Explore the words cloud of the BioExcel project. It provides you a very rough idea of what is the project "BioExcel" about.
The following table provides information about the project.
Coordinator |
KUNGLIGA TEKNISKA HOEGSKOLAN
Organization address contact info |
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 |
Take a look of project's partnership.
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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 |
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.
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.
year | authors and title | journal | last update |
---|---|---|---|
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-SantamarÃa GROmaÏs: 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; GelpÃ, Josep LluÃs; 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; GelpÃ, Josep LluÃs; 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; GelpÃ, Josep LluÃs; 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.