Blog

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.

Event review: What data-driven innovation means for business in Scotland

Author: Mark Sawyer
Posted: 6 Mar 2019 | 10:13

EPCC is at the heart of the Data Driven Innovation programme of  the Edinburgh and South East Scotland City Region Deal. This £661m programme will lead to the creation of major new data services for Scottish business, with EPCC providing the World Class Data Infrastructure (WCDI) that will underpin it.

Last week we hosted an event to explain the enormous potential of data-driven innovation for industry and to show how companies are already using data technologies to enhance commercial performance.

Proof-driven queries to preserve patient privacy

Author: Mike Jackson
Posted: 4 Mar 2019 | 09:42

StethoscopeIn our role as members of the Research Engineering Group of the Alan Turing Institute, Anna Roubickova and I worked with Efi Tsamoura and Benjamin Spencer (Department of Computer Science at the University of Oxford) on PDQ, a proof-driven query planner that has great potential within the realm of data science for medical research. 

EPCC at the 2019 Big Bang Fair

Author: Mario Antonioletti
Posted: 3 Mar 2019 | 17:28

For the fourth year running, from Wednesday 13th March to Saturday 16th of March,  EPCC will be attending the Big Bang Fair (BBF) at the NEC in Birmigham to demonstrate the wonders of supercomputing. The BBF encourages young people to adopt STEM-based subjects at school and later as a career – not only through universities but also apprenticeships and other career choices. This is also a great opportunity for our colleagues to undertake some outreach.

HPC-Europa3 visitor publishes paper in Physical Review Letters

Author: Guest blogger
Posted: 1 Mar 2019 | 12:33

Former HPC-EUROPA3 visitor Dr Mats Simmermacher, Dr Adam Kirrander (Mats' host from the University of Edinburgh's School of Chemistry), and their collaborators from Edinburgh and Copenhagen have recently published a paper in the prestigious Physical Review Letters where they discuss a new effect in ultrafast X-ray scattering. 

What is MPI “nonblocking” for? Correctness and performance

Author: Daniel Holmes
Posted: 27 Feb 2019 | 15:53

The MPI Standard states that nonblocking communication operations can be used to “improve performance… by overlapping communication with computation”. This is an important performance optimisation in many parallel programs, especially when scaling up to large systems with lots of inter-process communication.

However, nonblocking operations can also help with making a code correct – without introducing additional dependencies that can degrade performance.

The Julia programming language

Author: Magnus Morton
Posted: 22 Feb 2019 | 16:09

Julia logo

Peeved with Python? Revolted by R? SAS make you sad? The Julia Language may be for you. Recently reaching version 1.0, Julia claims to be more than just another data science language.

In this post I’ll give a tour of some of the more interesting features of Julia, and its implementation.

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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Tracy Peet
+44 (0) 131 650 5362
t.peet@epcc.ed.ac.uk