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HTMoL: full-stack solution for remote access, visualization, and analysis of molecular dynamics trajectory data

  • Mauricio Carrillo-Tripp
  • Leonardo Alvarez-Rivera
  • Omar Israel Lara-Ramírez
  • Francisco Javier Becerra-Toledo
  • Adan Vega-Ramírez
  • Emmanuel Quijas-Valades
  • Eduardo González-Zavala
  • Julio Cesar González-Vázquez
  • Javier García-Vieyra
  • Nelly Beatriz Santoyo-Rivera
  • Sergio Victor Chapa-Vergara
  • Amilcar Meneses-Viveros
Article
  • 52 Downloads

Abstract

Research on biology has seen significant advances with the use of molecular dynamics (MD) simulations. The MD methodology enables explanation and discovery of molecular mechanisms in a wide range of natural processes and biological systems. The need to readily share the ever-increasing amount of MD data has been hindered by the lack of specialized bioinformatic tools. The difficulty lies in the efficient management of the data, i.e., in sending and processing 3D information for its visualization. In this work, we present HTMoL, a plug-in-free, secure GPU-accelerated web application specifically designed to stream and visualize MD trajectory data on a web browser. Now, individual research labs can publish MD data on the Internet, or use HTMoL to profoundly improve scientific reports by including supplemental MD data in a journal publication. HTMoL can also be used as a visualization interface to access MD trajectories generated on a high-performance computer center directly. Furthermore, the HTMoL architecture can be leveraged with educational efforts to improve learning in the fields of biology, chemistry, and physics.

Keywords

Data sharing Data publishing Data streaming Graphical processing unit Webgl Web application Interactive structure Interactive dynamics 

Notes

Acknowledgements

The authors want to acknowledge all the persons involved in the review process. Their comments have helped to greatly improve this report and the functionality of the tool.

Funding

This work has been supported by the Consejo Nacional de Ciencia y Tecnología México (Grant Number 132376 to M.C.-T.).

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Copyright information

© Springer Nature Switzerland AG 2018

Authors and Affiliations

  • Mauricio Carrillo-Tripp
    • 1
  • Leonardo Alvarez-Rivera
    • 2
  • Omar Israel Lara-Ramírez
    • 3
  • Francisco Javier Becerra-Toledo
    • 2
  • Adan Vega-Ramírez
    • 2
  • Emmanuel Quijas-Valades
    • 2
  • Eduardo González-Zavala
    • 2
  • Julio Cesar González-Vázquez
    • 2
  • Javier García-Vieyra
    • 3
  • Nelly Beatriz Santoyo-Rivera
    • 2
  • Sergio Victor Chapa-Vergara
    • 3
  • Amilcar Meneses-Viveros
    • 3
  1. 1.Biomolecular Diversity LabCentro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Unidad MonterreyApodacaMéxico
  2. 2.Ingeniería en SistemasInstituto Tecnológico Superior de IrapuatoIrapuatoMéxico
  3. 3.Departamento de ComputaciónCentro de Investigación y de Estudios Avanzados del Instituto Politécnico NacionalCiudad de MéxicoMéxico

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