For each of our BioExcel training events we make a limited number of travel bursaries available. We ask the beneficiaries of the BioExcel travel grant to write a blog post for us, either about their experiences at the course, their research interests (in layman’s terms) or a relevant scientific topic.
The following blog posts were submitted by some of our travel-grant beneficiaries from the 2017 Hands-on Introduction to HPC training workshop.
Biomedical Research Foundation of Academy of Athens (BRFAA)
BioExcel organizes several events and workshops, related to computing in Life Sciences. I, myself, had the opportunity to attend the workshop “Hands-on Introduction to HPC for Life Scientists”, which was held in the University of Edinburgh, between the 29th of November and the 1st of December, 2017.
The workshop was addressed to young researchers, working in the fields of Life Sciences and utilizing High-Performance Computing (HPC). Supercomputers, as they are referred to, provide researchers with the ability to study complex biological and biomolecular systems, utilizing an array of processors, binned into clusters, so they can work in parallel. This way, calculations which would need days, weeks or even months to complete on conventional desktop machines can finish in minutes or hours. Since I am currently working on Computer-Aided Drug Design, using my country’s national supercomputer, this workshop was a great opportunity for me to gain a deeper understanding of the methods, software and hardware I employ for my simulations, and, at the same time, invoke some thinking of how I could maximize the efficiency of said hardware.
In the course of these 3 days, specialized researchers from the supercomputer Archer, located in Edinburgh, provided us with information about the hardware architectures of a supercomputer, how parallelization can be achieved through software designed for that purpose, as well as the different aspects of the utilization of a system like this. Specifically, we became accustomed to accessing the supercomputer, submitting jobs through a batch scheduler, proper resource allocation, and dealing with errors that may arise during such a procedure. All these were achieved through a series of very informative presentations, which explained in detail the background necessary, as well as practical exercises, which enabled us to test the knowledge we had gained. I should not fail to mention that all the people assisting us were very polite and friendly, creating a comfortable and relaxing environment, that played a catalytic role in the whole learning procedure. The above, coupled with the very modern, and at the same time Medieval-ish venue of the University of Edinburgh, King’s Buildings, made this a great experience!
Returning home, I realized I was now more capable of understanding and manipulating our national supercomputer’s resources, in order to perform my calculations. This workshop has proven very beneficial for me and my present and future work, giving me a stimulus to delve more into the field of HPC and its utilization in the fields of Life Sciences.
Dr Alpesh Thakker
School of Medical and Dental Science, University of Birmingham
I am Dr Alpesh Thakker working as a postdoctoral researcher at School of Medical and Dental Science, University of Birmingham. My day to day research involves generating high dimensional data using mass spectrometry and NMR techniques. The data analysis is the bottleneck for both of these technologies as it involves pre-processing and treatment of raw data files for comparative and exploratory analysis and when the numbers of samples are large, the computational power of the local CPU becomes the limitation. I was introduced to the resources that can automate/speed up the process of raw data files last year when the university of Birmingham had invested millions of pound to launch the high performance computing service in the form of Bluebear HPC that was made available free of cost to all the research institutes within the university.
One of the limitations to not being able to utilise these available resources effectively was lack of knowledge about using the command line interface in linux environment as well as lack of structured training aimed at life scientists. While browsing for available resources on internet to help me understand the architecture, terminology as well as the basic processes to effectively use the computational power, I came across the BioExcel website which provided wealth of knowledge related to the concepts of HPC and various training events that are organised throughout the year.
The opportunity to attend these 3 day workshop on HPC helped me understand the basic concepts of HPC as well as the protocols to efficiently use the resources and computational power of the available system. It not only helped me improve my knowledge regarding the HPC but also helped in overcoming the fear that an average life science scientist has about dealing with computational related problems.