BioExcel’s webinar series continue with an introduction of the workflow tool, MDStudio. The webinar is part of the collaborative work plan between BioExcel and Vrije Universiteit Amsterdam.

Abstract

Molecular Dynamics (MD) is becoming an essential method in the research toolkit of academic and applied science. Common practice is to combine MD with other in silico modelling, simulation and data analysis techniques into functional workflows. These have become complex entities over the years with significant software and hardware requirements and domain-level expertise to be handled correctly, preventing routine use by novice and expert users alike.

Our Molecular and Computational Toxicology research group at the Vrije Universiteit Amsterdam develops MD-based workflows with a practical focus on drug development. To ensure user-friendliness of our workflows and promote wide-spread application of MD-based methods we have recently launched the MDStudio software platform. MDStudio uses the modern concept of “software as microservices” as the basis of constructing workflows with a number of major benefits:

  1. Open platform approach: any method can become a microservice through a thin language agnostic container exposing a standardized API to talk to others via a router over a network regardless of the database, hardware and software environment. Interoperability guaranteed!
  2. Flexible workflows: Users can interact with microservices and implement workflows at several levels of abstraction in a near language agnostic way: script based, re-computable interactive notebooks or a full graphical user interface. Fast workflow based prototyping and development making the impact of MDStudio truly greater than the sum of its parts!
  3. (Multi) user-friendly: Research is teamwork! MDStudio is multi-user ready enabling research teams to collaborate on projects through workflows, anywhere, anytime and anyplace.
  4. Heterogeneous scalability: MDStudio uses a self-contained, containerized, client-server architecture that can be deployed on many different platforms. Microservices natively scale from multi-core desktops to HPC clusters and cloud environments. Requiring only a network connection to communicate, they can be deployed on physically isolated hardware tailored to the requirements of a research team.

We welcome your state-of-the-art method as microservice in a growing MDStudio ecosystem!

Presenter

Marc van Dijk, MMS Division of Molecular and Computational Toxicology, Vrije Universiteit Amsterdam,  The Netherlands

m4.van.dijk@vu.nl

Dr. Marc van Dijk (orcid.org/0000-0002-3773-9357) studied Biology at Utrecht University and obtained his Master’s degree in Biomolecular Sciences and specialization in structural biology in 2005.
Subsequently, he performed his PhD research at the NMR Department of the Bijvoet Center for structural biology at Utrecht University. Marc obtained his PhD degree in 2010, on the topic of protein-DNA interaction modelling using molecular simulation techniques. Thereafter, he has been involved in various research projects as post-doctoral researcher at the Cambridge University (UK), Utrecht University and VU University Amsterdam where he currently holds a Senior Scientist position. His research focuses on the study of biomolecular interactions using computational molecular modeling and simulation techniques. Marc is currently involved in the Dutch e-Science center project “Enhancing protein-Drug binding prediction” where he is involved in method development for accurate protein-drug binding affinity prediction using free-energy methods. Part of this project is the MDStudio software platform for microservice based molecular dynamics workflows where Marc is project coordinator and lead developer.

Title: MDStudio, microservice based molecular dynamics workflows
Date: 11th October, 2017
Time: 14:00 UTC / 15:00 BST / 16:00 CEST

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