Centre of Excellence for Biomolecular Research

Deliverables

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

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

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

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

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

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

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