Deliverables
Definition of the incubation plan, description of its components and implementation strategy. Software documentation and usage summary. Best practice for documentation, regression tests, benchmarking, etc.
Second Report on Fast Track ApplicationsSecond report on research outcomes from fast track applications including a first best practices section to help external users of the underlying codes to quickly set up their own applications eg in the context of task 24
Dissemination Action PlanA detailed and comprehensive report on the dissemination actions that will be carried out by the project.
Intermediate Report on VVUQ, Exemplar Research Integration and Community ApplicationsThis report will describe the results of VVUQ technique application in Task 25 and the exemplar integration research as well as review achievements with community application codes
CompBioMed2 Compute and Data Services Strategic PlanThis deliverable will define of the strategies for the design of services portfolio and the operational service processes needed for the maintenance and delivery of CompBioMed compute and data services.
First Report on VVUQ Strategies and Community Application CodesThis report will describe the VVUQ strategies and techniques developed in Task 25 and review the community application codes with best prospects for parallelisation and deployment by Task 24
Project HandbookWP1 will produce a project handbook outlining the project’s procedures, legal obligations and reporting processes, to assist each partner.
First Report on Fast Track Application ReadinessReport on the applications and research being undertaken within the CompBioMed2 environment based on the initial, Fast Track deployment.
Report on Dissemination and InnovationA report on dissemination and innovation activities produced by the project at the midterm point
Quality Assurance PlanTo manage the project’s quality control process, a Quality Assurance Plan will be created to assist internal reviewers in monitoring all deliverables before they are finalised and submitted to the Commission. The deliverable will also contain a detailed risk analysis and contingency planning.
Report on Establishment of the Community EngagementA report on the report on the establishment of the users’ engagement portal and of the HPC-M community of practice.
Ethics ReportThis report will be initiated in M6 and maintained as a running log of the types of data used in CompBioMed2. The report will keep detailed information on the procedures for data collection, storage, protection, retention, and destruction, and confirmation that they comply with national and EU legislation.
Advanced Report on Biomedical ApplicationsTechnical report on results of code improvement focussing on robustness efficiency usability etc Report on software incubation
Report on Maintenance and Development of CompBioMed Computational ServicesThis report will describe the status of the CompBioMed service portfolio at the halfway point of the project lifetime For each of the identified services we will provide a technical description of its components access mechanism used and einfrastructure usage
Analytics Requirements AnalysisThis report will assess the potential for applying analytics techniques to CompBioMed2 project data
Innovation PlanA detailed innovation plan, to be adhered to by all members of the consortium, to promote the innovation and commercialisation aspects of this project.
Task 3.1 will produce an initial Data Management Plan for the project. This will be updated over the course of the project as its needs evolve.
Publications
Author(s):
Zainab Altai, Marco Viceconti, Amaka C. Offiah, Xinshan Li
Published in:
Biomechanics and Modeling in Mechanobiology, Issue 17/4, 2018, Page(s) 1001-1009, ISSN 1617-7959
Publisher:
Springer Verlag
DOI:
10.1007/s10237-018-1008-9
Author(s):
Brooke E. Husic, Nicholas E. Charron, Dominik Lemm, Jiang Wang, Adrià Pérez, Maciej Majewski, Andreas Krämer, Yaoyi Chen, Simon Olsson, Gianni de Fabritiis, Frank Noé, Cecilia Clementi
Published in:
The Journal of Chemical Physics, Issue 153/19, 2020, Page(s) 194101, ISSN 0021-9606
Publisher:
American Institute of Physics
DOI:
10.1063/5.0026133
Author(s):
Alfonso Santiago, Miguel Zavala-Aké, Ricard Borrell, Guillaume Houzeaux, Mariano Vázquez
Published in:
Journal of Fluids and Structures, Issue 96, 2020, Page(s) 103009, ISSN 0889-9746
Publisher:
Academic Press
DOI:
10.1016/j.jfluidstructs.2020.103009
Author(s):
Shunzhou Wan, Robert C. Sinclair, Peter V. Coveney
Published in:
Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Issue 379/2197, 2021, ISSN 1364-503X
Publisher:
Royal Society of London
DOI:
10.1098/rsta.2020.0082
Author(s):
P. S. Zun, A. J. Narracott, P. C. Evans, B. J. M. van Rooij, A. G. Hoekstra
Published in:
Biomechanics and Modeling in Mechanobiology, Issue 19/2, 2020, Page(s) 681-692, ISSN 1617-7959
Publisher:
Springer Verlag
DOI:
10.1007/s10237-019-01239-w
Author(s):
P. S. Zun, A. J. Narracott, C. Chiastra, J. Gunn, A. G. Hoekstra
Published in:
Cardiovascular Engineering and Technology, Issue 10/4, 2019, Page(s) 568-582, ISSN 1869-408X
Publisher:
Springer Pub. Co.,
DOI:
10.1007/s13239-019-00431-4
Author(s):
Ivan Benemerito, Erica Montefiori, Alberto Marzo and Claudia Mazzà
Published in:
Applied Sciences, 2022, ISSN 2076-3417
Publisher:
MDPI
DOI:
10.3390/app122412932
Author(s):
C. Winsor, X. Li, M. Qasim, C.R. Henak, P.J. Pickhardt, H. Ploeg, M. Viceconti
Published in:
Bone, Issue 143, 2021, Page(s) 115759, ISSN 8756-3282
Publisher:
Elsevier BV
DOI:
10.1016/j.bone.2020.115759
Author(s):
David W. Wright, Fouad Husseini, Shunzhou Wan, Christophe Meyer, Herman van Vlijmen, Gary Tresadern, Peter V. Coveney
Published in:
Advanced Theory and Simulations, Issue 3/1, 2019, Page(s) 1900194, ISSN 2513-0390
Publisher:
John Wiley & Sons
DOI:
10.1002/adts.201900194
Author(s):
Vytautas Gapsys, Laura Pérez-Benito, Matteo Aldeghi, Daniel Seeliger, Herman van Vlijmen, Gary Tresadern, Bert L. de Groot
Published in:
Chemical Science, Issue 11/4, 2020, Page(s) 1140-1152, ISSN 2041-6520
Publisher:
Royal Society of Chemistry
DOI:
10.1039/c9sc03754c
Author(s):
Hector Martinez-Navarro, Ana Mincholé, Alfonso Bueno-Orovio, Blanca Rodriguez
Published in:
Scientific Reports, Issue 9/1, 2019, ISSN 2045-2322
Publisher:
Nature Publishing Group
DOI:
10.1038/s41598-019-53221-2
Author(s):
Alejandro Varela-Rial, Maciej Majewski, Alberto Cuzzolin, Gerard Martínez-Rosell, Gianni De Fabritiis
Published in:
Journal of Chemical Information and Modeling, Issue 60/6, 2020, Page(s) 2673-2677, ISSN 1549-9596
Publisher:
American Chemical Society
DOI:
10.1021/acs.jcim.0c00143
Author(s):
Christos Kotsalos, Jonas Latt, Bastien Chopard
Published in:
Journal of Computational Physics, Issue 398, 2019, Page(s) 108905, ISSN 0021-9991
Publisher:
Academic Press
DOI:
10.1016/j.jcp.2019.108905
Author(s):
Britt J. M. van Rooij, Gábor Závodszky, Alfons G. Hoekstra, David N. Ku
Published in:
Scientific Reports, Issue 10/1, 2020, ISSN 2045-2322
Publisher:
Nature Publishing Group
DOI:
10.1038/s41598-020-74518-7
Author(s):
Alexander Heifetz, Inaki Morao, M. Madan Babu, Tim James, Michelle W. Y. Southey, Dmitri G. Fedorov, Matteo Aldeghi, Michael J. Bodkin, Andrea Townsend-Nicholson
Published in:
Journal of Chemical Theory and Computation, Issue 16/4, 2020, Page(s) 2814-2824, ISSN 1549-9618
Publisher:
American Chemical Society
DOI:
10.1021/acs.jctc.9b01136
Author(s):
Stefan Doerr, Maciej Majewski, Adrià Pérez, Andreas Krämer, Cecilia Clementi, Frank Noe, Toni Giorgino, Gianni De Fabritiis
Published in:
Journal of Chemical Theory and Computation, Issue 17/4, 2021, Page(s) 2355-2363, ISSN 1549-9618
Publisher:
American Chemical Society
DOI:
10.1021/acs.jctc.0c01343
Author(s):
F. Levrero-Florencio, F. Margara, E. Zacur, A. Bueno-Orovio, Z.J. Wang, A. Santiago, J. Aguado-Sierra, G. Houzeaux, V. Grau, D. Kay, M. Vázquez, R. Ruiz-Baier, B. Rodriguez
Published in:
Computer Methods in Applied Mechanics and Engineering, Issue 361, 2020, Page(s) 112762, ISSN 0045-7825
Publisher:
Elsevier BV
DOI:
10.1016/j.cma.2019.112762
Author(s):
R. Pons, A. Guala, J. F. Rodríguez-Palomares, J. C. Cajas, L. Dux-Santoy, G. Teixidó-Tura, J. J. Molins, M. Vázquez, A. Evangelista, J. Martorell
Published in:
Royal Society Open Science, Issue 7/2, 2020, Page(s) 191752, ISSN 2054-5703
Publisher:
Royal Society Publishing
DOI:
10.1098/rsos.191752
Author(s):
Sharp Chim Yui Lo, J. W. S. McCullough, P. V. Coveney
Published in:
Scientific Reports, 2022, ISSN 2045-2322
Publisher:
Nature Publishing Group
DOI:
10.1038/s41598-022-21923-9
Author(s):
José Jiménez-Luna, Laura Pérez-Benito, Gerard Martínez-Rosell, Simone Sciabola, Rubben Torella, Gary Tresadern, Gianni De Fabritiis
Published in:
Chemical Science, Issue 10/47, 2019, Page(s) 10911-10918, ISSN 2041-6520
Publisher:
Royal Society of Chemistry
DOI:
10.1039/c9sc04606b
Author(s):
Adrià Pérez, Pablo Herrera-Nieto, Stefan Doerr, Gianni De Fabritiis
Published in:
Journal of Chemical Theory and Computation, Issue 16/7, 2020, Page(s) 4685-4693, ISSN 1549-9618
Publisher:
American Chemical Society
DOI:
10.1021/acs.jctc.0c00205#
Author(s):
Mark Taylor, Marco Viceconti, Pinaki Bhattacharya, Xinshan Li
Published in:
Journal of the Mechanical Behavior of Biomedical Materials, Issue 118, 2021, Page(s) 104434, ISSN 1751-6161
Publisher:
Elsevier BV
DOI:
10.1016/j.jmbbm.2021.104434
Author(s):
Andrea Townsend-Nicholson, Nojood Altwaijry, Andrew Potterton, Inaki Morao, Alexander Heifetz
Published in:
Current Opinion in Structural Biology, Issue 55, 2019, Page(s) 178-184, ISSN 0959-440X
Publisher:
Elsevier BV
DOI:
10.1016/j.sbi.2019.04.005
Author(s):
Andrew Potterton, Fouad S. Husseini, Michelle W. Y. Southey, Mike J. Bodkin, Alexander Heifetz, Peter V. Coveney, Andrea Townsend-Nicholson
Published in:
Journal of Chemical Theory and Computation, Issue 15/5, 2019, Page(s) 3316-3330, ISSN 1549-9618
Publisher:
American Chemical Society
DOI:
10.1021/acs.jctc.8b01270
Author(s):
Mateusz K. Bieniek, Agastya P. Bhati, Shunzhou Wan, Peter V. Coveney
Published in:
Journal of Chemical Theory and Computation, Issue 17/2, 2021, Page(s) 1250-1265, ISSN 1549-9618
Publisher:
American Chemical Society
DOI:
10.1021/acs.jctc.0c01179
Author(s):
Karim Zouaoui Boudjeltia, Christos Kotsalos, Daniel Ribeiro Sousa, Alexandre Rousseau, Christophe Lelubre, Olivier Sartenaer, Michael Piagnerelli, Jérôme Dohet‐Eraly, Frank Dubois, Nicole Tasiaux, Bastien Chopard, Alain Van Meerhaeghe
Published in:
Annals of the New York Academy of Sciences, Issue 1485/1, 2021, Page(s) 71-82, ISSN 0077-8923
Publisher:
New York Academy of Sciences
DOI:
10.1111/nyas.14489
Author(s):
Alexander Heifetz, Tim James, Michelle Southey, Inaki Morao, Matteo Aldeghi, Laurie Sarrat, Dmitri G Fedorov, Mike J Bodkin, Andrea Townsend-Nicholson
Published in:
Current Opinion in Structural Biology, Issue 55, 2019, Page(s) 85-92, ISSN 0959-440X
Publisher:
Elsevier BV
DOI:
10.1016/j.sbi.2019.03.021
Author(s):
Alexander Gheorghiu, Peter V. Coveney, Alya A. Arabi
Published in:
Physical Chemistry Chemical Physics, Issue 23/10, 2021, Page(s) 6252-6265, ISSN 1463-9076
Publisher:
Royal Society of Chemistry
DOI:
10.1039/d0cp06218a
Author(s):
Pablo Herrera-Nieto, Adrià Pérez, Gianni De Fabritiis
Published in:
Journal of Chemical Information and Modeling, Issue 60/10, 2020, Page(s) 5003-5010, ISSN 1549-9596
Publisher:
American Chemical Society
DOI:
10.1021/acs.jcim.0c00381
Author(s):
Z. Altai, M. Viceconti, X. Li, A.C. Offiah
Published in:
Clinical Radiology, Issue 75/1, 2020, Page(s) 78.e9-78.e16, ISSN 0009-9260
Publisher:
W. B. Saunders Co., Ltd.
DOI:
10.1016/j.crad.2019.08.026
Author(s):
Andrea Townsend-Nicholson
Published in:
Interface Focus, Issue 10/6, 2020, Page(s) 20200003, ISSN 2042-8898
Publisher:
Royal Society Publishing
DOI:
10.1098/rsfs.2020.0003
Author(s):
D. Nepal, S Kang, K. M. Adstedt, K. Kanhaiya, M. R. Bockstaller, L. C. Brinson, M. J. Buehler, P. V. Coveney, K. Dayal, J. A. El-Awady, L. C. Henderson, D. L. Kaplan, S. Keten, N. A. Kotov, G. C. Schatz, S. Vignolini, F. Vollrath, Y. Wang, B. I. Yakobson, V. V. Tsukruk, H. Heinz
Published in:
Nature Materials, 2022, ISSN 1476-4660
Publisher:
Nature
DOI:
10.1038/s41563-022-01384-1
Author(s):
Shunzhou Wan, Gary Tresadern, Laura Pérez‐Benito, Herman Vlijmen, Peter V. Coveney
Published in:
Advanced Theory and Simulations, Issue 3/1, 2019, Page(s) 1900195, ISSN 2513-0390
Publisher:
John Wiley & Sons
DOI:
10.1002/adts.201900195
Author(s):
S. Wan, A. Bhati, D. Wright, I. Wall, A. Graves, D. Green, P. V. Coveney
Published in:
J. Chem. Inf. Model., 2022, ISSN 1549-960X
Publisher:
ACS
DOI:
10.1021/acs.jcim.2c00255
Author(s):
Peter V. Coveney, Roger R. Highfield
Published in:
Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Issue 379/2197, 2021, ISSN 1364-503X
Publisher:
Royal Society of London
DOI:
10.1098/rsta.2020.0067
Author(s):
Marco Viceconti, Muhammad Qasim, Pinaki Bhattacharya, Xinshan Li
Published in:
Current Osteoporosis Reports, Issue 16/3, 2018, Page(s) 216-223, ISSN 1544-1873
Publisher:
Current Science Inc.
DOI:
10.1007/s11914-018-0438-8
Author(s):
D. Groen, H. Arabnejad, D. Suleimenova, W. Edeling, E. Raffin, Y. Xue, K. Bronik, N. Monnier, P. V. Coveney
Published in:
Computer Physics Communications, 2022, ISSN 0010-4655
Publisher:
Elsevier BV
DOI:
10.1016/j.cpc.2022.108596
Author(s):
Zainab Altai, Muhammad Qasim, Xinshan Li, Marco Viceconti
Published in:
Clinical Biomechanics, Issue 68, 2019, Page(s) 137-143, ISSN 0268-0033
Publisher:
Pergamon Press Ltd.
DOI:
10.1016/j.clinbiomech.2019.06.004
Author(s):
Sha Li, Bastien Chopard, Jonas Latt
Published in:
Journal of Computational Science, Issue 38, 2019, Page(s) 101045, ISSN 1877-7503
Publisher:
Elsevier BV
DOI:
10.1016/j.jocs.2019.101045
Author(s):
Peter V. Coveney, Roger R. Highfield
Published in:
Journal of Computational Science, Issue 46, 2020, Page(s) 101093, ISSN 1877-7503
Publisher:
Elsevier BV
DOI:
10.1016/j.jocs.2020.101093
Author(s):
B. J. M. van Rooij, G. Závodszky, A. G. Hoekstra, D. N. Ku
Published in:
Interface Focus, Issue 11/1, 2021, Page(s) 20190126, ISSN 2042-8898
Publisher:
Royal Society Publishing
DOI:
10.1098/rsfs.2019.0126
Author(s):
Zainab Altai, Erica Montefiori, Bart van Veen, Margaret A. Paggiosi, Eugene V. McCloskey, Marco Viceconti, Claudia Mazzà, Xinshan Li
Published in:
PLOS ONE, Issue 16/2, 2021, Page(s) e0245121, ISSN 1932-6203
Publisher:
Public Library of Science
DOI:
10.1371/journal.pone.0245121
Author(s):
Philip W. Fowler
Published in:
Interface Focus, Issue 10/6, 2020, Page(s) 20190141, ISSN 2042-8898
Publisher:
Royal Society Publishing
DOI:
10.1098/rsfs.2019.0141
Author(s):
J. W. S. McCullough, R. A. Richardson, A. Patronis, R. Halver, R. Marshall, M. Ruefenacht, B. J. N. Wylie, T. Odaker, M. Wiedemann, B. Lloyd, E. Neufeld, G. Sutmann, A. Skjellum, D. Kranzlmüller, P. V. Coveney
Published in:
Interface Focus, Issue 11/1, 2021, Page(s) 20190119, ISSN 2042-8898
Publisher:
Royal Society Publishing
DOI:
10.1098/rsfs.2019.0119
Author(s):
Shunzhou Wan, Andrew Potterton, Fouad S. Husseini, David W. Wright, Alexander Heifetz, Maciej Malawski, Andrea Townsend-Nicholson, Peter V. Coveney
Published in:
Interface Focus, Issue 10/6, 2020, Page(s) 20190128, ISSN 2042-8898
Publisher:
Royal Society Publishing
DOI:
10.1098/rsfs.2019.0128
Author(s):
Benjamin Csippa, Dániel Gyürki, Gábor Závodszky, István Szikora, György Paál
Published in:
Cardiovascular Engineering and Technology, Issue 11/1, 2020, Page(s) 1-13, ISSN 1869-408X
Publisher:
Springer Pub. Co.,
DOI:
10.1007/s13239-019-00445-y
Author(s):
Pablo Herrera-Nieto, Adrià Pérez, Gianni De Fabritiis
Published in:
Scientific Reports, Issue 10/1, 2020, ISSN 2045-2322
Publisher:
Nature Publishing Group
DOI:
10.1038/s41598-020-69322-2
Author(s):
Benjamin Czaja, Mario Gutierrez, Gábor Závodszky, David de Kanter, Alfons Hoekstra, Omolola Eniola-Adefeso
Published in:
PLOS Computational Biology, Issue 16/3, 2020, Page(s) e1007716, ISSN 1553-7358
Publisher:
PLOS
DOI:
10.1371/journal.pcbi.1007716
Author(s):
Christos Kotsalos, Jonas Latt, Joel Beny, Bastien Chopard
Published in:
Interface Focus, Issue 11/1, 2021, Page(s) 20190116, ISSN 2042-8898
Publisher:
Royal Society Publishing
DOI:
10.1098/rsfs.2019.0116
Author(s):
A. Wade, A. P. Bhati, S. Wan, P. V. Coveney
Published in:
J. Chem. Theory Comput, 2022, ISSN 1549-9626
Publisher:
ACS
DOI:
10.1021/acs.jctc.2c00114
Author(s):
B. J. M. van Rooij, G. Závodszky, V. W. Azizi Tarksalooyeh, A. G. Hoekstra
Published in:
Journal of The Royal Society Interface, Issue 16/159, 2019, Page(s) 20190148, ISSN 1742-5689
Publisher:
The Royal Society
DOI:
10.1098/rsif.2019.0148
Author(s):
Benjamin Czaja, Gábor Závodszky, Alfons Hoekstra
Published in:
Computational Science – ICCS 2020 - 20th International Conference, Amsterdam, The Netherlands, June 3–5, 2020, Proceedings, Part VI, Issue 12142, 2020, Page(s) 403-409, ISBN 978-3-030-50432-8
Publisher:
Springer International Publishing
DOI:
10.1007/978-3-030-50433-5_31
Author(s):
Alexander Heifetz, Andrea Townsend-Nicholson
Published in:
Quantum Mechanics in Drug Discovery, Issue 2114, 2020, Page(s) 177-186, ISBN 978-1-0716-0281-2
Publisher:
Springer US
DOI:
10.1007/978-1-0716-0282-9_12
Author(s):
Alexander Heifetz, Tim James, Michelle Southey, Inaki Morao, Dmitri G. Fedorov, Mike J. Bodkin, Andrea Townsend-Nicholson
Published in:
Quantum Mechanics in Drug Discovery, Issue 2114, 2020, Page(s) 163-175, ISBN 978-1-0716-0281-2
Publisher:
Springer US
DOI:
10.1007/978-1-0716-0282-9_11
Author(s):
Alexander Heifetz, Vladimir Sladek, Andrea Townsend-Nicholson, Dmitri G. Fedorov
Published in:
Quantum Mechanics in Drug Discovery, Issue 2114, 2020, Page(s) 187-205, ISBN 978-1-0716-0281-2
Publisher:
Springer US
DOI:
10.1007/978-1-0716-0282-9_13
Author(s):
Matthew Habgood, Tim James, Alexander Heifetz
Published in:
Quantum Mechanics in Drug Discovery, Issue 2114, 2020, Page(s) 207-229, ISBN 978-1-0716-0281-2
Publisher:
Springer US
DOI:
10.1007/978-1-0716-0282-9_14
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