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BioExcel Workflows Interest Group Newsletter #3

This is the third 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: Microservice-based molecular dynamics workflows

In case you missed it, we would like to remind you that BioExcel's webinar on making microservice-based workflows with MDstudio, by Marc van Dijk, starts this Wednesday - it's still not too late to register!

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

BioExcel Community Forum (2017-11-22 / 2017-11-23)

Next month we are welcoming you to the BioExcel Community Forum in Amsterdam. Spanning one-and-half days at the end of November 2017, there are co-located sessions from across the BioExcel Interest Groups; attendants can of course freely transition between sessions during the day.

We specially hope you would like to attend to take part in the Workflows Interest Group sessions. The Entry-Level Users IG and Workflows IG are running a combined unconference-style programme, where participants get to influence the direction of the event rather than passively listening.

After an initial round table to find out the interests of those present, we will discuss a number of different MD tools and related workflows. This will be followed by presentation of what BioExcel is doing with such tools.

The next session will be a “bring-your-own-workflow” session in which participants will discuss the MD workflows with a chance to ask experts questions and discuss potential solutions.

Additional time will be available for a final hands-on session which will allow us to dig deeper based on the interests of the group, breaking out into smaller groups that try out techniques and software.

There is also a chance to do an informal 5 minute lightning talk about whatever topic you think might be of interest to the interest group. We intend this to be a networking event, helping you to build new connections with other participants and the BioExcel community.

The Community Forum 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 Amsterdam!

Title: BioExcel Community Forum
Date: 22 November 2017 - 23 November 2017
Place: Lloyd Hotel & Cultural Embassy, Amsterdam, Netherlands

CWL User Guide published

The Common Workflow Language (CWL) community, which BioExcel is participating in, has published a step-by-step user guide to CWL. If you have not had a go with CWL yet, how about having a look? You may also check also out the recording from our earlier BioExcel webinar on Common Workflow Language presented by CWL co-founder Michael Crusoe.

BioExcel at SuperComputing 2017

Are you going to The International Conference for High Performance Computing, Networking, Storage and Analysis (SC17) in Colorado? Look out for BioExcel folks, including Erik Lindahl, Rosa Badia, Adam Carter and Erwin Laure!

BioExcel is featured in the SC17 Birds-of-a-Feather session European Exascale Projects, presented by the ETP4HPC European HPC Exascale Effort.

Several BioExcel partners have booths at SC17:
BSC (#1975), EPCC (#201), Forschungszentrum Jülich (#401)
Feel free to come have a chat!

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?
Contact or

Other news

You may have spotted that the Nobel Prize for Physics 2017 went to LIGO researchers, but did you know that LIGO used 20 million hours of calculations on the MareNostrum Supercomputer? MareNostrum is managed by Barcelona Supercomputing Center (BSC), a BioExcel partner. You may also be interested to know that LIGO's calculations facilitate large scale Pegasus workflows running on a variety of compute infrastructure; each.pyCBC workflow have 60,000 compute tasks, 5000 input files (10 GB) and 60,000 output files (60 GB).
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