Life sciences is a diverse area of research that relies on some of the most intense computing to achieve its mission.
From modeling molecules, proteins and cell-membranes through to large scale "virtual human" computational biology of cardiology, haematology and neurology - advances in health-care and the wider field of life sciences use significant and large-scale computing to bring valuable benefits to society such as drug discovery, personalized medicine and clinical diagnosis or guidance.
Next generation sequencing is transforming genomics and bioinformatics. Long running sequencing operations require substantial computing clusters to deliver patient results in clinically-relevant timeframes, for as many patients as possible - whilst bioinformaticians strive to analyze trends and patterns within their vast databanks of human genomes.
The urgency of high performance computing on this work continues to increase - and needs every assistance to achieve faster throughput.
Allinea's tools help Life Science researchers and developers to accelerate the performance of their code and to spend less time struggling with bugs, whilst system owners achieve higher throughput from their technology. Analyzing core issues within the application software such as I/O and threads and processor usage means no ounce of performance is left behind.
Our Success Stories
When Dr. Aurel Neic, postdoctoral researcher at the Institute of Biophysics, Medical University of Graz, and his team wanted to develop a simulation framework for the human heart, he turned, like so many scientific researchers, to the power of the supercomputer.
His research group develops a simulation framework called the Cardiac arrythmia Research Package (CaRP). The team uses Allinea Forge to assist in developing and debugging the highly parallel numerical code and its associated management code.
The team has also started to use Allinea MAP for profiling and looking deep into the performance of their code with the aim of speeding up blood flow simulations and research.
These are exciting times at the Earlham Institute. The planet will be home to 9 billion people by 2050 - and with the population soaring and crop yields plateauing, scientists must work to increase calorie production by 60% in three decades time.
This important life science research at the Earlham Institute applies computational science and biotechnology to help find the answers to this and other pressing world food problems. It's a complex problem - agricultural genomes can be massive - wheat, for example, has an 8x longer genome than the human genome - but is considerably less understood.
With genomes to map of this size, the computing task is highly intensive - often tasks are run for two weeks on dozens of high powered Intel Xeon cores simultaneously. Accelerating performance of their main code can deliver immediate impact on the scientists work - with sequencing completing faster, and also increasing the number of genomes that can be sequenced by the same supercomputer.
Using Allinea's tools, the Earlham team have gained new insight into the performance of their code - and achieved a 50% speed up. The team are delighted with the faster, all-encompassing view of behaviour and huge application speed up Allinea MAP and Performance Reports has given them and feel confident that their research will be able to isolate any wheat gene within the next two to three years.
Researchers at University College London (UCL) modelling intracranial blood flow have been able to reach a major milestone by using development tools from Allinea Software.
A massive simulation using 50,000 processor cores on the UK’s largest supercomputer, ARCHER, became possible after solving an application crash that only occurred at this high scale. ARCHER is the UK’s flagship Cray XC30 system, which is managed by Edinburgh Parallel Computing Centre (EPCC) on behalf of EPSRC and other UK research councils.
UCL’s HemeLB software applies computational fluid dynamics to model blood flow around cerebral vessels and simulate pressure at points of weakness such as aneurysms. Using data from MRI scans of a patient’s blood vessels, the group anticipates that simulations will one day help to decide the best clinical option for individual patients.
The UCL team and Allinea Software were brought together by the EU CRESTA project – which is preparing applications for future extreme-scale computing. Running applications at extreme scales poses challenges, which Allinea Software’s tools help to solve.