Sharing Data from Molecular Simulations
Year: 2019
Type: article
Abstract: Given the need for modern researchers to produce open, reproducible scientific output, the lack of standards and best practices for sharing data and workflows used to produce and analyze molecular dynamics (MD) simulations has become an important issue in the field. There are now multiple well-established packages to perform molecular dynamics simulations, often highly tuned for exploiting specific classes of hardware, each with strong communities surrounding them, but with very limited interoperability/transferability options. Thus, the choice of the software package often dictates the workflow for both simulation production and analysis. The level of detail in documenting the workflows and analysis code varies greatly in published work, hindering reproducibility of the reported results and the ability for other researchers to build on these studies. An increasing number of researchers are motivated to make their data available, but many challenges remain in order to effectively share and reuse simulation data. To discuss these and other issues related to best practices in the field in general, we organized a workshop in November 2018 ( https://bioexcel.eu/events/workshop-on-sharing-data-from-molecular-simulations/ ). Here, we present a brief overview of this workshop and topics discussed. We hope this effort will spark further conversation in the MD community to pave the way toward more open, interoperable, and reproducible outputs coming from research studies using MD simulations.
Authors: Mark Abraham, Rossen Apostolov, Jonathan Barnoud, Paul Bauer, Christian Blau, Alexandre M.J.J. Bonvin, Matthieu Chavent, John Chodera, Karmen Čondić-Jurkić, Lucie Delemotte, Helmut Grubmüller, Rebecca J. Howard, E. Joseph Jordan, Erik Lindahl, O. H. Samuli Ollila, Jana Selent, Daniel G. A. Smith, Phillip J. Stansfeld, Johanna K.S. Tiemann, Mikael Trellet, Christopher Woods, Artem Zhmurov
Institutions: Science for Life Laboratory, KTH Royal Institute of Technology, University of Groningen, Utrecht University, Université Toulouse III - Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, Memorial Sloan Kettering Cancer Center, Max Planck Institute for Biophysical Chemistry, Stockholm University, University of Helsinki, Universitat Pompeu Fabra, Hospital Del Mar, Municipal Institute for Medical Research, Hospital del Mar Research Institute, Molecular Sciences Software Institute, University of Oxford, Leipzig University, University of Bristol
Language: English
Subfield: Information Systems and Management
Field: Decision Sciences
Domain: Social Sciences
Open Access status: green
Funders: National Science Foundation, Wellcome Trust, University of Warwick, European Commission, University of Bristol, Deutsche Forschungsgemeinschaft, Max-Planck-Gesellschaft, Centre National de la Recherche Scientifique, Science for Life Laboratory, Horizon 2020 Framework Programme, Medical Research Council, Engineering and Physical Sciences Research Council, Biotechnology and Biological Sciences Research Council
Awards: Centre of Excellence for Biomolecular Research, G2005278011, G2291362457, G3159704455, The UK High-End Computing Consortium for Biomolecular Simulation, BioExcel Centre of Excellence for ComputationalBiomolecular Research, Assembly and Dynamics of Bacterial Chemosensory Signaling Arrays, G4330362853, S2I2: Impl: The Molecular Sciences Software Institute, The Lipoprotein Biogenesis Pathway: An Emerging Structural Target for Novel Antibiotics, G4937468798, G5045220161, The Lipoprotein Biogenesis Pathway: An Emerging Structural Target for Novel Antibiotics, G5066350998, Sustainable RSE Careers for Sustainable Software Development, G52543226, G5580141040, G5927648607, MemProtMD: A resource for membrane proteins, The UK High-End Computing Consortium for Biomolecular Simulation, Triggering assembly of the twin-arginine translocase, G8567706437, G8875621885, G8903667313, G9000158989, Functional dynamics of the KATP channel
OpenAlex ID: W2974666250