BioExcel CoE Newsletter #7

Dear reader,

Tomorrow we have the next webinar in our educational series on "How to choose compute resources for your team". As a follow up to it, next week we will look into the specifics of choosing Cloud and HTC resources. Hurry up and sign up for both! As you know, all webinars have a live Q&A session at the end to ask presenters directly.

This week is also the deadline to register for the "Hybrid Methods in Molecular Simulations" workshop. Isn't it great to learn all about QM/MM, coarse grained MD etc. while enjoying the beauty of Sardinia (Italy)? We certainly think so!

If southern Europe isn't your thing, you are welcome to Stockholm (Sweden) for the awesome BioExcel/PRACE Spring School. Have you ever been to lectures and hands-on tutorials by the very core developers of the 4 big applications for molecular modelling and simulations - GROMACS, AMBER, NAMD and VMD? Probably not because the Spring School is the first such event!

Then, in the UK we have the Summer School on "Foundation skills for HPC". That's in July (weather's fine!) but the deadline is also coming close.

All events above are free of charge, and we even offer travel bursaries. So, please, hurry up!

As some of you know, BioExcel works very closely with the Open PHACTS foundation. In one of our projects, we use the pharmacological data provided through the Open PHACTS' APIs. Recently our organizations signed a formal agreement for strategic partnership.

The integrative modelling interest group has a brand new page. There you can find regular updates with tips&tricks, interviews, events and notable publications covering this exciting domain. 

To all GROMACS users - there's a new patch release 2016.2! Let your friendly sysadmin know about it and kindly ask to consider an upgrade.

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.

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Webinar #12: "How to choose compute resources for your team" (2017-03-08)

Webinar: "How to choose compute resources for your team" (2017-03-08)

BioExcel’s webinar series continues with Lee Larcombe from ELIXIR-UK and University of Edinburgh, who will take us through the benefits and challenges of using local compute resources. Starting from some things to consider when resourcing your research, to what can feasibly be done on a laptop or desktop computer, a workstation, up to a local clusters. What considerations need to be …

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Webinar #13: "Accessing Cloud & HTC Resources in BioExcel" (2017-03-15)

Webinar: "Accessing Cloud & HTC Resources in BioExcel" (2017-03-15)

BioExcel’s webinar series continues with Steven Newhouse from EMBL-EBI, who will discuss Cloud versus HTC (High Throughput Computing) resources, what is the difference and when you should use which. What type and volume of resources are available and where? Should you apply as an individual or as part of an organisation? How should you discover and access the resource? What are the …

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Workshop on Hybrid Methods in Molecular Simulation

Workshop on Hybrid Methods in Molecular Simulation

Deadline for the registration March 10th

BioExcel is sponsoring the first workshop on Hybrid Methods in Molecular Simulation that will be held on April 3-4 at the Sala SEARCH of the Cagliari's city hall. The workshop will be a highly informal forum for PhD students, postdocs and (mostly) early stage researchers to present and exchange new ideas. Particularly important in this respect will be the poster …

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PRACE Spring School 2017 - HPC for Life Sciences - in collaboration with BioExcel

BioExcel/PRACE Spring School 2017 - HPC for Life Sciences

Deadline for the registration March 17th.

Date: Monday 10 – Thursday 13 April 2017 Venue: KTH Main Campus, Stockholm, Sweden Application opens: 23rd January 2017 Application deadline: Friday 17th March 2017 Participation: First-come, first-served Contact: Vera Matser Registration fee: £0, participants will need to cover their own accommodation and transport cost BioExcel will be providing a limited number of fixed amount travel bursaries for this event. If you would like to …

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Foundation skills for HPC in computational biomolecular research - BioExcel Summer School

Foundation skills for HPC in computational biomolecular research - BioExcel Summer School

Date: Monday 3 - Friday 7 July 2017 Venue: European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom Application opens: Friday January 13 2017 Application deadline: Friday April 28 2017 Participation: Open application with selection Contact: Charlotte Pearton Registration fee: £0, participants will need to cover their own accommodation and transport cost BioExcel will be providing …

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Partnership between BioExcel and Open PHACTS Foundation

Partnership between BioExcel and Open PHACTS Foundation

We are very pleased to announce that BioExcel has recently formed a strategic partnership with the Open PHACTS Foundation. The foundation provides the Open PHACTS Discovery Platform, which has matured since 2011 into an  important source of publicly available pharmacological linked data in a single integrated and open infrastructure. Open PHACTS supports data standards, interoperability and public understanding of drug …

Read more.

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New GROMACS Release: 2016.2

New GROMACS Release: 2016.2

The official release of GROMACS 2016.2 is available! This release fixes several issues found since 2016, and incorporates all the fixes found in the 5.1.4 release, and a few since. We encourage all users of the 2016 series to update to 2016.2. Please see the link to the release notes below for more details. You can find the code, documentation, …

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Parse and manipulate PDB files with shell and PyMol

Parse and manipulate PDB files with shell and PyMol

Many tasks we are performing in Integrative Modelling involve 3D structures of molecules. Visualising them, modifying them to fit a particular program requirements or just parsing them to analyse them can sometimes be time-consuming. We are presenting here two approaches to quickly and easily manipulate PDB files. Shell scripting (based on PDB-tools suite) Several short and efficient python scripts have been gathered in …

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ask.bioexcel.eu

Ask.Bioexcel.eu

Ask.Bioexcel.eu, is a forum to support the community for computational biomolecular research in academia and industry, with particular focus on biomolecular simulation and modelling and using high-performance computing (HPC) and high-throughput computing (HTC). Anyone is free to register (sign in with email or your Google/GitHub/Yahoo account), please feel free to ask questions and contribute to the existing threads! …

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Follow us / get in touch!

 

It's all here: http://bioexcel.eu/contact

Notably, you should know about Ask.BioExcel.eu - bookmark that one :)

Twitter, G+, LinkedIn... we're there, see the links at the bottom.

Code repositories - yes, it's Github where we'll keep all new code: https://github.com/bioexcel

Chat channel - drop by our gitter channel for an informal chat: https://gitter.im/bioexcel/general

Video channel - here are the recordings of the webinars!

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