Deliverables Documents, reports (23) Dissemination report and updated plan This document will report on the status and outcome of the dissemination/outreach activities, and present plans about their execution in the second half of the project. Long-term hardware/software assessment for pilot applications and the general community A report discussing future hardware developments and their impact on the pilot applications; update to D1.3 Selection and Establishment of User Groups A report detailing the selection of User Groups and how they were established including the provision of social media and other collaborative tools Quality assurance and risk management plan. This deliverable will discuss the overall quality monitoring process for the project (such as deliverables and milestone completion) and the overall risk management strategy. The risks will be regularly assessed in the yearly management report. The deliverable will also include the targets of the KPIs and success criteria, which will be followed-up in the management reports. Revised business plan - update A revision of D5.2 based on additional work with external consulting company. Initial business plan. An initial business plan based on the sketch in this proposal and initial experiences in WP3 will be developed. Consultancy Modalities and Funding Options, Half-time Update Yearly Update of the Consultancy Modalities and Funding Options User feedback and future roadmap. This deliverable will collect user feedback and identify future developments for the BioExcel supported environments. Specification of software engineering, testing & QA A report specifying the software engineering, testing, and quality assurance aspects of the project. Roadmap of future hardware and long-term development plan for each pilot application. A report discussing future hardware developments and their impact on the pilot applications. Training report and updated plan This document will report on the status of the generated training material, its usage and recommendation for its further improvements. The document will also contain evaluation of the completed training activities and recommendations for future ones. Recommendations for BioExcel training programme. This document will report on the outcome from the evaluation of the training needs and the plans for further training activities. Dissemination and outreach plan This document will outline the overall plan for dissemination and outreach activities. Revised business plan. A revision of D5.1 based on further experiences in WP3. Final report on dissemination and training This document will present a final report on the dissemination, outreach and training activities. Consultancy Proposals Update Update on the Consultancy Proposals Efficacy of Feedback Process A report on the efficacy of the feedback process. This deliverable will also cover the project’s agreed measures of success. Governance and Business plan A proposed governance structure with defined roles, responsibilities and internal communication processes will be developed together with the final revised business plan. This will also include proposals for a legal structure to be implemented for the CoE after the funding period is over. According to the recommendations at the 2nd EC review an external consultant, contracted under Article 10, will be used to validate the business plan. State of the art and Gap analysis This deliverable will report state of the art of portable environments for computing, will identify technological gaps based on the defined use cases and initial user feedback from WP3, and propose an initial roadmap. Management plan Initial deliverable stating the management organization and planning for the entire project. Consultancy Proposals. A report summarising the consultancy proposals developed by the BioExcel partners either for their benefit or for a collaborating organisation Competency framework, mapping to current training & initial training plan Working with our users, we will agree on the competencies that they require to make the most of HPC for their research and then match these competencies to those already provided by existing training programmes so that we can focus on developing new training that meets currently unmet needs. Consultancy Modalities and Funding Options, Final Update Final Update of Consultancy Modalities and Funding Options Other (4) Final release of workflows and modular tools for user services. The final release will try to integrate user feedback provided in D2.3 and build a development plan for future developments. First project release of all pilot applications Public release of the pilot applications with documentation. First release of workflows blocks and portals The fist release of the customized environments as laid out in D2.1 will provide pilot users the opportunity to evaluate our platform and provide feedback. Final project releases of pilot applications Final public release of the pilot applications, including task-level parallelism and throughput modules, as well as a report of software achievements in the project and strategies for best usage of extreme-scale resources. Publications Conference proceedings (3) The Archive and Package (arcp) URI scheme Author(s): Stian Soiland-Reyes Marcos Cáceres Published in: 2018 IEEE 14th International Conference on e-Science (e-Science), 2018, Page(s) 5, ISBN 978-1-5386-9156-4 Publisher: IEEE DOI: 10.1109/eScience.2018.0001 I'll take that to go: Big data bags and minimal identifiers for exchange of large, complex datasets Author(s): Kyle Chard, Mike D'Arcy, Ben Heavner, Ian Foster, Carl Kesselman, Ravi Madduri, Alexis Rodriguez, Stian Soiland-Reyes, Carole Goble, Kristi Clark, Eric W. Deutsch, Ivo Dinov, Nathan Price, Arthur Toga Published in: 2016 IEEE International Conference on Big Data (Big Data), 2016, Page(s) 319-328, ISBN 978-1-4673-9005-7 Publisher: IEEE DOI: 10.1109/BigData.2016.7840618 Developing a Benchmark Suite for Semantic Web Data from Existing Workflows Author(s): Troumpoukis, Antonis; Charalambidis, Angelos; Mouchakis, Giannis; Konstantopoulos, Stasinos; Siebes, Ronald; de Boer, Victor; Soiland-Reyes, Stian; Digles, Daniela Published in: Proceedings of the Workshop on Benchmarking Linked Data (BLINK 2016) co-located with the 15th International Semantic Web Conference (ISWC), Issue 1700, 2016, ISSN 1613-0073 Publisher: CEUR-WS DOI: 10.5281/zenodo.159568 Peer reviewed articles (41) Enabling precision medicine via standard communication of HTS provenance, analysis, and results Author(s): 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 Published in: PLOS Biology, Issue 16/12, 2018, Page(s) e3000099, ISSN 1545-7885 Publisher: PLOS DOI: 10.1371/journal.pbio.3000099 Robust Cross-Platform Workflows: How Technical and Scientific Communities Collaborate to Develop, Test and Share Best Practices for Data Analysis Author(s): 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 Published in: Data Science and Engineering, Issue 2/3, 2017, Page(s) 232-244, ISSN 2364-1185 Publisher: Springer Nature Switzerland DOI: 10.1007/s41019-017-0050-4 Protein–ligand pose and affinity prediction: Lessons from D3R Grand Challenge 3 Author(s): Panagiotis I. Koukos, Li C. Xue, Alexandre M. J. J. Bonvin Published in: Journal of Computer-Aided Molecular Design, Issue 33/1, 2019, Page(s) 83-91, ISSN 0920-654X Publisher: Kluwer Academic Publishers DOI: 10.1007/s10822-018-0148-4 Large-scale prediction of binding affinity in protein–small ligand complexes: the PRODIGY-LIG web server Author(s): Anna Vangone, Joerg Schaarschmidt, Panagiotis Koukos, Cunliang Geng, Nevia Citro, Mikael E Trellet, Li C Xue, Alexandre M J J Bonvin Published in: Bioinformatics, 2018, ISSN 1367-4803 Publisher: Oxford University Press DOI: 10.1093/bioinformatics/bty816 A Membrane Protein Complex Docking Benchmark Author(s): Panagiotis I. Koukos, Inge Faro, Charlotte W. van Noort, Alexandre M.J.J. Bonvin Published in: Journal of Molecular Biology, Issue 430/24, 2018, Page(s) 5246-5256, ISSN 0022-2836 Publisher: Academic Press DOI: 10.1016/j.jmb.2018.11.005 Consistent Prediction of Mutation Effect on Drug Binding in HIV-1 Protease Using Alchemical Calculations Author(s): Tomas Bastys, Vytautas Gapsys, Nadezhda T. Doncheva, Rolf Kaiser, Bert L. de Groot, Olga V. Kalinina Published in: Journal of Chemical Theory and Computation, Issue 14/7, 2018, Page(s) 3397-3408, ISSN 1549-9618 Publisher: American Chemical Society DOI: 10.1021/acs.jctc.7b01109 Permeability and ammonia selectivity in aquaporin TIP2;1: linking structure to function Author(s): Viveca Lindahl, Pontus Gourdon, Magnus Andersson, Berk Hess Published in: Scientific Reports, Issue 8/1, 2018, ISSN 2045-2322 Publisher: Nature Publishing Group DOI: 10.1038/s41598-018-21357-2 Defining distance restraints in HADDOCK Author(s): Alexandre M. J. J. Bonvin, Ezgi Karaca, Panagiotis L. Kastritis, João P. G. L. M. Rodrigues Published in: Nature Protocols, Issue 13/7, 2018, Page(s) 1503-1503, ISSN 1754-2189 Publisher: Nature Publishing Group DOI: 10.1038/s41596-018-0017-6 GROmaρs: A GROMACS-Based Toolset to Analyze Density Maps Derived from Molecular Dynamics Simulations Author(s): Rodolfo Briones, Christian Blau, Carsten Kutzner, Bert L. de Groot, Camilo Aponte-Santamaría Published in: Biophysical Journal, Issue 116/1, 2019, Page(s) 4-11, ISSN 0006-3495 Publisher: Biophysical Society DOI: 10.1016/j.bpj.2018.11.3126 iSEE: Interface structure, evolution, and energy-based machine learning predictor of binding affinity changes upon mutations Author(s): Cunliang Geng, Anna Vangone, Gert E. Folkers, Li C. Xue, Alexandre M. J. J. Bonvin Published in: Proteins: Structure, Function, and Bioinformatics, Issue 87/2, 2019, Page(s) 110-119, ISSN 0887-3585 Publisher: Wiley-Liss Inc DOI: 10.1002/prot.25630 Performance of HADDOCK and a simple contact-based protein–ligand binding affinity predictor in the D3R Grand Challenge 2 Author(s): 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 Published in: Journal of Computer-Aided Molecular Design, Issue 32/1, 2018, Page(s) 175-185, ISSN 0920-654X Publisher: Kluwer Academic Publishers DOI: 10.1007/s10822-017-0049-y Distinguishing crystallographic from biological interfaces in protein complexes: role of intermolecular contacts and energetics for classification Author(s): Katarina Elez, Alexandre M. J. J. Bonvin, Anna Vangone Published in: BMC Bioinformatics, Issue 19/S15, 2018, ISSN 1471-2105 Publisher: BioMed Central DOI: 10.1186/s12859-018-2414-9 SpotOn: High Accuracy Identification of Protein-Protein Interface Hot-Spots Author(s): 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 Published in: Scientific Reports, Issue 7/1, 2017, ISSN 2045-2322 Publisher: Nature Publishing Group DOI: 10.1038/s41598-017-08321-2 M3: an integrative framework for structure determination of molecular machines Author(s): Ezgi Karaca, João P G L M Rodrigues, Andrea Graziadei, Alexandre M J J Bonvin, Teresa Carlomagno Published in: Nature Methods, Issue 14/9, 2017, Page(s) 897-902, ISSN 1548-7091 Publisher: Nature Publishing Group DOI: 10.1038/nmeth.4392 Protein Flexibility and Synergy of HMG Domains Underlie U-Turn Bending of DNA by TFAM in Solution Author(s): Anna Rubio-Cosials, Federica Battistini, Alexander Gansen, Anna Cuppari, Pau Bernadó, Modesto Orozco, Jörg Langowski, Katalin Tóth, Maria Solà Published in: Biophysical Journal, Issue 114/10, 2018, Page(s) 2386-2396, ISSN 0006-3495 Publisher: Biophysical Society DOI: 10.1016/j.bpj.2017.11.3743 Alchemical Free Energy Calculations for Nucleotide Mutations in Protein–DNA Complexes Author(s): Vytautas Gapsys, Bert L. de Groot Published in: Journal of Chemical Theory and Computation, Issue 13/12, 2017, Page(s) 6275-6289, ISSN 1549-9618 Publisher: American Chemical Society DOI: 10.1021/acs.jctc.7b00849 Targeting RNA structure in SMN2 reverses spinal muscular atrophy molecular phenotypes Author(s): 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 Published in: Nature Communications, Issue 9/1, 2018, ISSN 2041-1723 Publisher: Nature Publishing Group DOI: 10.1038/s41467-018-04110-1 The Differential Response of Proteins to Macromolecular Crowding Author(s): Michela Candotti, Modesto Orozco Published in: PLOS Computational Biology, Issue 12/7, 2016, Page(s) e1005040, ISSN 1553-7358 Publisher: Public Library of Science (PLoS) DOI: 10.1371/journal.pcbi.1005040 PMut: a web-based tool for the annotation of pathological variants on proteins, 2017 update Author(s): Víctor López-Ferrando, Andrea Gazzo, Xavier de la Cruz, Modesto Orozco, Josep Ll Gelpí Published in: Nucleic Acids Research, 2017, ISSN 0305-1048 Publisher: Oxford University Press DOI: 10.1093/nar/gkx313 Prediction and validation of protein intermediate states from structurally rich ensembles and coarse-grained simulations Author(s): Laura Orellana, Ozge Yoluk, Oliver Carrillo, Modesto Orozco, Erik Lindahl Published in: Nature Communications, Issue 7, 2016, Page(s) 12575, ISSN 2041-1723 Publisher: Nature Publishing Group DOI: 10.1038/ncomms12575 Long-timescale dynamics of the Drew?Dickerson dodecamer Author(s): Pablo D. Dans, Linda Danil?ne, Ivan Ivani, Tom?? Dr?ata, Filip Lanka?, Adam Hospital, J?rgen Walther, Ricard Illa Pujagut, Federica Battistini, Josep Lluis Gelp?, Richard Lavery, Modesto Orozco Published in: Nucleic Acids Research, Issue 44/9, 2016, Page(s) 4052-4066, ISSN 0305-1048 Publisher: Oxford University Press DOI: 10.1093/nar/gkw264 pyPcazip: A PCA-based toolkit for compression and analysis of molecular simulation data Author(s): Ardita Shkurti, Ramon Goni, Pau Andrio, Elena Breitmoser, Iain Bethune, Modesto Orozco, Charles A. Laughton Published in: SoftwareX, Issue 5, 2016, Page(s) 44-50, ISSN 2352-7110 Publisher: Elsevier B.V. DOI: 10.1016/j.softx.2016.04.002 BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data Author(s): Adam Hospital, Pau Andrio, Cesare Cugnasco, Laia Codo, Yolanda Becerra, Pablo D. Dans, Federica Battistini, Jordi Torres, Ramón Goñi, Modesto Orozco, Josep Ll. Gelpí Published in: Nucleic Acids Research, Issue 44/D1, 2016, Page(s) D272-D278, ISSN 0305-1048 Publisher: Oxford University Press DOI: 10.1093/nar/gkv1301 Parmbsc1: a refined force field for DNA simulations Author(s): Ivan Ivani, Pablo D Dans, Agnes Noy, Alberto Pérez, Ignacio Faustino, Adam Hospital, Jürgen Walther, Pau Andrio, Ramon Goñi, Alexandra Balaceanu, Guillem Portella, Federica Battistini, Josep Lluis Gelpí, Carlos González, Michele Vendruscolo, Charles A Laughton, Sarah A Harris, David A Case, Modesto Orozco Published in: Nature Methods, 2015, ISSN 1548-7091 Publisher: Nature Publishing Group DOI: 10.1038/nmeth.3658 Proton Dynamics in Protein Mass Spectrometry Author(s): Jinyu Li, Wenping Lyu, Giulia Rossetti, Albert Konijnenberg, Antonino Natalello, Emiliano Ippoliti, Modesto Orozco, Frank Sobott, Rita Grandori, Paolo Carloni Published in: The Journal of Physical Chemistry Letters, Issue 8/6, 2017, Page(s) 1105-1112, ISSN 1948-7185 Publisher: American Chemical Society DOI: 10.1021/acs.jpclett.7b00127 Environmental and genetic factors support the dissociation between ?-synuclein aggregation and toxicity Author(s): Anna Villar-Piqu?, Tom?s Lopes da Fonseca, Ricardo Sant?Anna, ?va M?nika Szeg?, Luis Fonseca-Ornelas, Raquel Pinho, Anita Carija, Ellen Gerhardt, Caterina Masaracchia, Enrique Abad Gonzalez, Giulia Rossetti, Paolo Carloni, Claudio O. Fern?ndez, Debora Foguel, Ira Milosevic, Markus Zweckstetter, Salvador Ventura, Tiago Fleming Outeiro Published in: Proceedings of the National Academy of Sciences, Issue 113/42, 2016, Page(s) E6506-E6515, ISSN 0027-8424 Publisher: National Academy of Sciences DOI: 10.1073/pnas.1606791113 Challenges of docking in large, flexible and promiscuous binding sites Author(s): Martin Kotev, Robert Soliva, Modesto Orozco Published in: Bioorganic & Medicinal Chemistry, Issue 24/20, 2016, Page(s) 4961-4969, ISSN 0968-0896 Publisher: Pergamon Press Ltd. DOI: 10.1016/j.bmc.2016.08.010 dMM-PBSA: A New HADDOCK Scoring Function for Protein-Peptide Docking Author(s): Dimitrios Spiliotopoulos, Panagiotis L. Kastritis, Adrien S. J. Melquiond, Alexandre M. J. J. Bonvin, Giovanna Musco, Walter Rocchia, Andrea Spitaleri Published in: Frontiers in Molecular Biosciences, Issue 3, 2016, ISSN 2296-889X Publisher: Frontiers DOI: 10.3389/fmolb.2016.00046 The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes Author(s): G.C.P. van Zundert, J.P.G.L.M. Rodrigues, M. Trellet, C. Schmitz, P.L. Kastritis, E. Karaca, A.S.J. Melquiond, M. van Dijk, S.J. de Vries, A.M.J.J. Bonvin Published in: Journal of Molecular Biology, Issue 428/4, 2016, Page(s) 720-725, ISSN 0022-2836 Publisher: Academic Press DOI: 10.1016/j.jmb.2015.09.014 Molecular dynamics characterization of the conformational landscape of small peptides: A series of hands-on collaborative practical sessions for undergraduate students Author(s): João P.G.L.M. Rodrigues, Adrien S.J. Melquiond, Alexandre M.J.J. Bonvin Published in: Biochemistry and Molecular Biology Education, Issue 44/2, 2016, Page(s) 160-167, ISSN 1470-8175 Publisher: American Society for Biochemistry and Molecular Biology Inc. DOI: 10.1002/bmb.20941 The DisVis and PowerFit Web Servers: Explorative and Integrative Modeling of Biomolecular Complexes Author(s): G.C.P. van Zundert, M. Trellet, J. Schaarschmidt, Z. Kurkcuoglu, M. David, M. Verlato, A. Rosato, A.M.J.J. Bonvin Published in: Journal of Molecular Biology, Issue 429/3, 2017, Page(s) 399-407, ISSN 0022-2836 Publisher: Academic Press DOI: 10.1016/j.jmb.2016.11.032 Exploring the interplay between experimental methods and the performance of predictors of binding affinity change upon mutations in protein complexes Author(s): Cunliang Geng, Anna Vangone, Alexandre M.J.J. Bonvin Published in: Protein Engineering Design and Selection, Issue 29/8, 2016, Page(s) 291-299, ISSN 1741-0126 Publisher: Oxford University Press DOI: 10.1093/protein/gzw020 Copernicus, a hybrid dataflow and peer-to-peer scientific computing platform for efficient large-scale ensemble sampling Author(s): Iman Pouya, Sander Pronk, Magnus Lundborg, Erik Lindahl Published in: Future Generation Computer Systems, Issue 71, 2017, Page(s) 18-31, ISSN 0167-739X Publisher: Elsevier BV DOI: 10.1016/j.future.2016.11.004 Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2 Author(s): Dari Kimanius, Björn O Forsberg, Sjors HW Scheres, Erik Lindahl Published in: eLife, Issue 5, 2016, ISSN 2050-084X Publisher: eLife Sciences Publications DOI: 10.7554/eLife.18722 Changes in the free-energy landscape of p38? MAP kinase through its canonical activation and binding events as studied by enhanced molecular dynamics simulations Author(s): Antonija Kuzmanic, Ludovico Sutto, Giorgio Saladino, Angel R Nebreda, Francesco L Gervasio, Modesto Orozco Published in: eLife, Issue 6, 2017, ISSN 2050-084X Publisher: eLife Sciences Publications DOI: 10.7554/eLife.22175 Accurate and Rigorous Prediction of the Changes in Protein Free Energies in a Large-Scale Mutation Scan Author(s): Vytautas Gapsys, Servaas Michielssens, Daniel Seeliger, Bert L. de?Groot Published in: Angewandte Chemie International Edition, Issue 55/26, 2016, Page(s) 7364-7368, ISSN 1433-7851 Publisher: John Wiley & Sons Ltd. DOI: 10.1002/anie.201510054 Multiscale simulation of DNA Author(s): Pablo D Dans, J?rgen Walther, Hansel G?mez, Modesto Orozco Published in: Current Opinion in Structural Biology, Issue 37, 2016, Page(s) 29-45, ISSN 0959-440X Publisher: Elsevier BV DOI: 10.1016/j.sbi.2015.11.011 Structure of the bacterial plant-ferredoxin receptor FusA Author(s): Rhys Grinter, Inokentijs Josts, Khedidja Mosbahi, Aleksander W. Roszak, Richard J. Cogdell, Alexandre M. J. J. Bonvin, Joel J. Milner, Sharon M. Kelly, Olwyn Byron, Brian O. Smith, Daniel Walker Published in: Nature Communications, Issue 7, 2016, Page(s) 13308, ISSN 2041-1723 Publisher: Nature Publishing Group DOI: 10.1038/ncomms13308 pmx Webserver: A User Friendly Interface for Alchemistry Author(s): Vytautas Gapsys, Bert L. de Groot Published in: Journal of Chemical Information and Modeling, Issue 57/2, 2017, Page(s) 109-114, ISSN 1549-9596 Publisher: American Chemical Society DOI: 10.1021/acs.jcim.6b00498 The Multiple Roles of Waters in Protein Solvation Author(s): Adam Hospital, Michela Candotti, Josep Llu?s Gelp?, Modesto Orozco Published in: The Journal of Physical Chemistry B, Issue 121/15, 2017, Page(s) 3636-3643, ISSN 1520-6106 Publisher: American Chemical Society DOI: 10.1021/acs.jpcb.6b09676 Structural basis of a histidine-DNA nicking/joining mechanism for gene transfer and promiscuous spread of antibiotic resistance Author(s): Radoslaw Pluta, D. Roeland Boer, Fabián Lorenzo-Díaz, Silvia Russi, Hansel Gómez, Cris Fernández-López, Rosa Pérez-Luque, Modesto Orozco, Manuel Espinosa, Miquel Coll Published in: Proceedings of the National Academy of Sciences, Issue 114/32, 2017, Page(s) E6526-E6535, ISSN 0027-8424 Publisher: National Academy of Sciences DOI: 10.1073/pnas.1702971114 Other (22) BioExcel Whitepaper on Scientific Software Development Author(s): 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 Published in: Issue 3, 2018 Publisher: openAIRE DOI: 10.5281/zenodo.1194633 BioExcel Deliverable 3.4 - Efficacy of Feedback Processes Author(s): Carter, Adam; Harrow, Ian; Abraham, Mark; Hospital, Adam; Matser, Vera; Noack, Holger; Apostolov, Rossen Published in: Issue 3, 2017 Publisher: BioExcel DOI: 10.5281/zenodo.1060843 BioExcel Deliverable 1.2 – First project release of all pilot applications Author(s): Abraham, Mark; Ippoliti, Emiliano; Bonvin, Alexandre; de Groot, Bert; Soiland-Reyes, Stian Published in: Issue 6, 2017 Publisher: BioExcel DOI: 10.5281/zenodo.574459 BioExcel Deliverable 4.1 – Dissemination and Outreach Plan Author(s): Apostolov, Rossen Published in: Issue 37, 2016 Publisher: BioExcel DOI: 10.5281/zenodo.264250 BioExcel Deliverable 4.2 - Competency framework, mapping to current training & initial training plan Author(s): Matser, Vera Published in: Issue 31, 2016 Publisher: BioExcel DOI: 10.5281/zenodo.264231 BioExcel Deliverable 2.1 – State of the art and gap analysis Author(s): 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. Published in: Issue 35, 2016 Publisher: BioExcel DOI: 10.5281/zenodo.263963 BioExcel Deliverable 3.1 - Selection and Establishment of User Groups Author(s): Carter, Adam; Harrow, Ian; Apostolov, Rossen; Soiland-Reyes, Stian; de Groot, Bert; Abraham, Mark Published in: Issue 36, 2016 Publisher: BioExcel DOI: 10.5281/zenodo.264011 BioExcel Deliverable 3.3 – Consultancy Modalities and Funding Options, Half-time Update Author(s): Carter, Adam; Harrow, Ian Published in: Issue 6, 2017 Publisher: BioExcel DOI: 10.5281/zenodo.574613 BioExcel Deliverable 5.1 - Initial Business Plan Author(s): Noack, Holger; Harrow, Ian; Bonvin, Alexandre; Carter, Adam; Apostolov, Rossen; Laure, Erwin Published in: Issue 28, 2016 Publisher: BioExcel DOI: 10.5281/zenodo.263932 BioExcel Deliverable 6.2 – Quality Assurance and Risk Management Plan Author(s): Apostolov, Rossen Published in: Issue 25, 2016 Publisher: BioExcel DOI: 10.5281/zenodo.263934 BioExcel Deliverable 6.1 - Management Plan Author(s): Apostolov, Rossen; Laure, Erwin Published in: Issue 26, 2015 Publisher: BioExcel DOI: 10.5281/zenodo.263933 BioExcel Deliverable 2.2 – First Release of Workflow Blocks and Portals Author(s): 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 Published in: Issue 16, 2016 Publisher: BioExcel DOI: 10.5281/zenodo.263965 BioExcel Deliverable 1.1 - Specification of software engineering, testing & QA Author(s): Abraham, Mark; Bonvin, Alexandre; Melquiond, Adrien; Ippoliti, Emiliano; de Groot, Bert Published in: Issue 17, 2016 Publisher: BioExcel DOI: 10.5281/zenodo.263908 BioExcel Deliverable 4.3 - Recommendations for BioExcel Training Programme Author(s): Matser, Vera Published in: Issue 18, 2016 Publisher: BioExcel DOI: 10.5281/zenodo.263926 BioExcel Deliverable 3.2 – Consultancy Proposals Author(s): Carter, Adam Published in: Issue 9, 2017 Publisher: BioExcel DOI: 10.5281/zenodo.574607 BioExcel Deliverable 1.3 - Roadmap of future hardware and long-term development plan for each pilot application Author(s): Apostolov, Rossen; Abraham, Mark; Laure, Erwin; Lindahl, Erik; Bonvin, Alexandre; de Groot, Bert; Ippoliti, Emiliano Published in: Issue 6, 2017 Publisher: BioExcel DOI: 10.5281/zenodo.574605 BioExcel Deliverable 5.2 - Revised Business Plan Author(s): Noack, Holger; Harrow, Ian; Bonvin, Alexandre; Carter, Adam; Apostolov, Rossen; Laure, Erwin Published in: Issue 6, 2017 Publisher: BioExcel DOI: 10.5281/zenodo.574634 BioExcel Deliverable 4.5 – Training report and updated plan Author(s): Matser, Vera Published in: Issue 6, 2017 Publisher: BioExcel DOI: 10.5281/zenodo.574620 GROMACS 2019.1 Manual Author(s): Lindahl; Abraham; Hess; van der Spoel Published in: Issue 25, 2018 Publisher: BioExcel DOI: 10.5281/zenodo.2564761 GROMACS 2019 Manual Author(s): Lindahl; Abraham; Hess; van der Spoel Published in: Issue 1, 2018 Publisher: BioExcel DOI: 10.5281/zenodo.2424485 Mechanism of Structural Tuning of the Hepatitis C Virus Human Cellular Receptor CD81 Large Extracellular Loop Author(s): Eva S. Cunha, Pedro Sfriso, Adriana L. Rojas, Pietro Roversi, Adam Hospital, Modesto Orozco, Nicola G.A. Abrescia Published in: Structure, Issue 25/1, 2017, Page(s) 53-65 Publisher: Cell Press DOI: 10.1016/j.str.2016.11.003 BioExcel Deliverable 4.4 – Dissemination Report and Updated Plan Author(s): Apostolov, Rossen; Matser, Vera; White, Mirren; Harrow, Ian Published in: Issue 1, 2017 Publisher: BioExcel DOI: 10.5281/zenodo.574614 Non-peer reviewed articles (2) BioExcel Deliverable 2.3 - User Feedback and Future Roadmap Author(s): Hospital, Adam; Gelpí, Josep Lluís; Dianes, Jose A.; Andrio, Pau; White, Darren J.; Ippoliti, Emiliano; Melquiond, Adrien; Gapsys, Vytautas Published in: Zenodo, Issue 3, 2017, ISSN 0000-0000 Publisher: BioExcel DOI: 10.5281/zenodo.1060946 Software release for BioExcel pilot applications Author(s): Mark Abraham Published in: Zenodo, Issue 2, 2018, ISSN 0000-0000 Publisher: BioExcel DOI: 10.5281/zenodo.1473684 Searching for OpenAIRE data... 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