PATC/CompBioMed Winter School 2019 reviews from travel grantees

“CompBioMed Travel grant for the BSC Winter School – Report This February I had the opportunity to attend to a High-Performance Computing course in Barcelona thanks to the sponsorship of CompBioMed and the organization of PRACE. I am sure all of you have had the opportunity to visit Barcelona, and if not, I strongly encourage you to go as soon as possible. You will not only find a beautiful city by the Mediterranean ocean, but also vibrant technological and biomedical hub, with excellent public transport and first-class universities. Trust me, I am from Madrid. The course took place at the Campus Nord, where the Barcelona Supercomputing Center (BSC) is located, a neighborhood full of university and research buildings together with elegant villas and palaces. Throughout the first sessions, the attendants could learn the basics of HPC: OpenMP, MPI, SLURM, etc. And we got the opportunity to practice with some introductory exercises to get a feel about what it is to work and run experiments in a supercomputer. Once the basics were clear, we then enjoyed the talks presented by different researchers who work either at BSC or at other partner institutions. All of them had a topic in common: The Virtual Human. An ambitious project whose goal is to simulate all the biology behind a human being to enhance basic research, drug discovery, treatment recovery, etc. Every talk was truly interesting, but, perhaps because I am interested in tech-transfer and entrepreneurship, my personal favorite was given by the people at Acellera. They are a young Spanish Start-Up who offer drug discovery solutions such as PlayMolecule, a repository of applications for molecule modeling and prediction. The last day we had the privilege to participate in a tour to the heart of the BSC: Mare Nostrum IV, one of the most powerful supercomputers in Europe, with a speed of 13.7 petaflops. For the curious ones, it is located inside a deconsecrated chapel (perhaps reminding us about the role of technology in our world).” 

“Between 13th – 15th February 2019, the “Short Course on HPC-based Computational Bio-Medicine” within the UPC Campus Nord took place. During these three intensive days, about 25 students and young researchers in Bioengineering and related fields were attending 12 different seminars in close relationship with supercomputing and parallelization. At the beginning of the course, when Mariano Vazquez opened it, most of us did not even knew what a supercomputer was. Step by step and with the help of researchers from all over the world, we got used to cluster use and command prompt interface. On Wednesday, the morning started with an overall review of HPC systems but once we were quite familiar with “our” MareNostrum and for the rest of the day, more detailed and specific topics began to be addresed. “Zoom in on blood” by University of Amsterdam gave us a practical approach to the use of supercomputers in understanding the behaviour of blood cells in our body. To finalize the afternoon, Adrià Perez was the person in charge of introduce “PlayMolecule” and some of its molecular modelling applications in computation. The second day took off with a practical application of image registration using parallelization and, personally, one of the most interesting sessions in my opinion due to its clinical uses. To follow, BSC researchers described us the basics for an efficient and effective simulation when using parallelization strategies. After lunch, Jazmín Aguado-Sierra was the responsible for giving us a biophysical and biomechanical point of view of the multiscale model simulations. Despite its complexity, “Alya Red Cardiac Computational Model” awakened a lot of interest amongst us, especially among the ones who have already finish our undergraduate studies. To finish the day, a hands-on session with molecular sequencing was performed by University College London. Third day’s morning began strong with Guillermo Marín and Paul Melis. These two young researchers gave us the keys for a better graphics understanding and making, especially with 2D/3D scientific datasets and the need of supercomputers use for creating them. To conclude the official sessions, Mariana Pereira showed us that it is not mandatory to have many years of experience in research to create outstanding projects in mixing Computation and Biosciences. On Friday afternoon the PATC course came to an end after the wonderful visit to know MareNostrum: the most powerful supercomputer in Spain and fifth in Europe, which was built in a chapel. Without doubt the guided tour did not disappoint us and the beauty hidden behind a lot of colourful tidied wires is really unexpected.” 

“My name is XXXX and I live in Madrid. First of all, I did not imagine that I could get the scholarship that was offered, but it was a luck because thanks to the scholarship I could go to the course with the permission of my work. Currently I am dedicated to biomedical engineering in a hospital in Madrid, working in an operating room specialized in cardiology; also, I am helping with hospital projects in a foundation known as FIC. In spite of being working, I am in my last year of career at the European University of Madrid. My first day in the course was a bit surprising, I had never programmed into a supercomputer. Thanks to the explanations I was able to understand its operation and the best thing was to be able to carry out different tasks. For me, the best talk was on the second day: ‘HPC Multi-Scale computational modeling using Alya Red’ because I already knew the concept of Alya before and it seems very interesting to me. Due to be working in the area of cardiology is a topic that I have very present in my day to day and there were many new things I could learn and then I could tell the rest of my colleagues in the hospital upon my return. It was very nice to meet Andrea Townsend-Nicholson; apart from giving good explanations and teaching in a very easy way, she was a very close person and always with something to teach. The last day was the visit to MareNostrum. I can speak for myself and for the rest of the classmates that we were all with their mouths open, the site was amazing. It is a marvel and a unique opportunity to have been there and see how it is working something so incredible. To conclude, it was a great experience that I hope to repeat at another time, not only because of the number of things that can be learned, but also to meet such good and incredible people that make things like Alya possible. Thanks, CompBioMed and BSC for this great opportunity.” 

Since the moment I learned about the existence of this course thanks to my Biomedical Engineering professor, Borja Rodriguez, I immediately felt a necessity to attend to this unique opportunity. Upon reading what kind of work was being done in this institution, it seemed it fit perfectly with what I was looking for in order to expand on my academic knowledge: a combination between programming and biomedical sciences. So finally, I decided to get on board onto this event. First of all, the BSC is located at the UPC campus in Barcelona, which gives it all of the advantages of being in such an advanced and modernized city. This created a great environment to work in. All of the lectures and workshops given throughout this course were held at one of the UPC buildings, which allowed for our group to have access to great installations and to directly connect to the Supercomputer. The courses themselves had great variety on the topics they focused in: from Data Visualization to Computational Modelling of objects such as red blood cells, proteins and even functional pharmaceutical molecules. The courses were set up in such a way, so it was easy to learn progressively, first learning the basic commands to log into the supercomputer and navigate through it, and as the courses came by be able to perform much more complicated tasks, as the ones mentioned with anteriority. Although not all of the speakers provided us with hands-on workshops but carried highly in-depth lectures which helped us understand what their company was aiming to accomplish, and how they benefited from supercomputing in order to achieve these goals. It all finally concluded with the visit to the Supercomputing Centre. For me personally, it was a unique experience, being able to see with our own eyes one of the biggest technological accomplishments present in Barcelona. Seeing how the most advanced gadgets blend in with the architecture of an old church is just astonishing, and thanks to how carefully and with how much detail the center explains and shows how the supercomputer has been evolving throughout the years, really makes you appreciate the importance and value that this facility holds. Overall, I’m glad I have been able to form part of this experience. Not only I have been able to gain a great amount of programming skills, but also expand my knowledge upon many different topics I had very little to no idea about before attending to this course. It has also helped me understand my potential role in the job market once in graduate as a Biomedical Engineering, and how I could help today’s and future’s society in so many different ways. Lastly, I would like to thank the BSC for offering me this opportunity and hope in the future I can apply all the knowledge gained to my professional career.

The CompBioMed course was one intriguing event that happened to fall into my mail inbox one January morning. Without much thought I hurriedly applied and began preparing for the trip to the MareNostrum supercomputer. I found the event interesting because it dived deep into the crossroads between Biomedical and Computer Sciences, where the true research and development for more sustainable futures occur. All this collaboration between universities from across borders thanks to the efforts of funding programs from the EU comes together in the lively, gorgeous city of Barcelona.
Right off the bat we got to the UPC campus where we were greeted by the team orchestrating the whole event and got our hands to work getting familiar with the work environment which meant for us (students of Biomedical Engineering backgrounds) to drop the notions of what was a user-friendly OS and focus on the functionality and command-based window. After getting familiar with the Linux OS we went through a series of lectures-workshops which were planned to take into account about our collective level and experience working with supercomputers.
One of the workshop-lecture which I thoroughly enjoyed was the lecture given by the UCL team led Andrea Townsend-Nicholson which actively took part in the day-to-day life of transforming a research laboratory from being 98% experimental to a mere 36% experimental by introducing simulations in their research process, that way they saved resources and were better able to focus their research on more fructiferous paths.
And finally, as a special treat, after playing around and getting our hands on the projects developed and tested in the MareNostrum supercomputer we got to be a part of special people who get to actually visit and explore the reformed chapel which currently holds the MareNostrum in the UPC campus. As we watched the current technology we were taken through the motions of the upkeep, what it entails for the university to keep up such a costly device, and we also got to see where the MareNostrum comes from.