MolSSI/BioExcel Workshop on Workflows in Biomolecular Simulations: POSTPONED TO FALL 2020

Organizers: Shentenu Jha and Sam Ellis

Location:  Virginia Tech Executive Briefing Center in Arlington, Virginia

Dates: Expected Fall 2020


The Centre of Excellence for Computational Biomolecular Research (BioExcel) and the Molecular Sciences Software Institute (MolSSI) are jointly organizing workshops on the development and application of workflow solutions for biomolecular modeling and simulations. 

This first event was hosted by BioExcel in Barcelona, Spain (Dec. 2018), which focused on workflow tool developers. A broad selection of experts in workflow manager tools, particularly those appropriate to biomolecular simulation pipelines, met to discuss the existing opportunities and emerging trends in how workflow systems are utilized. The results of that workshop are summarized in this report.  

A follow-up workshop is taking place this year from 31 March to 2 April 2020, this time hosted by the MolSSI in Arlington, VA — minutes from Washington DC.  The aim of this meeting is to connect developers with end user groups. Like in 2018, the event will be by invitation only, but anyone interested in attending – developer or end user – please contact our local organizers.  MolSSI will provide lodging for up to three nights at the Holiday Inn, Balston, as well as breakfast and lunch.  All other expenses should be incurred by attendees. 


Workflows are an increasingly important aspect of biomolecular simulation science. Over the years there have been a variety of projects around the world to develop workflow systems that would be well suited to the demands of this type of research, but to date it has been difficult to achieve widespread community uptake. One of the main problems is the missing gap between biomolecular simulation scientists and workflow system developers. Understanding the existing capabilities of these systems can greatly improve efficiency, reproducibility, complexity and flexibility in complex pipelines, eventually enabling new and better science. 

The purpose of this workshop is to bring together workflow system developers and biomolecular simulation experts with the aim to foster a dialogue between them that will help:

  • Workflow system tool developers to test the potential of existing capabilities for real-life applications and to learn from expert end users what the broader requirements for (bio-)molecular applications and workflows are.
  • Biomolecular simulation experts to understand how to transform their complex scientific projects into biomolecular workflows and learn from tool developers how workflow software can help improve their pipelines. 

As with the first workshop organized by BioExcel and MolSSI, it is not the intention for this workshop to be a place for projects to make “sales pitches” – rather, we seek workflow system developers willing and able to discuss both the strengths and weaknesses of their approaches together with experts in the biomolecular simulation tools and try to work together to build complex pipelines to solve real scientific problems. 


The workshop will start with presentations given by the biomolecular simulation domain experts about possible scientific projects to be tackled using software pipelines, followed by short presentations from workflow system tool developers about their tool’s capabilities. After all presentations, domain experts will pair with tool developers according to the potential of a particular tool/workflow system to address their scientific project needs. 

These pairs, with the possibility to choose more than one workflow system per scientific project, will meet together for the whole second day of the workshop in a hackathon-like session, with the aim of translating abstract requirements into concrete solutions, identify gaps, shape development roadmaps, and start making and testing a possible solution together.

During the last day of the meeting, solutions designed in the hackathon session will be shared through presentations with special focus on the suitability of a particular workflow system to solve a particular scientific problem, and the common difficulties found in building the various types of workflows. 


Day 1: 

  • Presentations and Pairing
    • Domain Experts present on their workflows
    • Tool Developers discuss their tool
    • Create pairings of Domain Experts and Tool developers for “hacking”

Day 2: 

  • Hackathon session
    • 2 Sessions: Morning and Afternoon
    • For each session, 1-2 Domain Experts work with each Tool Developer to “hack” on their application of the tool

Day 3: 

  • Discussions and Conclusions
    • Lightning Talk(s) by Tool Developers and Domain Experts to discuss the difficulties/positives of building their applications
    • Conclusions & wrap-up session

WHO SHOULD ATTEND: MolSSI and BioExcel are inviting domain experts and developers of tool/workflow developers. If you did not receive an invitation and wish to take part, contact Samuel Ellis (