Scalable Software Services for Life Science

Scientific Articles

(For authors only) Acknowledgement formulations

For publications by people working on the project:

"This work has been partially funded by the EU Commission (contract INFSO-RI-261523) through collaboration with ScalaLife"

For publications that were facilitated through ScalaLife (e.g. help of experts, etc.)

"This work makes use of results produced by the ScalaLife project which is co-funded by the European Commission (under contract number INFSO-RI-261523). More information is available at http://www.scalalife.eu".

 

Scientific Publications

  1. (Journal) Tim Meyer, Marco D’Abramo, Adam Hospital, Manuel Rueda, Carles Ferrer-Costa, Alberto Pérez, Oliver Carrillo, Jordi Camps, Carles Fenollosa, Dmitry Repchevsky, Josep Lluis Gelpí, and Modesto Orozco: MoDEL (Molecular Dynamics Extended Library): A Database of Atomistic Molecular Dynamics Trajectories, 18/11, P. 1399-1409, (2010), (doi:10.1016/j.str.2010.07.013).
  2. (Book chapter) Modesto Orozco, Laura Orellana, Adam Hospital, Athi N. Naganathan, Agustí Emperador, Oliver Carrillo and J.L.Gelpí: Coarse Grained Representation of Protein Flexibility. Foundations, Successes and Shortcomings,  In "Computational Chemistry Methods in Structural Biology". Advances in Protein Chemistry and Structural Biology, vol. 80. Ed. C. Christov. Elsevier (2010)
    Note: Articles (1) and (2) are directly related to the achivements in WP7-Interface Definitions & Data Exchange
  3. (Journal) Z. Rinkevicius, N. A. Murugan, J. Kongsted, K. Aidas, A. H. Steindal, and H. Ågren, "Density Functional Theory/Molecular Mechanics Approach for Electronic g-Tensors of Solvated Molecules", J. Phys. Chem. B., http://pubs.acs.org/doi/abs/10.1021/jp1108653
    Note: Article (3) is directly related to the achivements in Dalton software
  4. (Proceedings) Rossen Apostolov, Lilit Axner, Hans Agren, Eduard Ayugade, Mihai Duta, Jose Luis Gelpi, Judit Gimenez, Ramon Goni, Berk Hess, Ferdinand Jamitzky, Dieter Kranzmuller, Jesus Labarta, Erwin Laure, Erik Lindahl, Modesto Orozco, Magnus Peterson, Helmut Satzger, AnneTrefethen, "ScalaLife - Scalable Software Services for Life Science", in Proceedings of 9th HealthGrid conference (2011)
    Note: Article (4) is directly related to the ScalaLife Competence Center
  5. (Proceedings) Xavier Aguilar, Michael Schliephake, Olav Vahtras, Judit Gimenez and Erwin Laure, "Scaling Dalton, a molecular electronic structure program" in 7th IEEE International Conference on eScience (eScience 2011)
  6. (Journal) Z. Rinkevicius, N. A. Murugan, J. Kongsted, B. Frecuş, A. H. Steindal, and H. Ågren, "Density Functional Restricted–Unrestricted/Molecular Mechanics Theory for Hyperfine Coupling Constants of Molecules in Solution", J. Chem. Theory Comput., Articles ASAP,  2011. DOI: 10.1021/ct2003572
    Note: Articles (5) and (6) are directly related to the achivements in Dalton software
  7. (Online) ScalaLife in Scientific Computer World: http://www.bsc.cat/about-bsc/press/bsc-in-the-media/visualising-future-medicine or http://www.scientific-computing.com/signIn.php?issue_id=22&pageStartFrom=42
  8. (Journal) Joakim P. M. Jämbeck, Alexander P. Lyubartsev, "An Extension and Further Validation of an All-Atomistic Force Field for Biological Membranes", J. Chem. Theory Comput., DOI: 10.1021/ct300342n, June 26, 2012
  9. (White paper) Simen Reine,Thomas Kjærgaard, Trygve Helgaker, Olav Vahtras, Zilvinas Rinkevicius, Bogdan Frecus, Thomas W. Keal, Andrew Sunderland, Paul Sherwood, Michael Schliephake, Xavier Aguilar, Lilit Axner, Maria Francesca Iozzi, Ole Widar Saastad, Judit Gimenez, "Petascaling and Performance Analysis of DALTON on Different Platforms", PRACE white paper: (http://www.prace-ri.eu/IMG/pdf/Petascaling_and_Performance_Analysis_of_D...)
  10. (White paper) Fabio Affinito, Andrew Emerson, Leandar Litov, Peicho Petkov, Rossen Apostolov, Lilit Axner, Berk Hess, Erik Lindahl, Maria Francesca Iozzi, "Performance Analysis and Petascaling Enabling of GROMACS", PRACE white paper (http://www.prace-ri.eu/IMG/pdf/Performance_Analysis_and_Petascaling_Enab...)
  11. (Journal) Joakim P.M. Jämbeck and Alexander P. Lyubartsev, "Another Piece of the Membrane Puzzle: Extending Slipids Further", J. Chem. Theory Comput., DOI: 10.1021/ct300777p
  12. (Proceedings) Rossen Apostolov, Hans Agren, Lilit Axner, Eduard Ayguade, Mihai Duta, Jose Luis Gelpi, Judit Gimenez, Ramon Goni,
    Berk Hess, Ferdinand Jamitzky, Dieter Kranzmueller, Jesus Labarta, Erwin Laure, Erik Lindahl, Modesto Orozco, Magnus Peterson,
    Helmut Satzger, Albert Solernou, Anne Trefethen, "ScalaLife – Scalable Software Services for Life Sciences" in eChallenges e-2012 Conference Proceedings, (2012). View paper
  13. (Journal) Pedro Sfriso, Agusti Emperador, Laura Orellana, Adam Hospital, Josep Lluis Gelpí, and Modesto Orozco, "Finding Conformational Transition Pathways from Discrete Molecular Dynamics Simulations", J. Chem. Theory Comput., 2012, 8 (11), pp 4707–4718, DOI: 10.1021/ct300494q (August 23, 2012)
  14. (Journal) Xavier Aguilar, Michael Schliephake, Olav Vahtras, Judit Gimenez, Erwin Laure, "Scalability analysis of Dalton, a molecular structure program", Future Generation Computer Systems, Volume 29, Issue 8, October 2013, Pages 2197–2204, doi:10.1016/j.future.2013.04.013
  15. (Journal) Jaime Axel Rosal Sandberg and Zilvinas Rinkevicius, "An algorithm for the efficient evaluation of two-electron repulsion integrals over contracted Gaussian-type basis functions", J. Chem. Phys. 137, 234105 (2012)
  16. (Journal) Adam Hospital, Pau Andrio, Carles Fenollosa, Dmjan Cicin-Sain, Modesto Orozco and Josep Ll. Gelpí. "MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations.Bioinformatics. ;28(9):1278-1279.  (2102) DOI: 10.1093/bioinformatics/bts139
    Note: Article (16) is directly related to the achivements in WP7-Interface Definitions & Data Exchange
  17. (Journal) Raimondi, F.; Felline, A.; Portella, G.; Orozco, M and Fanelli, F. “Light on the structural communication in Ras GTPases”, J. Biomol. Struct. and Dyn. iFirst, 31(2),142-57, 2013; doi: 10.1080/07391102.2012.698379
  18. (Journal) Carrillo, O., Laughton, C. and Orozco, M. “Fast Atomistic Molecular Dynamics Simulations from Essential Dynamics Samplings”, J. Chem. Theory Comput., 2012, 8 (3), pp 792–799, DOI: 10.1021/ct2007296
  19. (Journal) Fernanda Rodriguez, Sarah L. Rouse, Claudia E. Tait, Jeffrey Harmer, Antonio De Riso, Christiane R. Timmel, Mark S. P. Sansom, Ben C. Berks and Jason R. Schnell, "Structural model for the protein-translocating element of the twin-arginine transport system",
  20. (Journal) Agusti Emperador, Albert Solernou, Pedro Sfriso, Carles Pons, Josep Lluis Gelpi, Juan Fernandez-Recio and Modesto Orozco, "Efficient Relaxation of Protein–Protein Interfaces by Discrete Molecular Dynamics Simulations",
    J. Chem. Theory Comput., 2013, 9 (2), pp 1222–1229,DOI: 10.1021/ct301039e.
  21. (Brochure) Satzger et. al, "Supercomputing at the Leading Edge", published by Gauss Centre for Supercompuing, for ISC2013 (2013)
  22. (Proceedings) A. Solernou, J. Thiyagalingam, M. C. Duta, A. E. Trefethen, "The Effect of Topology-Aware Process and Thread Placement on Performance and Energy", Lect. Notes Comput. Sci., 7905., 2013
  23. (Online, guest feature in InsideHPC) Bader, David, "Understanding the Human Condition with Big Data and HPC", 28 May 2013
  24. (Proceedings) Pronk, S.; Larsson, P.; Pouya, I.; Bowman, G.R.; Haque, I.S.; Beauchamp, K.; Hess, B.; Pande, V.S.; Kasson, P.M.; Lindahl, E., "Copernicus: A new paradigm for parallel adaptive molecular dynamics," High Performance Computing, Networking, Storage and Analysis (SC), 2011 International Conference for , vol., no., pp.1,10, 12-18 Nov. 2011
  25. (Journal) Pronk, S., Páll, S., Schulz, R., Larsson, P., Bjelkmar, P., Apostolov, R., Shirts, M. R., et al. (2013). GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics (Oxford, England), 29(7), 845–854. doi:10.1093/bioinformatics/btt055
  26. (Proceedings) Greiner, M., Elts, E., Briesen, H. Molecular Dynamics Simulations as a predictive tool for the behavior of fats in high-pressure processes. In Proceedings of the VII international conference on Simulation and Modelling in the Food and Bio-Industry “FOODSIM’2012”, p. 10-14, Freising, Germany, 2012, ISBN: 978-90-77381-72-4; EAN: 978-90-77381-72-4.
  27. (Journal) Szilárd Páll, Berk Hess, A flexible algorithm for calculating pair interactions on SIMD architectures, Computer Physics Communications, Available online 13 June 2013, ISSN 0010-4655, http://dx.doi.org/10.1016/j.cpc.2013.06.003.
  28. (In preparation) Szilárd Páll, Berk Hess, and Erik Lindahl, Heterogeneous GPU acceleration in GROMACS. 2013
  29. (Journal) Magnus Lundborg, Rossen Apostolov, Daniel Spangberg, Anders Gardenas, David van der Spoel, Erik Lindahl, "Efficient and Extensible Format, Library and API for Binary Trajectory Data from Molecular Simulations", 2013, JCC (accepted with minor revisions)
  30. (journal) Murugan, N.; Apostolov, Rossen; Rinkevicius, Zilvinas; Kongsted, Jacob; Lindahl, Erik; Ågren, Hans, “Association dynamics, linear and non-linear optical properties of an N-acetylaladanamide probe in a POPC membrane”, JACS,  135 (36), pp 13590–13597, http://dx.doi.org/10.1021/ja407326n, 2013
  31. (journal) Jaime Axel Rosal Sandberg, Zilvinas Rinkevicius, "New recurrence relations for analytic evaluation of two-electron repulsion integrals over highly contracted gaussian-type orbitals", (In preparation)
  32. (Brochure) Helmut Satzger, Rossen Apostolov, Lilit Axner, Mihai Duta, Judit Gimenez, Ramon Goni, Berk Hess, Ferdinand Jamitzky, Erwin Laure, Albert Solernou, Momme Allalen, Christoph Bernau, Zilvinas Rinkevicius, Modesto Orozco, Josep Lluis Gelpí, Agusti Emperador, “How the ScalaLife project integrates software developers, computing centres and life science researchers“, InSIDE Journal on Innovation Supercomputing in Germany, Spring 2013, vol. 11, No.1, http://inside.hlrs.de/pdfs/inSiDE_spring2013.pdf
  33. (Book chapter) Carsten Kutzner , Rossen Apostolov, Berk Hess, and Helmut Grubmuller, “Scaling of the GROMACS 4.6 molecular dynamics code on SuperMUC”, volume in "Advances of Parallel Computing" series
  34. (White paper) Ramon Goni, Rossen Apostolov, Magnus Lundborg, Christoph Bernau, Ferdinand Jamitzky, Erwin Laure, Erik Lindhal, Pau Andrio, Yolanda Becerra, Modesto Orozco, Josep Lluís Gelpi, "Standards for data handling", 2013.
  35. (in preparation) "Pushing the Scaling Limits of Life Science software"
  36. (in preparation) "Accelerating Gromacs using Convey FPGAs"
  37. (journal) Sarah L. Rouse, Julien Marcoux, Carol V. Robinson, Mark S.P. Sansom, Dodecyl Maltoside Protects Membrane Proteins In Vacuo, Biophysical Journal, Volume 105, Issue 3, 6 August 2013, Pages 648-656, ISSN 0006-3495, http://dx.doi.org/10.1016/j.bpj.2013.06.025. (http://www.sciencedirect.com/science/article/pii/S0006349513007042)
  38. (journal) Guillaume Roussel, Sarah L. Rouse, Mark S.P. Sansom, Catherine Michaux, Eric A. Perpète, The role of 2-methyl-2,4-pentanediol in sodium dodecyl sulfate micelle dissociation unveiled by dynamic light scattering and molecular dynamics simulations, Colloids and Surfaces B: Biointerfaces, Available online 30 October 2013, ISSN 0927-7765, http://dx.doi.org/10.1016/j.colsurfb.2013.10.023.
  39. Ekaterina Elts, Maximilian M. Greiner, and Heiko Briesen, "Data Filtering for Effective Analysis of Crystal–Solution Interface Molecular Dynamics Simulations", March 6, 2014, http://pubs.acs.org/doi/abs/10.1021/ct400808d, Journal of Chemical Theory and Computation
     

Poster presentations

  1. Joakim P. M. Jämbeck, Alexander P. Lyubartsev, "Stockholm lipids: a refined all-atom force field for phospholipids", SeRC Third Annual Meeting 24 April 2012, Stockholm.  View poster.
  2. Szilárd Páll, Berk Hess, Erik Lindahl: Poster: 3D Tixels: A Highly Efficient Algorithm For GPU/CPU-acceleration of Molecular Dynamics on Heterogeneous Parallel Architectures. SC Companion 2011: 71-72
     
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Stockholm Lipids Poster at SeRC Meeting.pdf14.1 MB
eChallenges_ref_73_doc_7985.pdf665.45 KB