Longbow: A Lightweight Remote Job Submission Tool

Gebbie-Rayet, James; Shannon, Gareth; Loeffler, Hannes H.; Laughton, Charles A.

doi:10.5334/jors.95

Cited by 10 publications

(2 citation statements)

References 15 publications

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“…In addition to handling the communication between the two UIs, the API connects them with a python-based back-end that translates the commands issued on the user interfaces into GROMACS-PLUMED2 , input files. The python back-end also handles remote deployment of molecular simulations on compute resources using the Longbow library . Both the API and the python back-end are stored in a Docker container .…”

Section: Methodsmentioning

confidence: 99%

Combining Virtual Reality Visualization with Ensemble Molecular Dynamics to Study Complex Protein Conformational Changes

Juárez-Jiménez

Tew

Connor

et al. 2020

J. Chem. Inf. Model.

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Molecular dynamics (MD) simulations are increasingly used to elucidate relationships between protein structure, dynamics and their biological function. Currently it is extremely challenging to perform MD simulations of large-scale structural rearrangements in proteins that occur on millisecond timescales or beyond, as this requires very significant computational resources, or the use of cumbersome 'collective variable' enhanced sampling protocols. Here we describe a framework that combines ensemble MD simulations and virtual-reality visualization (eMD-VR) to enable users to interactively generate realistic descriptions of large amplitude, millisecond timescale protein conformational changes in proteins. Detailed tests demonstrate that eMD-VR substantially decreases the computational cost of folding simulations of a WW domain, without the need to define collective variables a priori. We further show that eMD-VR generated pathways can be combined with Markov State Models to describe the thermodynamics and kinetics of large-scale loop motions in the enzyme cyclophilin A.Our results suggest eMD-VR is a powerful tool for exploring protein energy landscapes in bioengineering efforts.

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Section: Methodsmentioning

confidence: 99%

Combining Virtual Reality Visualization with Ensemble Molecular Dynamics to Study Complex Protein Conformational Changes

Juárez-Jiménez

Tew

Connor

et al. 2020

J. Chem. Inf. Model.

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“…BioExcel CoE joined together some of the most important HPC WFMS around the world in a dedicated workshop (2018), with the goal of identifying specific software gaps and opportunities for improved workflow practices. 118 A representation of the most popular WFMS in the field were present in the workshop: Parsl 119 , AdaptiveMD, 120 PyCOMPSs, 121 BioSimSpace, 122 LongBow, 123 FireWorks, 124 Swift, 125 ExTASY, 126 , 127 and RADICAL. 128 , 129 Although sharing many of the most important features (automation, data control flow, task management, dependency graph), each WFMS has its own design goal, and adoption of one versus another implies a thorough analysis of the particular research project needs and the WFMS features.…”

Section: Taking Advantage Of High Performance Computingmentioning

confidence: 99%

Pre‐exascale HPC approaches for molecular dynamics simulations. Covid‐19 research: A use case

Wieczór

Genna

Aranda

et al. 2022

WIREs Comput Mol Sci

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Exascale computing has been a dream for ages and is close to becoming a reality that will impact how molecular simulations are being performed, as well as the quantity and quality of the information derived for them. We review how the biomolecular simulations field is anticipating these new architectures, making emphasis on recent work from groups in the BioExcel Center of Excellence for High Performance Computing. We exemplified the power of these simulation strategies with the work done by the HPC simulation community to fight Covid‐19 pandemics. This article is categorized under: Data Science > Computer Algorithms and Programming Data Science > Databases and Expert Systems Molecular and Statistical Mechanics > Molecular Dynamics and Monte‐Carlo Methods

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Reactive inkjet printing of polyethylene glycol and isocyanate based inks to create porous polyurethane structures

Schuster

Hirth

Weber

2018

J of Applied Polymer Sci

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Reactive inkjet printing offers a direct way to create polymeric structures in situ on a substrate. Therefore, two component polyurethane formulations can be utilized to be used in multicomponent inkjet printing. In this contribution, the use of polyethylene glycol (M = 200 g mol −1 ), glycerol ethoxylate (M = 1,000 g mol −1 ), and water (blowing agent) in combination with aliphatic 1,6-hexamethylene diisocyanate or aromatic methylene diphenyl diisocyanate for reactive inkjet printing is evaluated. The inks are jettable on a Dimatix DMP-3000 inkjet printer using a 10 pL piezo driven drop-on-demand printhead showing stable droplet formation. Solid films on glass are formed using a drop-by-drop printing strategy. Layer-by-Layer strategy gives best results on polycarbonate substrates forming porous polyurethane structures.

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Longbow: A Lightweight Remote Job Submission Tool

Cited by 10 publications

References 15 publications

Combining Virtual Reality Visualization with Ensemble Molecular Dynamics to Study Complex Protein Conformational Changes

Combining Virtual Reality Visualization with Ensemble Molecular Dynamics to Study Complex Protein Conformational Changes

Pre‐exascale HPC approaches for molecular dynamics simulations. Covid‐19 research: A use case

Reactive inkjet printing of polyethylene glycol and isocyanate based inks to create porous polyurethane structures

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