BioExcel Building Blocks People & References

People & References

The BioExcel Building Blocks library is a collaboration from different research groups, all of them involved in the BioExcel centre of Excellence.

People

Main Developers

Pau Andrio

Software Research Engineer

BSC - CNS - Life Sciences, INB Computational Node 2

Genís Bayarri

Full Stack Developer

IRB Barcelona - Molecular Modeling and Bioinformatics
 

Laia Codó

Software Research Engineer

BSC - CNS - Life Sciences, INB Computational Node 2

Luis Jordà

Research Student

BSC - CNS - Life Sciences, INB Computational Node 2
 

Coordinators

Adam Hospital

Research Associate

IRB Barcelona - Molecular Modeling and Bioinformatics
 

Modesto Orozco

Group Leader

IRB Barcelona - Molecular Modeling and Bioinformatics
 

Josep Lluís Gelpí

INB - Computational Group Manager

BSC - CNS - Life Sciences, INB Computational Node 2

Contributors

Ania Niewielska (EBI), Alberto Eusebi (EBI), Felix Xavier Amaladoss (EBI), Stian Soiland-Reyes (UNIMAN), Robin Long (UNIMAN), Douglas Lowe (UNIMAN), Carole Goble (UNIMAN), Rosa Maria Badia (BSC), Daniele Lezzi (BSC), Javier Conejero (BSC), Jorge Ejarque (BSC), Marc del Pino (BSC)

References

BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows.
Pau Andrio, Adam Hospital, Javier Conejero, Luis Jordá, Marc Del Pino, Laia Codo, Stian Soiland-Reyes, Carole Goble, Daniele Lezzi, Rosa M. Badia, Modesto Orozco & Josep Ll. Gelpi.
Nature Scientific Data, 09/2019, Volume 6, Issue 1, p.169, (2019)

Towards FAIR principles for research software
Lamprecht Anna-Lena, Garcia Leyla, Kuzak Mateusz, Martinez Carlos, Arcila Ricardo, Martin Del Pico Eva, Dominguez Del Angel Victoria, van de Sandt Stephanie, Ison Jon, Martinez Paula Andrea, McQuilton Peter, Valencia Alfonso. Harrow Jennifer. Psomopoulos Fotis, Gelpi Josep Ll., Chue Hong Neil, Goble Caroleu, Capella-Gutierrez, Salvador. 10.3233/DS-190026. Data Science, vol. Pre-press, no. Pre-press, pp. 1-23, 2019

GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers
Mark James Abraham, Teemu Murtola, Roland Schulz, Szilárd Páll, Jeremy C.Smith, Berk Hess, Erik Lindahl.
ScienceDirect, Volumes 1–2, September 2015, Pages 19-25

More bang for your buck: Improved use of GPU nodes for GROMACS 2018
Carsten Kutzner, Szilárd Páll, Martin Fechner, Ansgar Esztermann, Bert L. de Groot, Helmut Grubmüller.
Journal of Computational Chemistry, Volume 40, Issue 27. October 15, 2019.Pages 2418-2431.

pmx: Automated protein structure and topology generation for alchemical perturbations
Vytautas Gapsys, Servaas Michielssens, Daniel Seeliger, Bert L. de Groot.
Journal of Computational Chemistry, Volume 36, Issue 5. February 15, 2015.

Open Babel: An open chemical toolbox.
O'Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR.
Journal of Cheminformatics, 2011 Oct 7;3:33. doi: 10.1186/1758-2946-3-33.

ACPYPE - AnteChamber PYthon Parser interfacE
Alan W Sousa da Silva & Wim F Vranken.
BMC Research Notes, 5, Article number: 367 (2012).

Biopython: freely available Python tools for computational molecular biology and bioinformatics.
Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczynski B, de Hoon MJ.
Bioinformatics, 2009 Jun 1;25(11):1422-3. doi: 10.1093/bioinformatics/btp163. Epub 2009 Mar 20.

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data
Daniel R. Roe, Thomas E. Cheatham, III
J. Chem. Theory Comput. 2013, 9, 7, 3084-3095. https://doi.org/10.1021/ct400341p.

AMBER 2018
D.A. Case, I.Y. Ben-Shalom, S.R. Brozell, D.S. Cerutti, T.E. Cheatham, III, V.W.D. Cruzeiro, T.A. Darden, R.E. Duke, D. Ghoreishi, M.K. Gilson, H. Gohlke, A.W. Goetz, D. Greene, R Harris, N. Homeyer, S. Izadi, A. Kovalenko, T. Kurtzman, T.S. Lee, S. LeGrand, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, D.J. Mermelstein, K.M. Merz, Y. Miao, G. Monard, C. Nguyen, H. Nguyen, I. Omelyan, A. Onufriev, F. Pan, R. Qi, D.R. Roe, A. Roitberg, C. Sagui, S. Schott-Verdugo, J. Shen, C.L. Simmerling, J. Smith, R. Salomon-Ferrer, J. Swails, R.C. Walker, J. Wang, H. Wei, R.M. Wolf, X. Wu, L. Xiao, D.M. York and P.A. Kollman (2018), University of California, San Francisco.