BioExcel CoE Newsletter #6

Dear reader,

Happy New 2017! We hope that everyone had a good time during the holidays and is already back to science!

The BioExcel team has been busy filling up this year's calendar with exciting events in the hope to help everyone get better at modelling and simulations.

We start with the PATC training course next week in Barcelona on using the COMP Superscalar (COMPSs) framework for distributed infrastructures and workflows. Then in April we have the joint BioExcel/PRACE Spring School which is bringing together the main developers of the top applications for Molecular Dynamics simulations and visualization: GROMACS, NAMD, AMBER and VMD. Morning lectures and afternoon hands-on sessions will give both beginners and advanced users a great opportunity to learn more (and get a really cool T-shirt!). Although winter is still in here (at least in our northern hemisphere), we have already opened the registration for our Summer School, which takes place in the first week of July. More on that in another newsletter, for now make sure to register!

Our team has been active in setting up the stage for exciting activities in the various Interest Groups. Notably, right before the Christmas holidays, took place the inauguration meeting of the "Practical Applications for Industry" IG. This group supports and places emphasis on the practical applications of computational biomolecular research. It considers and shares published use cases of relevance to industry to understand the impact and benefit of biomolecular modelling and simulations. We expect those aspects, which generate most interest, will emerge to guide provision of practical support and advice. This is important for expanding usage of the core applications and developing our sustainability plans. More information about the group’s activities, shared resources and communications can be found on the dedicated Industry IG web page. We should also mention that this autumn, around the end of November, we are planning a big Community Forum which will host all the different Interest Groups. You can expect more on this in future newsletters.

Validation of PDB structures is crucial for the correct modelling of your systems (otherwise, frankly, the simulations will produce a few TB of junk trajectories). For that reason we highly recommend our next webinar in early February on "Assessing structure quality in the PDB archive". As usual, we will have a Q&A session at the end for your questions. Then, in mid-February comes the next webinar on "Robust solutions for cryoEM fitting and visualisation of interaction space". Our partners at Utrecht University will talk about the algorithms behind PowerFit and DisVis, two really user-friendly tools. Please join us as new or current users with your questions and feedback, and of course, at any time head straight to the dedicated sections in the Ask.BioExcel.eu forums: DisVis is here, and PowerFit is here.

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

BioExcel/PRACE Spring School 2017 - HPC for Life Sciences

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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Practical Applications for Industry Interest Group

Purpose The Industry IG has been formed to support the practical application of software and workflows that harness Molecular Modelling and Simulations, being used in an industry setting. Activities The group will focus on interests that are relevant to industry. This will include 1) Published use case applications e.g. virtual screening, antibody engineering and mutations; 2) BioExcel pilot use cases …

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Webinar: Assessing structure quality in the PDB archive (2017-02-08)

Webinar: Assessing structure quality in the PDB archive (2017-02-08)

The next webinar in BioExcel's webinar series on computational methods and applications for biomolecular research will take place on 8th February. Matthew Conroy, a scientific curator at EMBL-EBI will present his talk, "Assessing structure quality in the PDB Archive". Models in the PDB archive are an interpretation of the experimental data. This webinar will look at how the worldwide PDB (wwPDB) is validating …

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Webinar: Robust solutions for cryoEM fitting and visualisation of interaction space (2017-02-15)

Webinar: Robust solutions for cryoEM fitting and visualisation of interaction space (2017-02-15)

BioExcel's webinar series on computational methods and applications for biomolecular research continues on 15th February. (Please note the revised date for this webinar, which is different from the date previously advertised). In this webinar Gydo van Zundert, Mikael Trellet and Jörg Schaarschmidt from Utrecht University will together offer a presentation entitled "Robust solutions for cryoEM fitting and visualisation of interaction space". The …

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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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