BioExcel Building Blocks, a Software Library for Interoperable Biomolecular Simulation Workflows

Overview

Journal Sci Data

Specialty Science

Date 2019 Sep 12

PMID 31506435

Citations 11

Authors

Pau Andrio

Adam Hospital

Javier Conejero

Luis Jorda

Marc Del Pino

Laia Codo

Stian Soiland-Reyes

Carole Goble

Daniele Lezzi

Rosa M Badia

Modesto Orozco

Josep Ll Gelpi

Affiliations

Soon will be listed here.

Abstract

In the recent years, the improvement of software and hardware performance has made biomolecular simulations a mature tool for the study of biological processes. Simulation length and the size and complexity of the analyzed systems make simulations both complementary and compatible with other bioinformatics disciplines. However, the characteristics of the software packages used for simulation have prevented the adoption of the technologies accepted in other bioinformatics fields like automated deployment systems, workflow orchestration, or the use of software containers. We present here a comprehensive exercise to bring biomolecular simulations to the "bioinformatics way of working". The exercise has led to the development of the BioExcel Building Blocks (BioBB) library. BioBB's are built as Python wrappers to provide an interoperable architecture. BioBB's have been integrated in a chain of usual software management tools to generate data ontologies, documentation, installation packages, software containers and ways of integration with workflow managers, that make them usable in most computational environments.

Citing Articles

Comprehensive detection and characterization of human druggable pockets through binding site descriptors.

Comajuncosa-Creus A, Jorba G, Barril X, Aloy P Nat Commun. 2024; 15(1):7917.

PMID: 39256431 PMC: 11387482. DOI: 10.1038/s41467-024-52146-3.

Developments and applications of the OPTIMADE API for materials discovery, design, and data exchange.

Evans M, Bergsma J, Merkys A, Andersen C, Andersson O, Beltran D Digit Discov. 2024; 3(8):1509-1533.

PMID: 39118978 PMC: 11305395. DOI: 10.1039/d4dd00039k.

Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows.

Bayarri G, Andrio P, Gelpi J, Hospital A, Orozco M PLoS Comput Biol. 2024; 20(6):e1012173.

PMID: 38900779 PMC: 11189206. DOI: 10.1371/journal.pcbi.1012173.

Rapid proteome-wide prediction of lipid-interacting proteins through ligand-guided structural genomics.

Chou J, Decosto C, Chatterjee P, Dassama L bioRxiv. 2024; .

PMID: 38352308 PMC: 10862712. DOI: 10.1101/2024.01.26.577452.

Thermodynamics and kinetics of DNA and RNA dinucleotide hybridization to gaps and overhangs.

Ashwood B, Jones M, Radakovic A, Khanna S, Lee Y, Sachleben J Biophys J. 2023; 122(16):3323-3339.

PMID: 37469144 PMC: 10465710. DOI: 10.1016/j.bpj.2023.07.009.

References

. Protein Data Bank: the single global archive for 3D macromolecular structure data. Nucleic Acids Res. 2018; 47(D1):D520-D528. PMC: 6324056. DOI: 10.1093/nar/gky949. View

Thibault J, Cheatham 3rd T, Facelli J . iBIOMES Lite: summarizing biomolecular simulation data in limited settings. J Chem Inf Model. 2014; 54(6):1810-9. PMC: 4076027. DOI: 10.1021/ci500173w. View

Jo S, Cheng X, Lee J, Kim S, Park S, Patel D . CHARMM-GUI 10 years for biomolecular modeling and simulation. J Comput Chem. 2016; 38(15):1114-1124. PMC: 5403596. DOI: 10.1002/jcc.24660. View

. UniProt: a worldwide hub of protein knowledge. Nucleic Acids Res. 2018; 47(D1):D506-D515. PMC: 6323992. DOI: 10.1093/nar/gky1049. View

Wilkinson M, Senger M, Kawas E, Bruskiewich R, Gouzy J, Noirot C . Interoperability with Moby 1.0--it's better than sharing your toothbrush!. Brief Bioinform. 2008; 9(3):220-31. DOI: 10.1093/bib/bbn003. View

Rueda M, Ferrer-Costa C, Meyer T, Perez A, Camps J, Hospital A . A consensus view of protein dynamics. Proc Natl Acad Sci U S A. 2007; 104(3):796-801. PMC: 1783393. DOI: 10.1073/pnas.0605534104. View

Hospital A, Andrio P, Fenollosa C, Cicin-Sain D, Orozco M, Gelpi J . MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations. Bioinformatics. 2012; 28(9):1278-9. DOI: 10.1093/bioinformatics/bts139. View

Beisken S, Meinl T, Wiswedel B, de Figueiredo L, Berthold M, Steinbeck C . KNIME-CDK: Workflow-driven cheminformatics. BMC Bioinformatics. 2013; 14:257. PMC: 3765822. DOI: 10.1186/1471-2105-14-257. View

Roopra S, Knapp B, Omasits U, Schreiner W . jSimMacs for GROMACS: a Java application for advanced molecular dynamics simulations with remote access capability. J Chem Inf Model. 2009; 49(10):2412-7. DOI: 10.1021/ci900248f. View

10.

van der Kamp M, Schaeffer R, Jonsson A, Scouras A, Simms A, Toofanny R . Dynameomics: a comprehensive database of protein dynamics. Structure. 2010; 18(4):423-35. PMC: 2892689. DOI: 10.1016/j.str.2010.01.012. View

11.

Hospital A, Faustino I, Collepardo-Guevara R, Gonzalez C, Gelpi J, Orozco M . NAFlex: a web server for the study of nucleic acid flexibility. Nucleic Acids Res. 2013; 41(Web Server issue):W47-55. PMC: 3692121. DOI: 10.1093/nar/gkt378. View

12.

Hospital A, Andrio P, Cugnasco C, Codo L, Becerra Y, Dans P . BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data. Nucleic Acids Res. 2015; 44(D1):D272-8. PMC: 4702913. DOI: 10.1093/nar/gkv1301. View

13.

Kota P . GUIMACS - a Java based front end for GROMACS. In Silico Biol. 2007; 7(1):95-9. View

14.

Ayton G, Noid W, Voth G . Multiscale modeling of biomolecular systems: in serial and in parallel. Curr Opin Struct Biol. 2007; 17(2):192-8. DOI: 10.1016/j.sbi.2007.03.004. View

15.

Dans P, Walther J, Gomez H, Orozco M . Multiscale simulation of DNA. Curr Opin Struct Biol. 2015; 37:29-45. DOI: 10.1016/j.sbi.2015.11.011. View

16.

Miller B, Singh R, Klauda J, Hodoscek M, Brooks B, Woodcock 3rd H . CHARMMing: a new, flexible web portal for CHARMM. J Chem Inf Model. 2008; 48(9):1920-9. PMC: 2676146. DOI: 10.1021/ci800133b. View

17.

Kaushik G, Ivkovic S, Simonovic J, Tijanic N, Davis-Dusenbery B, Kural D . RABIX: AN OPEN-SOURCE WORKFLOW EXECUTOR SUPPORTING RECOMPUTABILITY AND INTEROPERABILITY OF WORKFLOW DESCRIPTIONS. Pac Symp Biocomput. 2016; 22:154-165. PMC: 5166558. DOI: 10.1142/9789813207813_0016. View

18.

Pronk S, Pouya I, Lundborg M, Rotskoff G, Wesen B, Kasson P . Molecular simulation workflows as parallel algorithms: the execution engine of Copernicus, a distributed high-performance computing platform. J Chem Theory Comput. 2015; 11(6):2600-8. DOI: 10.1021/acs.jctc.5b00234. View

19.

Pronk S, Pall S, Schulz R, Larsson P, Bjelkmar P, Apostolov R . GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics. 2013; 29(7):845-54. PMC: 3605599. DOI: 10.1093/bioinformatics/btt055. View

20.

Afgan E, Baker D, Batut B, van den Beek M, Bouvier D, cech M . The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic Acids Res. 2018; 46(W1):W537-W544. PMC: 6030816. DOI: 10.1093/nar/gky379. View