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BioExcel CoE Newsletter #10
Dear reader,
Summer is over in Europe, however we have prepared a lot of exciting activities, especially for the rainy autumn days.
The preparations for the BioExcel Community Forum are in full swing. This won't be the regular "talks-coffee-talks-lunch-etc..." type of conference but rather a highly interactive gathering of students and researchers for engaging and stimulating discussions. All of the interest groups will have dedicated sessions, which will give you the opportunity to meet the core developers of our main applications and platforms. The venue is really cool, and right in the heart of Amsterdam! Hurry up with sign-up - registration is free!
If you can't make it to the forum, consider coming over to Edinburgh for the "Hands-on introduction to HPC for Life Sciences" course. All are welcome as no previous HPC experience is required! And if "structural bioinformatics" is a skill you'd like to add to your LinkedIn profile, join the EMBL-EBI course in Hinxton.
BioExcel is one of the main supporters of the development of the Common Workflow Language (CWL). Our efforts, presented in the "CWL viewer" poster, were acknowledged with the F1000 award at this year's ISMB/ECCB conference. Congratulations to Stian Soiland-Reyes and the rest of the team!
Talking about workflows - our next webinar is something you don't want to miss, especially if you're doing MD simulations. Our collaborators from Vrije Universiteit Amsterdam, the group of Daan Geerke, will present "MDStudio, microservice based molecular dynamics workflows". MDStudio is a great platform, so make sure to register for the talk.
What else? The GROMACS 2016.4 update is out now, if you find any issues with it, drop a question at the support forums. And last but not least - the September edition of the Integrative Modelling Interest Group's newsletter is already out. There you will find as always a great interview, several notable new publications and of course your favorite "Tips & Tricks" on using ChimeraX.
Stay tuned for more exciting news next month!
Rossen Apostolov
BioExcel Manager
* You are receiving this mail either because you subscribed for the BioExcel's newsletter through the website or you attended one of our webinar events. Since we are organizing regularly more of the latter, we thought you'd like to know about them. You can, of course, always unsubscribe (link is at the bottom) but we hope you'd like to stay in touch.

BioExcel Community Forum (22-23 November, 2017)
BioExcel Community Forum (22-23 November, 2017)
Join us in Amsterdam for BioExcel's first Community Forum A networking event with a programme of small interactive working groups aligned with the BioExcel Interest Groups 22nd-23rd November, 2017 Lloyd Hotel & Cultural Embassy, Amsterdam Free - Register at: https://www.eventbrite.co.uk/e/bioexcel-community-forum-tickets-35807737908 The BioExcel Community Forum provides an opportunity for members of BioExcel's interest groups and other members of the BioExcel community to …
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Hands-on Introduction to HPC for Life Scientists
Hands-on Introduction to HPC for Life Scientists
Date: Wednesday 29th November - Friday 1st December 2017 Venue: EPCC, James Clerk Maxwell Building (JCMB 3305), University of Edinburgh Application opens: Sunday June 23 2017 Participation: First come, first served Contact: Vera Matser Registration fee: £0 Register here This course provides an introduction to High-Performance Computing (HPC) for researchers in the life sciences, using ARCHER as a platform for hands-on …
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F1000 Poster Award to BioExcel's CWL Viewer at ISMB
F1000 Poster Award to BioExcel's CWL Viewer at ISMB
BioExcel was well represented at the ISMB/ECCB 2017 conference - perhaps you picked up one of our t-shirts? One surprise was that our Common Workflow Language Viewer poster (doi:10.7490/f1000research.1114375.1) won a F1000 Poster Award! The poster presents the CWL Viewer, a web rendering of portable workflow executions defined in the Common Workflow Language. CWL Poster at …
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Webinar: "MDStudio, microservice based molecular dynamics workflows" (2017-10-11)
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 University of 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 …
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GROMACS Release 2016.4
Hi GROMACS users, The official release of GROMACS 2016.4 is available! This release fixes several issues found since 2016.3, including disabling the broken support for automatic PME tuning in mdrun for group-scheme simulations, and various other fixes. It also implements production-ready support for CUDA 9 + Volta generation GPUs, along with other portability enhancements. It incorporates all the fixes found in the 5.1.4 release, and a few since. …
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ChimeraX, a new version of Chimera available on SBgrid
Introduction UCSF Chimera is one of the most popular molecular viewer. It is currently developed by the Resource for Biocomputing, Visualization, and Informatics at University of California, San Francisco. Among its many features, Chimera is probably the best software for the interactive visualisation and analysis density maps. It allows for a fine-tuning of the density maps and provides built-in algorithms for the …
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