Support for science

Active matter in an active city

Author: Guest blogger
Posted: 9 Jul 2019 | 13:39

Giuseppe Negro undertook an HPC-Europa3 visit based in Edinburgh from 15/04/19–27/05/19. He gives us a brief overview of his visit and the work he undertook.

Hi everyone! My name is Giuseppe Negro and I am a PhD student at the University of Bari in Italy. I work in computational modelling of soft matter systems with Prof. Giuseppe Gonnella and with my collegue Livio Nicola Carenza, who was also an HPC-Europa3 visitor in Edinburgh, at the Department of Physics in Bari. I visited EPCC under the HPC-Europa3 transnational access programme, and I was hosted by Prof. D. Marenduzzo at the Department of Physics and Astronomy of the University of Edinburgh located at the James Clerk Maxwell Building.

HPC for urgent decision-making

Author: Nick Brown
Posted: 5 Jul 2019 | 11:13

The EU VESTEC research project is focused on the use of HPC for urgent decision-making and the project team will be running a workshop at SC’19.

VESTEC will build a flexible toolchain to combine multiple data sources, efficiently extract essential features, enable flexible scheduling and interactive supercomputing, and realise 3D visualisation environments for interactive explorations.

Taking the sting out of gout

Author: Amy Krause
Posted: 1 Jul 2019 | 10:48

 

 

 

 

Gout is estimated to affect 2.5% of the UK population, and is increasing globally in association with cardiovascular disease and obesity. EPCC has been working with Dr Philip Riches of the MRC Institute of Genetics and Molecular Medicine to develop a new app that could lead to improved treatment and better quality of life for patients.

Gout is a type of arthritis caused by excess uric acid in the blood. It is characterised by sudden attacks of intense pain that result in reduced quality of life, work absence and disability. The standard treatment for the condition involves close monitoring of blood urate levels and medication, but the high level of health professional support required to ensure a long term cure of gout is rarely delivered: fewer than half of eligible patients receive preventive treatment and fewer than half of those on treatment receive an adequate dose of medication.

Computing for extreme conditions

Author: Rosa Filgueira
Posted: 27 Jun 2019 | 10:06

The DARE project is addressing the challenges of combining extreme data, extreme computation and extreme complexity in scientific research.

Virtually every scientific domain is experiencing an increase in the volume of data it produces, with growing computational power enabling more complex simulations. Although comparing these simulations with observation can improve models and understanding, it is highly data-intensive.

Powering biomolecular research through advanced computing

Author: Arno Proeme
Posted: 25 Jun 2019 | 15:51

BioExcel is a Centre of Excellence that supports academic and industrial researchers in the use of advanced computing in biomolecular research. It has received follow-on Horizon 2020 funding from the EU Commission to continue and expand its activities for a period of three years starting from January 2019.

UK astronomy enters multi-petabyte era

Author: George Beckett
Posted: 28 May 2019 | 10:43

The Large Synoptic Survey Telescope (LSST), which EPCC has been involved with for over a decade, will soon pass an important milestone as it moves from construction to commissioning.

Promoting Science on Computers to Schools - Workshop Event

Author: Clair Barrass
Posted: 16 Apr 2019 | 11:27

EPCC and EXDCI-2Funded by EXDCI-2, EPCC is organising a 2-day workshop in Edinburgh on 8-9 July 2019 to present ideas on how science and engineering can be supported from Raspberry Pis to large scale supercomputers. We are looking to investigate how to introduce these topics to school-age audiences including linking to existing school curricula. This will include examples of existing education materials and activities and looking ahead to current plans.

Software Sustainability Institute's Collaboration's Workshop: another success!

Author: Mario Antonioletti
Posted: 15 Apr 2019 | 10:41

Attendees at CW19. This year's Software Sustainability Institute's Collaboration's Workshop, CW19, was held from 1–3 April at the University of Loughborough. There were almost 70 attendees from all over the UK and further afield too - Germany, the Netherlands and the US. I am of the opinion that this is one of the best types networking workshops I have been to, possibly equalled by the UK RSE conferences.

Software Sustainability Institute's Collaborations Workshop 2019 (CW19)

Author: Mario Antonioletti
Posted: 19 Mar 2019 | 10:16

The Software Sustainability Institute's (SSI) Collaborations Workshop 2019 (CW19) will be held at the West Park Teaching Hub, Loughborough University, Loughborough from 1-3 April 2019. This year the workshop will be themed around topics based on interoperability, documentation, training, and sustainability. Keynote speakers will include Catherine Stihler, CEO of Open Knowledge International, and Franziska Heine (link points to a German article), Head of Software & Development at Wikimedia Deutschland. They will open the event on 1st April.

Spark-based genome analysis on Cray-Urika and Cirrus clusters

Author: Rosa Filgueira
Posted: 16 Jan 2019 | 11:06

Analysing genomics data is a complex and compute intensive task, generally requiring numerous software tools and large reference data sets, tied together in successive stages of data transformation and visualisation.

Typically in a cancer genomics analysis, both a tumour sample and a “normal” sample from the same individual are first sequenced using NGS systems and compared using a series of quality control stages. The first control stage, ‘Sequence Quality Control’ (which is optional), checks sequence quality and performs some trimming. While the second one, ‘Alignment’, involves a number of steps, such as alignment, indexing, and recalibration, to ensure that the alignment files produced are of the highest quality as well as several more to guarantee the variants are called correctly. Both stages compromise a series of intermediately computing and data-intensive steps that very often are handcrafted by researchers and/or analysts.

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