Hear from our 2019 BioExcel Summer School travel grant beneficiaries

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 or a relevant scientific topic.

The 2019 BioExcel Summer School took place in Sardinia, which included lectures and hands-on sessions on topics such as biomolecular docking, free energy calculations and more.

Jan Sayilgan
Koç University

Every morning during the BioExcel Summer School on Biomolecular Simulations 2019, we got on a bus around 08.30 a.m. from the hotel we stayed to go to the venue where the summer school took place. On the first morning, everyone was full of a fresh excitement as our bus was arriving to our destination. The scene was changing from sandy soil with Mediterranean scrub to packed green pine trees as our bus was climbing up a mountain. Our venue, the Science and Technology Park of Sardinia, was secluded on a mountain foothill surrounded by thousands of green pine trees like a medieval monastery. The monks and scientists may have one in common: Both do not wish to be disturbed by daily tumult. The Science and Technology Park of Sardinia is a perfect place for this kind of escape. As we got off the bus in front of the building, we realized that we had not yet reached the entrance. We also had to climb up many stairs to enter the building. The architect probably wanted to point out that doing science is not an easy job.

There were not monks in robes, but two great scientists and wonderful hosts Giuliano Malloci and Attilio Vargiu who welcomed us at the entrance. During the five days there were brilliant lectures and tutorials given by excellent scientists. The lectures I found most interesting because of my research area were the ones given on the first day by Mark Abraham on the overview of the molecular dynamics simulation software GROMACS and by Christian Blau on the theoretical part of the software. Also the lectures given on the second day by Attilio Vargiu on modeling molecular recognition through enhanced-sampling methods and integrative modelling of biomolecular complexes with HADDOCK by Alexandre Bonvin were for me the most valuable ones. In addition to the lectures and tutorials, we had a poster session, so we had the opportunity to gain an insight into each other’s research. Overall, the summer school organized by Vera Matser, Alexandre Bonvin, Giuliano Malloci and Attilio Vargiu was a great experience that I benefited from enormously.

Anna Verdino 
University of Salerno

I am Anna Verdino and last November 2018 I have started my Ph. D in Chemistry at the University of Salerno. When I knew the possibility to apply for the BioExcel Summer School on Biomolecular Simulations 2019, I was enthusiastic about the possibility to learn new, exciting techniques in the computational field to be applied to the study of proteins of interest. BioExcel Summer School on Biomolecular Simulations has been important to improve my background because I am currently working on the analysis of structural and functional effect caused by new and known genetic mutations in a rare disease, classic galactosemia, by computational approaches. I am also applying molecular dynamics simulations and docking approaches to model the conformational flexibility of wild-type and mutant enzyme and study the role of one known pharmaceutical chaperone in enzyme stabilization. The lessons and tutorials followed about docking and molecular dynamics have been productive to learning new techniques and solve several biological problems with my system that I was not able to manage before attending the school.  Moreover, thanks to this school, I have been able to meet people, exchange ideas and create new opportunities of collaboration that I think will be extremely useful for me in the future. For all these reasons, overall I think this has been an extremely positive experience both from a professional and personal point of view and I would be more than happy to repeat this wonderful experience in the future.

Daniil Mnevets
Belarusian State University

The BioExcel summer school is a great opportunity to get some insights into modern computational methods in biology. During the course of lectures by the developers and experts in presented software you are briefly introduced to the theory behind each technique in a very clear manner, so afterwards you could understand how to run the simulations by yourself. Besides that, there are tutorials where you could step by step run the simulation and try to apply the theory from lectures. The most awesome part of the school is the fact that lecturers were always ready to answer any of your questions; you could ask either something general or connected to your own studies and they were happy to help. The practical tips I obtained on the lectures and tutorials are already applied in my current projects.

Another part of the school I want to mention is definitely the community. The people at the summer school were very different, from various scientific fields and countries but still open minded and extremely friendly. I had a lot of scientific conversations and just ordinary talks all along the school time. During the poster session everyone was running around the presentations, trying to get some new information from others work, no one stayed away from the conversations there. The participants were always kind and friendly and I hope to keep in touch with them in future.

All in all, BioExcel is a great opportunity to broaden your knowledge in computational and structural biology, get deep insight into the algorithms of software for structural analysis, get plenty of useful tips how to improve the performance and find the correct parametrisation. Besides that, it is a pure scientific environment where you could find many interesting people and contacts for possible further collaborations or just to have a good conversation.

João Pedro Luís
University of Coimbra

“Life is like a box of chocolates, you never know what you’re gonna get” (Forrest Gump). Well, regarding the BioExcel Summer School here’s what I say: The school is like a box full of flavour and with the best of the best chocolates, you never feel full and you crave for more and more.

First, the location: Pula, in southern Sardinia (Italy). Amazing! We stayed in Hotel Flamingo which was great, near the beach and with a harmonious relationship with Nature (oh! friendly cats included!). It was the perfect place to get inspired and to relax after the lectures. And the weather was great also!

Second, the school: High quality! Filled with interesting topics, first we spread the towel to a very good GROMACS introduction by Mark Abraham followed by a deep dive to a more specifically focused session on AWH enhanced sampling by Christian Blau. It can be daunting to find the best pose under the warm sun, so next day we predicted the best ones with HADDOCK, in a very instructive lecture and hands-on session by Alexandre Bonvin and Charlotte Van Noort. To ride the waves of QM/MM and CP2K can be challenging, but Emiliano Ippoliti and Vaibhav Modi provided us precious learning and know-how to do it, on day three. Binding to the ocean was so strong that we learn how to calculate the energies from our seamulations using PMX, on the fourth day, with Bert de Groot and Vytautas Gapsys. Later that afternoon, a tutorial on metadynamics/HADDOCK, by Charlotte, Andrea Basciu and Attilio Vargiu, was the perfect stimulus to know how to sail this ship. Last day, a “Round table & Get answers” session, with a lot of questions/answers and suggestions, was the perfect end-of-week-cocktail.

Third, the people: Wonderful! I was bowled over by the generosity, talent, incredible atmosphere and professionalism of everyone involved in this school. People from different backgrounds, different cultures came together to share ideas, constructive feedback, bioinformatics tips and tricks and, most important, create a strong network of professional connections.

Fourth, personal and professional growth: BOOM!! It was a great experience! I learned of a lot of new things to improve my bioinformatics skills, discussed a few of the stumbling blocks that I’ve crossed upon while working on my project and, on a personal basis, it was definitely very enriching, mentally and socially. I thoroughly enjoyed being part of the BioExcel Summer School!

I take my hat off to all the organizers and participants of this event. Biggest thumbs up!!

 

 

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