Cavalli Stable Polycomb-dependent transgenerational inheritance of chromatin states in Drosophila published pages: , ISSN: 1061-4036, DOI: 10.1038/ng.3848 |
Nature Genetics | 2019-07-08 |
| 2016 |
Adam Hospital, Pau Andrio, Cesare Cugnasco, Laia Codo, Yolanda Becerra, Pablo D. Dans, Federica Battistini, Jordi Torres, Ramón Goñi, Modesto Orozco, Josep Ll. Gelpà BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data published pages: D272-D278, ISSN: 0305-1048, DOI: 10.1093/nar/gkv1301 |
Nucleic Acids Research 44/D1 | 2019-07-08 |
| 2016 |
Pablo D. Dans, Linda DanilÄne, Ivan Ivani, Tomáš DrÅ¡ata, Filip LankaÅ¡, Adam Hospital, Jürgen Walther, Ricard Illa Pujagut, Federica Battistini, Josep Lluis GelpÃ, Richard Lavery, Modesto Orozco Long-timescale dynamics of the Drew–Dickerson dodecamer published pages: 4052-4066, ISSN: 0305-1048, DOI: 10.1093/nar/gkw264 |
Nucleic Acids Research 44/9 | 2019-07-08 |
| 2016 |
Vincent Loubiere, Anna Delest, Aubin Thomas, Boyan Bonev, Bernd Schuettengruber, Satish Sati, Anne-Marie Martinez, Giacomo Cavalli Coordinate redeployment of PRC1 proteins suppresses tumor formation during Drosophila development published pages: 1436-1442, ISSN: 1061-4036, DOI: 10.1038/ng.3671 |
Nature Genetics 48/11 | 2019-07-08 |
| 2017 |
V?ctor L?pez-Ferrando, Andrea Gazzo, Xavier de?la?Cruz, Modesto Orozco, Josep Ll Gelp? PMut: a web-based tool for the annotation of pathological variants on proteins, 2017 update published pages: , ISSN: 0305-1048, DOI: 10.1093/nar/gkx313 |
Nucleic Acids Research | 2019-07-08 |
| 2017 |
François Le Dily, François Serra, Marc A. Marti-Renom 3D modeling of chromatin structure: is there a way to integrate and reconcile single cell and population experimental data? published pages: e1308, ISSN: 1759-0876, DOI: 10.1002/wcms.1308 |
Wiley Interdisciplinary Reviews: Computational Molecular Science | 2019-07-08 |
| 2017 |
Anton, Victor; Ramon-Cortes, Cristian; Ejarque, Jorge; Badia, Rosa M. Transparent Execution of Task-Based Parallel Applications in Docker with COMP Superscalar published pages: , ISSN: , DOI: 10.1109/PDP.2017.26 |
1 | 2019-07-08 |
| 2017 |
Alexandra Balaceanu, Marco Pasi, Pablo D. Dans, Adam Hospital, Richard Lavery, Modesto Orozco The Role of Unconventional Hydrogen Bonds in Determining BII Propensities in B-DNA published pages: 21-28, ISSN: 1948-7185, DOI: 10.1021/acs.jpclett.6b02451 |
The Journal of Physical Chemistry Letters 8/1 | 2019-07-08 |
| 2016 |
Boyan Bonev, Giacomo Cavalli Organization and function of the 3D genome published pages: 661-678, ISSN: 1471-0056, DOI: 10.1038/nrg.2016.112 |
Nature Reviews Genetics 17/11 | 2019-07-08 |
| 2018 |
Marc A. Marti-Renom, Genevieve Almouzni, Wendy A. Bickmore, Kerstin Bystricky, Giacomo Cavalli, Peter Fraser, Susan M. Gasser, Luca Giorgetti, Edith Heard, Mario Nicodemi, Marcelo Nollmann, Modesto Orozco, Ana Pombo, Maria-Elena Torres-Padilla Challenges and guidelines toward 4D nucleome data and model standards published pages: 1352-1358, ISSN: 1061-4036, DOI: 10.1038/s41588-018-0236-3 |
Nature Genetics 50/10 | 2019-06-29 |
| 2018 |
Thierry Cheutin, Giacomo Cavalli Loss of PRC1 induces higher-order opening of Hox loci independently of transcription during Drosophila embryogenesis published pages: , ISSN: 2041-1723, DOI: 10.1038/s41467-018-05945-4 |
Nature Communications 9/1 | 2019-06-29 |
| 2017 |
Bernd Schuettengruber, Henri-Marc Bourbon, Luciano Di Croce, Giacomo Cavalli Genome Regulation by Polycomb and Trithorax: 70 Years and Counting published pages: 34-57, ISSN: 0092-8674, DOI: 10.1016/j.cell.2017.08.002 |
Cell 171/1 | 2019-06-29 |
| 2017 |
Arka Chakraborty, Sébastien Lyonnais, Federica Battistini, Adam Hospital, Giorgio Medici, Rafel Prohens, Modesto Orozco, Josep Vilardell, Maria Solà DNA structure directs positioning of the mitochondrial genome packaging protein Abf2p published pages: 951-967, ISSN: 0305-1048, DOI: 10.1093/nar/gkw1147 |
Nucleic Acids Research 45/2 | 2019-06-29 |
| 2017 |
Boyan Bonev, Netta Mendelson Cohen, Quentin Szabo, Lauriane Fritsch, Giorgio L. Papadopoulos, Yaniv Lubling, Xiaole Xu, Xiaodan Lv, Jean-Philippe Hugnot, Amos Tanay, Giacomo Cavalli Multiscale 3D Genome Rewiring during Mouse Neural Development published pages: 557-572.e24, ISSN: 0092-8674, DOI: 10.1016/j.cell.2017.09.043 |
Cell 171/3 | 2019-06-29 |
| 2018 |
Quentin Szabo, Daniel Jost, Jia-Ming Chang, Diego I. Cattoni, Giorgio L. Papadopoulos, Boyan Bonev, Tom Sexton, Julian Gurgo, Caroline Jacquier, Marcelo Nollmann, Frédéric Bantignies, Giacomo Cavalli TADs are 3D structural units of higher-order chromosome organization in Drosophila published pages: eaar8082, ISSN: 2375-2548, DOI: 10.1126/sciadv.aar8082 |
Science Advances 4/2 | 2019-06-29 |
| 2017 |
Jinsen Li, Jared M. Sagendorf, Tsu-Pei Chiu, Marco Pasi, Alberto Perez, Remo Rohs Expanding the repertoire of DNA shape features for genome-scale studies of transcription factor binding published pages: 12877-12887, ISSN: 0305-1048, DOI: 10.1093/nar/gkx1145 |
Nucleic Acids Research 45/22 | 2019-06-29 |
| 2017 |
Mike Goodstadt, Marc A. Marti-Renom Challenges for visualizing three-dimensional data in genomic browsers published pages: 2505-2519, ISSN: 0014-5793, DOI: 10.1002/1873-3468.12778 |
FEBS Letters 591/17 | 2019-06-29 |
| 2017 |
Pablo D. Dans, Ivan Ivani, Adam Hospital, Guillem Portella, Carlos González, Modesto Orozco How accurate are accurate force-fields for B-DNA? published pages: gkw1355, ISSN: 0305-1048, DOI: 10.1093/nar/gkw1355 |
Nucleic Acids Research | 2019-06-29 |
| 2017 |
Bartomeu Mir, Israel Serrano, Diana Buitrago, Modesto Orozco, Núria Escaja, Carlos González Prevalent Sequences in the Human Genome Can Form Mini i-Motif Structures at Physiological pH published pages: 13985-13988, ISSN: 0002-7863, DOI: 10.1021/jacs.7b07383 |
Journal of the American Chemical Society 139/40 | 2019-06-29 |
| 2017 |
Diego I. Cattoni, Andrés M. Cardozo Gizzi, Mariya Georgieva, Marco Di Stefano, Alessandro Valeri, Delphine Chamousset, Christophe Houbron, Stephanie Déjardin, Jean-Bernard Fiche, Inma González, Jia-Ming Chang, Thomas Sexton, Marc A. Marti-Renom, Frédéric Bantignies, Giacomo Cavalli, Marcelo Nollmann Single-cell absolute contact probability detection reveals chromosomes are organized by multiple low-frequency yet specific interactions published pages: , ISSN: 2041-1723, DOI: 10.1038/s41467-017-01962-x |
Nature Communications 8/1 | 2019-06-29 |
| 2018 |
Yuki Ogiyama, Bernd Schuettengruber, Giorgio L. Papadopoulos, Jia-Ming Chang, Giacomo Cavalli Polycomb-Dependent Chromatin Looping Contributes to Gene Silencing during Drosophila Development published pages: 73-88.e5, ISSN: 1097-2765, DOI: 10.1016/j.molcel.2018.05.032 |
Molecular Cell 71/1 | 2019-06-29 |
| 2018 |
Aleksandar Kojic, Ana Cuadrado, Magali De Koninck, Daniel Giménez-Llorente, Miriam RodrÃguez-Corsino, Gonzalo Gómez-López, François Le Dily, Marc A. Marti-Renom, Ana Losada Distinct roles of cohesin-SA1 and cohesin-SA2 in 3D chromosome organization published pages: 496-504, ISSN: 1545-9993, DOI: 10.1038/s41594-018-0070-4 |
Nature Structural & Molecular Biology 25/6 | 2019-06-29 |
| 2018 |
Laura Pascual-Reguant, Enrique Blanco, Silvia Galan, François Le Dily, Yasmina Cuartero, Gemma Serra-Bardenys, Valerio Di Carlo, Ane Iturbide, Joan Pau Cebrià -Costa, Lara Nonell, Antonio GarcÃa de Herreros, Luciano Di Croce, Marc A. Marti-Renom, Sandra Peiró Lamin B1 mapping reveals the existence of dynamic and functional euchromatin lamin B1 domains published pages: , ISSN: 2041-1723, DOI: 10.1038/s41467-018-05912-z |
Nature Communications 9/1 | 2019-06-29 |
| 2018 |
Justina JankauskaitÄ—, Brian Jiménez-GarcÃa, Justas DapkÅ«nas, Juan Fernández-Recio, Iain H Moal SKEMPI 2.0: an updated benchmark of changes in protein–protein binding energy, kinetics and thermodynamics upon mutation published pages: , ISSN: 1367-4803, DOI: 10.1093/bioinformatics/bty635 |
Bioinformatics | 2019-06-29 |
| 2018 |
Alexandra Balaceanu, Alberto Pérez, Pablo D Dans, Modesto Orozco Allosterism and signal transfer in DNA published pages: 7554-7565, ISSN: 0305-1048, DOI: 10.1093/nar/gky549 |
Nucleic Acids Research 46/15 | 2019-06-29 |
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