Opendata, web and dolomites

BioExcel

Centre of Excellence for Biomolecular Research

Total Cost €

0

EC-Contrib. €

0

Partnership

0

Views

0

Project "BioExcel" data sheet

The following table provides information about the project.

Coordinator
KUNGLIGA TEKNISKA HOEGSKOLAN 

Organization address
address: BRINELLVAGEN 8
city: STOCKHOLM
postcode: 100 44
website: www.kth.se

contact info
title: n.a.
name: n.a.
surname: n.a.
function: n.a.
email: n.a.
telephone: n.a.
fax: n.a.

 Coordinator Country Sweden [SE]
 Project website http://www.bioexcel.eu
 Total cost 4˙782˙286 €
 EC max contribution 4˙782˙286 € (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  2018-12-31

 Partnership

Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    KUNGLIGA TEKNISKA HOEGSKOLAN SE (STOCKHOLM) coordinator 1˙084˙750.00
2    THE UNIVERSITY OF EDINBURGH UK (EDINBURGH) participant 1˙001˙226.00
3    EUROPEAN MOLECULAR BIOLOGY LABORATORY DE (HEIDELBERG) participant 598˙411.00
4    THE UNIVERSITY OF MANCHESTER UK (MANCHESTER) participant 345˙875.00
5    MAX-PLANCK-GESELLSCHAFT ZUR FORDERUNG DER WISSENSCHAFTEN EV DE (MUENCHEN) participant 315˙000.00
6    UNIVERSITEIT UTRECHT NL (UTRECHT) participant 279˙000.00
7    FORWARD TECHNOLOGIES AB SE (STOCKHOLM) participant 264˙500.00
8    FORSCHUNGSZENTRUM JULICH GMBH DE (JULICH) participant 259˙773.00
9    BARCELONA SUPERCOMPUTING CENTER - CENTRO NACIONAL DE SUPERCOMPUTACION ES (BARCELONA) participant 225˙000.00
10    FUNDACIO INSTITUT DE RECERCA BIOMEDICA (IRB BARCELONA) ES (BARCELONA) participant 225˙000.00
11    IAN HARROW CONSULTING LTD UK (HEMEL HEMPSTEAD) participant 183˙750.00

Map

 Project objective

Life Science research has become increasingly digital, and this development is accelerating rapidly. Biomolecular modelling techniques such as homology modelling, docking, and molecular simulation have advanced tremendously due to world-leading European research, resulting in extreme demands for better computational performance and throughput as these tools are used in applied research and industrial development. This research has direct influence on our daily life in areas such as health and medical applications, the development of new drugs, efficient drug delivery, biotechnology, environment, agriculture and food industry. Life Science is one of the largest and fastest growing communities in need of high-end computing, and it is a critically important industrial sector for Europe. However, compared to some other disciplines, the use of e-Infrastructure is still relatively new - many advanced techniques are not applied commercially due to limited experience. It requires significant support to: • Make e-Infrastructure useable by researchers who are not computing experts, • Improve the performance and applicability of key life science applications, • Handle large amounts of data in computational workflows.

BioExcel proposes to tackle these challenges by establishing a dedicated CoE for Biomolecular Research, covering structural and functional studies of the building blocks of living organisms - proteins, DNA, saccharides, membranes, solvents and small molecules like drug compounds - all areas where with large academic and industrial users bases in Europe. Specifically, BioExcel will • Improve the efficiency and scalability of important software packages for biomolecular research; • Improve the usability of ICT technologies for biomolecular researchers in academia and industry; • Promote best practices and train end users in making good use of both software and e-Infrastructure. • Develop appropriate governance structures and business plans for a sustainable CoE.

 Deliverables

List of deliverables.
Governance and Business plan Documents, reports 2019-09-09 16:45:52
Efficacy of Feedback Process Documents, reports 2019-09-09 16:45:52
Revised business plan - update Documents, reports 2019-09-09 16:45:52
Final release of workflows and modular tools for user services. Other 2019-09-09 16:45:52
Final project releases of pilot applications Other 2019-09-09 16:45:52
Consultancy Proposals Update Documents, reports 2019-09-09 16:45:52
User feedback and future roadmap. Documents, reports 2019-09-09 16:45:52
Final report on dissemination and training Documents, reports 2019-09-09 16:45:52
Consultancy Modalities and Funding Options, Final Update Documents, reports 2019-09-09 16:45:52
Long-term hardware/software assessment for pilot applications and the general community Documents, reports 2019-09-09 16:45:52
Consultancy Modalities and Funding Options, Half-time Update Documents, reports 2019-09-09 16:45:51
Consultancy Proposals. Documents, reports 2019-09-09 16:45:51
Selection and Establishment of User Groups Documents, reports 2019-09-09 16:45:51
Specification of software engineering, testing & QA Documents, reports 2019-09-09 16:45:51
State of the art and Gap analysis Documents, reports 2019-09-09 16:45:51
Roadmap of future hardware and long-term development plan for each pilot application. Documents, reports 2019-09-09 16:45:51
Quality assurance and risk management plan. Documents, reports 2019-09-09 16:45:51
Initial business plan. Documents, reports 2019-09-09 16:45:51
Competency framework, mapping to current training & initial training plan Documents, reports 2019-09-09 16:45:51
Training report and updated plan Documents, reports 2019-09-09 16:45:51
First release of workflows blocks and portals Other 2019-09-09 16:45:51
Dissemination report and updated plan Documents, reports 2019-09-09 16:45:51
Recommendations for BioExcel training programme. Documents, reports 2019-09-09 16:45:51
Dissemination and outreach plan Documents, reports 2019-09-09 16:45:51
Management plan Documents, reports 2019-09-09 16:45:51
Revised business plan. Documents, reports 2019-09-09 16:45:51
First project release of all pilot applications Other 2019-09-09 16:45:51

Take a look to the deliverables list in detail:  detailed list of BioExcel deliverables.

 Publications

year authors and title journal last update
List of publications.
2017 Carter, Adam; Harrow, Ian
BioExcel Deliverable 3.3 – Consultancy Modalities and Funding Options, Half-time Update
published pages: , ISSN: , DOI: 10.5281/zenodo.574613
6 2019-10-08
2017 Irina S. Moreira, Panagiotis I. Koukos, Rita Melo, Jose G. Almeida, Antonio J. Preto, Joerg Schaarschmidt, Mikael Trellet, Zeynep H. Gümüş, Joaquim Costa, Alexandre M. J. J. Bonvin
SpotOn: High Accuracy Identification of Protein-Protein Interface Hot-Spots
published pages: , ISSN: 2045-2322, DOI: 10.1038/s41598-017-08321-2
Scientific Reports 7/1 2019-10-08
2016 Apostolov, Rossen
BioExcel Deliverable 4.1 – Dissemination and Outreach Plan
published pages: , ISSN: , DOI: 10.5281/zenodo.264250
37 2019-10-08
2017 Matser, Vera
BioExcel Deliverable 4.5 – Training report and updated plan
published pages: , ISSN: , DOI: 10.5281/zenodo.574620
6 2019-10-08
2019 Rodolfo Briones, Christian Blau, Carsten Kutzner, Bert L. de Groot, Camilo Aponte-Santamaría
GROmaρs: A GROMACS-Based Toolset to Analyze Density Maps Derived from Molecular Dynamics Simulations
published pages: 4-11, ISSN: 0006-3495, DOI: 10.1016/j.bpj.2018.11.3126
Biophysical Journal 116/1 2019-10-08
2018 Mark Abraham
Software release for BioExcel pilot applications
published pages: , ISSN: 0000-0000, DOI: 10.5281/zenodo.1473684
Zenodo 2 2019-10-08
2016 Hospital, Adam; Montras, Anna; Soiland-Reyes, Stian; Bonvin, Alexandre; Melquiond, Adrien; Gelpí, Josep Lluís; Lezzi, Daniele; Newhouse, Steven; Dianes, Jose A.; Abraham, Mark; Apostolov, Rossen; Ippoliti, Emiliano; Carter, Adam; White, Darren J.
BioExcel Deliverable 2.1 – State of the art and gap analysis
published pages: , ISSN: , DOI: 10.5281/zenodo.263963
35 2019-10-08
2016 Matser, Vera
BioExcel Deliverable 4.3 - Recommendations for BioExcel Training Programme
published pages: , ISSN: , DOI: 10.5281/zenodo.263926
18 2019-10-08
2016 Noack, Holger; Harrow, Ian; Bonvin, Alexandre; Carter, Adam; Apostolov, Rossen; Laure, Erwin
BioExcel Deliverable 5.1 - Initial Business Plan
published pages: , ISSN: , DOI: 10.5281/zenodo.263932
28 2019-10-08
2018 Tomas Bastys, Vytautas Gapsys, Nadezhda T. Doncheva, Rolf Kaiser, Bert L. de Groot, Olga V. Kalinina
Consistent Prediction of Mutation Effect on Drug Binding in HIV-1 Protease Using Alchemical Calculations
published pages: 3397-3408, ISSN: 1549-9618, DOI: 10.1021/acs.jctc.7b01109
Journal of Chemical Theory and Computation 14/7 2019-10-08
2017 Abraham, Mark; Ippoliti, Emiliano; Bonvin, Alexandre; de Groot, Bert; Soiland-Reyes, Stian
BioExcel Deliverable 1.2 – First project release of all pilot applications
published pages: , ISSN: , DOI: 10.5281/zenodo.574459
6 2019-10-08
2018 Katarina Elez, Alexandre M. J. J. Bonvin, Anna Vangone
Distinguishing crystallographic from biological interfaces in protein complexes: role of intermolecular contacts and energetics for classification
published pages: , ISSN: 1471-2105, DOI: 10.1186/s12859-018-2414-9
BMC Bioinformatics 19/S15 2019-10-08
2019 Panagiotis I. Koukos, Li C. Xue, Alexandre M. J. J. Bonvin
Protein–ligand pose and affinity prediction: Lessons from D3R Grand Challenge 3
published pages: 83-91, ISSN: 0920-654X, DOI: 10.1007/s10822-018-0148-4
Journal of Computer-Aided Molecular Design 33/1 2019-10-08
2018 Abraham, Mark J.; Melquiond, Adrien S.J.; Ippoliti, Emiliano; Gapsys, Vytautas; Hess, Berk; Trellet, Mikael; Rodrigues, João P.G.L.M.; Laure, Erwin; Apostolov, Rossen; de Groot, Bert L.; Bonvin, Alexandre M.J.J.; Lindahl, Erik
BioExcel Whitepaper on Scientific Software Development
published pages: , ISSN: , DOI: 10.5281/zenodo.1194633
3 2019-10-08
2017 Apostolov, Rossen; Abraham, Mark; Laure, Erwin; Lindahl, Erik; Bonvin, Alexandre; de Groot, Bert; Ippoliti, Emiliano
BioExcel Deliverable 1.3 - Roadmap of future hardware and long-term development plan for each pilot application
published pages: , ISSN: , DOI: 10.5281/zenodo.574605
6 2019-10-08
2017 Hospital, Adam; Gelpí, Josep Lluís; Dianes, Jose A.; Andrio, Pau; White, Darren J.; Ippoliti, Emiliano; Melquiond, Adrien; Gapsys, Vytautas
BioExcel Deliverable 2.3 - User Feedback and Future Roadmap
published pages: , ISSN: 0000-0000, DOI: 10.5281/zenodo.1060946
Zenodo 3 2019-10-08
2018 Anna Rubio-Cosials, Federica Battistini, Alexander Gansen, Anna Cuppari, Pau Bernadó, Modesto Orozco, Jörg Langowski, Katalin Tóth, Maria Solà
Protein Flexibility and Synergy of HMG Domains Underlie U-Turn Bending of DNA by TFAM in Solution
published pages: 2386-2396, ISSN: 0006-3495, DOI: 10.1016/j.bpj.2017.11.3743
Biophysical Journal 114/10 2019-10-08
2016 Apostolov, Rossen
BioExcel Deliverable 6.2 – Quality Assurance and Risk Management Plan
published pages: , ISSN: , DOI: 10.5281/zenodo.263934
25 2019-10-08
2018 Panagiotis I. Koukos, Inge Faro, Charlotte W. van Noort, Alexandre M.J.J. Bonvin
A Membrane Protein Complex Docking Benchmark
published pages: 5246-5256, ISSN: 0022-2836, DOI: 10.1016/j.jmb.2018.11.005
Journal of Molecular Biology 430/24 2019-10-08
2017 Ezgi Karaca, João P G L M Rodrigues, Andrea Graziadei, Alexandre M J J Bonvin, Teresa Carlomagno
M3: an integrative framework for structure determination of molecular machines
published pages: 897-902, ISSN: 1548-7091, DOI: 10.1038/nmeth.4392
Nature Methods 14/9 2019-10-08
2018 Amparo Garcia-Lopez, Francesca Tessaro, Hendrik R. A. Jonker, Anna Wacker, Christian Richter, Arnaud Comte, Nikolaos Berntenis, Roland Schmucki, Klas Hatje, Olivier Petermann, Gianpaolo Chiriano, Remo Perozzo, Daniel Sciarra, Piotr Konieczny, Ignacio Faustino, Guy Fournet, Modesto Orozco, Ruben Artero, Friedrich Metzger, Martin Ebeling, Peter Goekjian, Benoît Joseph, Harald Schwalbe, Leonardo Sca
Targeting RNA structure in SMN2 reverses spinal muscular atrophy molecular phenotypes
published pages: , ISSN: 2041-1723, DOI: 10.1038/s41467-018-04110-1
Nature Communications 9/1 2019-10-08
2016 Carter, Adam; Harrow, Ian; Apostolov, Rossen; Soiland-Reyes, Stian; de Groot, Bert; Abraham, Mark
BioExcel Deliverable 3.1 - Selection and Establishment of User Groups
published pages: , ISSN: , DOI: 10.5281/zenodo.264011
36 2019-10-08
2017 Carter, Adam; Harrow, Ian; Abraham, Mark; Hospital, Adam; Matser, Vera; Noack, Holger; Apostolov, Rossen
BioExcel Deliverable 3.4 - Efficacy of Feedback Processes
published pages: , ISSN: , DOI: 10.5281/zenodo.1060843
3 2019-10-08
2019 Cunliang Geng, Anna Vangone, Gert E. Folkers, Li C. Xue, Alexandre M. J. J. Bonvin
iSEE: Interface structure, evolution, and energy-based machine learning predictor of binding affinity changes upon mutations
published pages: 110-119, ISSN: 0887-3585, DOI: 10.1002/prot.25630
Proteins: Structure, Function, and Bioinformatics 87/2 2019-10-08
2016 Abraham, Mark; Bonvin, Alexandre; Melquiond, Adrien; Ippoliti, Emiliano; de Groot, Bert
BioExcel Deliverable 1.1 - Specification of software engineering, testing & QA
published pages: , ISSN: , DOI: 10.5281/zenodo.263908
17 2019-10-08
2018 Alexandre M. J. J. Bonvin, Ezgi Karaca, Panagiotis L. Kastritis, João P. G. L. M. Rodrigues
Defining distance restraints in HADDOCK
published pages: 1503-1503, ISSN: 1754-2189, DOI: 10.1038/s41596-018-0017-6
Nature Protocols 13/7 2019-10-08
2018 Zeynep Kurkcuoglu, Panagiotis I. Koukos, Nevia Citro, Mikael E. Trellet, J. P. G. L. M. Rodrigues, Irina S. Moreira, Jorge Roel-Touris, Adrien S. J. Melquiond, Cunliang Geng, Jörg Schaarschmidt, Li C. Xue, Anna Vangone, A. M. J. J. Bonvin
Performance of HADDOCK and a simple contact-based protein–ligand binding affinity predictor in the D3R Grand Challenge 2
published pages: 175-185, ISSN: 0920-654X, DOI: 10.1007/s10822-017-0049-y
Journal of Computer-Aided Molecular Design 32/1 2019-10-08
2018 Lindahl; Abraham; Hess; van der Spoel
GROMACS 2019.1 Manual
published pages: , ISSN: , DOI: 10.5281/zenodo.2564761
25 2019-10-08
2016 Matser, Vera
BioExcel Deliverable 4.2 - Competency framework, mapping to current training & initial training plan
published pages: , ISSN: , DOI: 10.5281/zenodo.264231
31 2019-10-08
2017 Eva S. Cunha, Pedro Sfriso, Adriana L. Rojas, Pietro Roversi, Adam Hospital, Modesto Orozco, Nicola G.A. Abrescia
Mechanism of Structural Tuning of the Hepatitis C Virus Human Cellular Receptor CD81 Large Extracellular Loop
published pages: 53-65, ISSN: , DOI: 10.1016/j.str.2016.11.003
Structure 25/1 2019-10-08
2017 Noack, Holger; Harrow, Ian; Bonvin, Alexandre; Carter, Adam; Apostolov, Rossen; Laure, Erwin
BioExcel Deliverable 5.2 - Revised Business Plan
published pages: , ISSN: , DOI: 10.5281/zenodo.574634
6 2019-10-08
2017 Vytautas Gapsys, Bert L. de Groot
Alchemical Free Energy Calculations for Nucleotide Mutations in Protein–DNA Complexes
published pages: 6275-6289, ISSN: 1549-9618, DOI: 10.1021/acs.jctc.7b00849
Journal of Chemical Theory and Computation 13/12 2019-10-08
2018 Lindahl; Abraham; Hess; van der Spoel
GROMACS 2019 Manual
published pages: , ISSN: , DOI: 10.5281/zenodo.2424485
1 2019-10-08
2018 Viveca Lindahl, Pontus Gourdon, Magnus Andersson, Berk Hess
Permeability and ammonia selectivity in aquaporin TIP2;1: linking structure to function
published pages: , ISSN: 2045-2322, DOI: 10.1038/s41598-018-21357-2
Scientific Reports 8/1 2019-10-08
2016 Hospital, Adam; Montras, Anna; Gelpí, Josep Lluís; Badia, Rosa M.; Newhouse, Steven; Dianes, Jose A.; Andrio, Pau; Soiland-Reyes, Stian; White, Darren J; Carter, Adam; Ippoliti, Emiliano; Melquiond, Adrien; de Groot, Bert
BioExcel Deliverable 2.2 – First Release of Workflow Blocks and Portals
published pages: , ISSN: , DOI: 10.5281/zenodo.263965
16 2019-10-08
2017 Carter, Adam
BioExcel Deliverable 3.2 – Consultancy Proposals
published pages: , ISSN: , DOI: 10.5281/zenodo.574607
9 2019-10-08
2015 Apostolov, Rossen; Laure, Erwin
BioExcel Deliverable 6.1 - Management Plan
published pages: , ISSN: , DOI: 10.5281/zenodo.263933
26 2019-10-08
2018 Anna Vangone, Joerg Schaarschmidt, Panagiotis Koukos, Cunliang Geng, Nevia Citro, Mikael E Trellet, Li C Xue, Alexandre M J J Bonvin
Large-scale prediction of binding affinity in protein–small ligand complexes: the PRODIGY-LIG web server
published pages: , ISSN: 1367-4803, DOI: 10.1093/bioinformatics/bty816
Bioinformatics 2019-09-09
2017 Steffen Möller, Stuart W. Prescott, Lars Wirzenius, Petter Reinholdtsen, Brad Chapman, Pjotr Prins, Stian Soiland-Reyes, Fabian Klötzl, Andrea Bagnacani, Matúš Kalaš, Andreas Tille, Michael R. Crusoe
Robust Cross-Platform Workflows: How Technical and Scientific Communities Collaborate to Develop, Test and Share Best Practices for Data Analysis
published pages: 232-244, ISSN: 2364-1185, DOI: 10.1007/s41019-017-0050-4
Data Science and Engineering 2/3 2019-09-09
2018 Gil Alterovitz, Dennis Dean, Carole Goble, Michael R. Crusoe, Stian Soiland-Reyes, Amanda Bell, Anais Hayes, Anita Suresh, Anjan Purkayastha, Charles H. King, Dan Taylor, Elaine Johanson, Elaine E. Thompson, Eric Donaldson, Hiroki Morizono, Hsinyi Tsang, Jeet K. Vora, Jeremy Goecks, Jianchao Yao, Jonas S. Almeida, Jonathon Keeney, KanakaDurga Addepalli, Konstantinos Krampis, Krista M. Smith, Lydia Guo, Mark Walderhaug, Marco Schito, Matthew Ezewudo, Nuria Guimera, Paul Walsh, Robel Kahsay, Srikanth Gottipati, Timothy C. Rodwell, Toby Bloom, Yuching Lai, Vahan Simonyan, Raja Mazumder
Enabling precision medicine via standard communication of HTS provenance, analysis, and results
published pages: e3000099, ISSN: 1545-7885, DOI: 10.1371/journal.pbio.3000099
PLOS Biology 16/12 2019-09-09
2017 Adam Hospital, Michela Candotti, Josep Llu?s Gelp?, Modesto Orozco
The Multiple Roles of Waters in Protein Solvation
published pages: 3636-3643, ISSN: 1520-6106, DOI: 10.1021/acs.jpcb.6b09676
The Journal of Physical Chemistry B 121/15 2019-09-09

Are you the coordinator (or a participant) of this project? Plaese send me more information about the "BIOEXCEL" project.

For instance: the website url (it has not provided by EU-opendata yet), the logo, a more detailed description of the project (in plain text as a rtf file or a word file), some pictures (as picture files, not embedded into any word file), twitter account, linkedin page, etc.

Send me an  email (fabio@fabiodisconzi.com) and I put them in your project's page as son as possible.

Thanks. And then put a link of this page into your project's website.

The information about "BIOEXCEL" are provided by the European Opendata Portal: CORDIS opendata.

More projects from the same programme (H2020-EU.1.4.1.3.)

OCRE (2019)

Access to Commercial Services Through the EOSC-hub

Read More  

EXCELLERAT (2018)

The European Centre of Excellence for Engineering Applications

Read More  

INODE (2019)

INODE - Intelligent Open Data Exploration

Read More