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BioExcel Workflows Interest Group Newsletter #4

This is the fourth newsletter of the BioExcel Workflows interest group. As you probably know, BioExcel supports multiple workflow systems for computational biomolecular research, and we are keen to hear from you, either on our forum, or in our Gitter chat room. Feel free to get in touch with your questions about workflows, and we'll do our best to put you in contact with the experts!

Webinar: CWLEXEC: Run Common Workflow Language on HPC with IBM Spectrum LSF (2018-02-28)

We're proud to have IBM's Qingda Wang present BioExcel's upcoming webinar on CWLEXEC, a new open source tool for executing Common Workflow Language on HPC infrastructure using IBM Spectrum LSF. As you know, BioExcel have been supporting CWL with particular focus on interoperability, so we are very pleased to hear about this upcoming addition to the family of CWL workflow engines.

Title: CWLEXEC: A new open source tool to run CWL workflows on LSF
Presenter: Qingda Wang, Principal Architect, IBM Spectrum LSF Family Products and OEM
Date: Wed 28th February 2018
Time: 14:00 GMT / 15:00 CET

New to CWL? you may want to have a peek our previous webinar Introduction to Common Workflow Language which is available on YouTube and Slideshare.

Previous webinars

Did you miss some of our previous BioExcel webinars on workflows? The videos and slides are of course available:

ELIXIR Workflow and Tools interoperability

BioExcel's Josep Ll. Gelpí presented BioExcel and Common Workflow Language as part of ELIXIR Europe's Workflow and Tools interoperability plan at the ELIXIR Tools Platform face to face meeting last week. As part of BioExcel's partnership with ELIXIR we are also taking part in the implementation study of reuse, extension, scaling, and reproducibility of scientific workflows.

Photo by @biocrusoe

BioExcel Summer School on Biomolecular Simulations (Sardinia, 2018-06-17 / 2018-06-22)

In June 2018 BioExcel is hosting a week long summer school in Sardinia, Italy, full of lectures and hands-on sessions on:
  • Molecular Dynamics simulations
  • Biomolecular Docking
  • QM/MM
  • Free energy calculations
  • Advanced sampling methods (metadynamics)
Places are limited, so if you are interested, make sure you apply before end of March! Accommodation, food and airport shuttle are included in the registration fee.

The Summer School is also an excellent chance to get in touch with the lead BioExcel developers and have your say on future priorities. We are looking forward to seeing you in Sardinia!

Title: BioExcel Summer School on Biomolecular Simulations 2018
Date: Sunday 17 June 2018 - Friday 22 June 2018
Application deadline: 2018-03-30
Notification date: 2018-04-13
Place: Science and Technology Park of Sardinia, Sardinia, Pula, Italy

BioExcel at PASC 2018

Are you going to the The Platform for Advanced Scientific Computing (PASC) Conference 2018 in Basel, Switzerland? (Week starting 2018-07-02) Look out for BioExcel folks, including Rossen Apostolov, Stian Soiland-Reyes and Adam Hospital!

BioExcel and MolSSI (The Molecular Sciences Software Institute) are co-organizing a minisymposium at PASC:

Advances in Automation and Efficiency for the Exascale Era - Experiences from the Biomolecular Sciences
Life Sciences have become crucially dependent on software for analysis of experimental data, systems modelling and simulation, data integration across various repositories and databases etc. The dramatic increase of available tools has enabled scientists to perform ever more complex studies while taking advantage of modern high-end (HPC and HTC) compute facilities. Experimental facilities are producing staggering amounts of data which led to the rapid development of novel data analytics and machine learning techniques. We are at a stage where there is a need for additional focus on improving the interoperability of software applications, enable better coupling of tools with data sources and devising efficient workflows and libraries for the upcoming Exascale era in HPC. Such advances will considerably improve the productivity of researchers and allow them to address novel scientific problems. This mini-symposium brings together invited experts from two leading institutions in the field – BioExcel, the European Center of Excellence for Computational Biomolecular Research (, and MolSSI, Molecular Sciences Software Institute ( for USA to discuss the advances in this important field.

Further details on the program for the minisymposium and PASC will be available in March.

Upcoming events

Events by BioExcel and the wider workflow community:

Going a bit more hardcore?

Here are some high-performance and GPU events we have found in the HPC community:
Would you like your workflow/HPC event listed in the next newsletter?
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