BioExcel Building Blocks People & References

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

Main Developers

Coordinators

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)

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)

Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows
Genís Bayarri, Pau Andrio, Josep Lluís Gelpí, Adam Hospital & Modesto Orozco.
PLoS Comput Biol, 20(6): e1012173, 20 june 2024

BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations.
Genís Bayarri, Pau Andrio, Adam Hospital, Modesto Orozco & Josep Lluís Gelpí.
Nucleic Acids Research, Volume 50, Issue W1, 5 July 2022

BioExcel Building Blocks REST API (BioBB REST API), programmatic access to interoperable biomolecular simulation tools.
Genís Bayarri, Pau Andrio, Adam Hospital, Modesto Orozco & Josep Lluís Gelpí.
Bioinformatics, Volume 38, Issue 12, 15 June 2022

Making Canonical Workflow Building Blocks Interoperable across Workflow Languages.
Stian Soiland-Reyes, Genís Bayarri, Pau Andrio, Robin Long, Douglas Lowe, Ania Niewielska, Adam Hospital, Paul Groth.
Data Intelligence, 2022; 4 (2): 342–357. doi: https://doi.org/10.1162/dint_a_00135

The BioExcel methodology for developing dynamic, scalable, reliable and portable computational biomolecular workflows.
Jorge Ejarque, Pau Andrio, Adam Hospital, Javier Conejero, Daniele Lezzi, Josep LL. Gelpi, Rosa M. Badia.
arXiv, arXiv:2208.14130

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.