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.
Posted: 15 Jan 2019 | 11:52
The Fortissimo 2 project ended on 31 December 2018. Together with its predecessor (the plain old 'Fortissimo project') it has helped over 100 SMEs and mid-caps to run experiments that demonstrate the effectiveness of providing HPC services using a business model derived from cloud computing, thereby making it much lower risk for small companies to use HPC.
Posted: 8 Jan 2019 | 15:08
Earlier this year, HPE announced the Catalyst UK programme: a collaboration with Arm, SUSE and three UK universities to deploy one of the largest Arm-based high performance computing (HPC) installations in the world. EPCC was chosen as the site for one of these systems; the other two are the Universities of Bristol and Leicester.
EPCC's system (called 'Fulhame' after pioneering chemist Elizabeth Fulhame) was delivered and installed in early December. This HPE Apollo 70-based system consists of 64 compute nodes with two 32-core Cavium ThunderX2 processors (ie 4096 cores in total), 128GB of memory composed of 16 DDR4 DIMMs, and Mellanox InfiniBand interconnects. It will be made available to both industry and academia, with the aim to build applications that drive economic growth and productivity as outlined in the UK government’s Industrial Strategy.
Posted: 7 Jan 2019 | 15:14
The Advanced Computing Facility (ACF) on the outskirts of Edinburgh is the high performance computing data centre of EPCC.
Built in the 1970s and operated by EPCC since the turn of the millennium, the ACF site has had significant investment over the years. At present, there are three Computer Rooms, imaginatively called: Computer Room 1 (CR1), Computer Room 2 (CR2), and Computer Room 3 (CR3).
Posted: 14 Dec 2018 | 17:33
PickCells is image analysis software developed by the Centre for Regenerative Medicine (CRM) at The University of Edinburgh. PickCells allows biologists to explore multidimensional biological images of stem cell niches, organoids, and embryos. In late October, with the assistance of six researchers, we evaluated the usability of PickCells to help guide its future development.
To run our usability evaluation, we followed Steve Krug's highly-recommended and very readable book "Rocket Surgery Made Easy: The Do-It-Yourself Guide to Finding and Fixing Usability Problems". This book describes a practical way to carry out usability evaluations with minimal overhead.
Posted: 13 Dec 2018 | 16:34
EPCC has received funding via the Economic and Social Research Council (ESRC) to continue its work with the Scottish Administrative Data Research Partnership (S-ADRP).
The aim of the partnership is to enable research that leads to policy decisions that will in turn will help Scotland progress towards the vision outlined in the National Performance Framework. This framework helps to shape high level research priorities for Scottish Government, including tackling poverty, providing quality jobs and fair work for all, and ensuring that we live in inclusive, empowered, resilient and safe communities. S-ADRP consists of a number of Strategic Impact Programmes (SIPs) each dealing with a research priority.
Posted: 10 Dec 2018 | 10:59
By Raniere Silva, Community Officer at the Software Sustainability Institute.
The Software Sustainability Institute is pleased to announce applications to our Fellowship Programme 2019 are now open. Below we detail the application process and what to expect from us during the recruitment and post-recruitment stages.
Posted: 6 Dec 2018 | 16:12
In February EPCC will host an event to explain why data driven innovation is important for industry. We will also showcase how companies are already using data technologies to enhance commercial performance.
There is a lot of hype around big data and big computing for business, but it is undeniable that the influence of data-driven innovation will be profound.
The expertise and support available in Scotland has created a massive opportunity for our engineering and manufacturing sectors and, with the launch of the £500m Data-Driven Innovation (DDI) strand of the Edinburgh and South-East Scotland City Region Deal, this is an exciting time for exploring how technology can benefit business.
Posted: 26 Nov 2018 | 18:07
The community of Edinburgh research software engineers (CERSE) held their second gathering on Wednesday 21st November in the Edinburgh College of Art (ECA) main building.
The meeting was attended by around 50 participants, an interesting mix of researchers, software developers, systems admins and research support/management staff, from the University of Edinburgh and Heriot-Watt University. It is intended to keep these gatherings open to all Higher Education and research institutions of the Edinburgh area.
Posted: 20 Nov 2018 | 09:08
Pablo C. Cañizares came on an HPC-Europa3 visit to EPCC from 23 July–24 October 2018. In this blog article he summarises his visit.
Hi there! I'm Pablo C. Cañizares, a PhD student in Computer Science from the Complutense University of Madrid (UCM), Spain. I work in the Design and Testing of Reliable Systems group in the Computer Science Faculty of the UCM. I visited EPCC for three months under the HPC-Europa3 transnational access programme and was hosted by EPCC's Dr David Henty.