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 about their experience in the course.
The 2022 BioExcel Summer School took place in Sardinia, and included lectures and hands-on sessions on topics such as biomolecular docking, BioExcel Building Blocks, free energy calculations and more.
Giorgia Francesca Camagni
University of Padova
My name is Giorgia, and I feel very lucky to have had the opportunity to participate in the BioExcel Summer School on Biomolecular Simulation 2022 in Pula, Sardinia. With this post I would like to retrace the moments of this wonderful experience with you.
I cannot start without remembering the excitement, euphoria and agitation that grew in me as the day of departure approached. Finally, the day has arrived, I go to the airport and find that the flight is delayed (obviously!). As you can imagine, the anxiety level has increased. I already imagined that I could not arrive in time to take the last transfer bus provided by BioExcel to reach the hotel. Yes, I have a vivid imagination! Anyway, everything went smoothly! When I arrived at the Hotel Flamingo and settled into my room, even though I could not fall asleep due to the excitement, I was happy and excited to start this experience the next day. Every day at 8:30 a.m. the bus left to take us to the Science and Technology Park of Sardinia where the school was to take place. A structure immersed in the green hills. Until that moment I had not realized that I would have met so many boys, girls, and professors from my same research field and with whom I could have had so many exchanges.
Many interesting topics were covered during the school, including Molecular Dynamics, Binding Free energy, Docking and QM/MM, followed by the associated Tutorial. A perfect organization to explore the topic just explained. There was also a poster session, where it was possible to make their work known and receive lots of advice. It was a great and very informative experience. I talked all the time!
Of course, there was also room for fun. After the lessons we returned to the hotel, and we were able to relax by taking a swim in the sea and a good aperitif on the beach. One afternoon we went to visit the archaeological site of Nora and in the evening, we had dinner in an excellent restaurant in Pula. In short, it was a wonderful and very stimulating experience. I met some great people I am still in contact with today and the professors were very well trained and available for any conversation.
Do not miss it!
Marc Domingo Cabasés
Institut de Ciència de Materials de Barcelona (ICMAB-CSIC)
The BioExcel Summer School 2022 in Sardinia has been wonderful. It’s been an intense school week with a mix of theory lessons, software tutorials and science discussions. The course was organized in such a way that we first did the theoretical courses and then the corresponding tutorials, which was quite appropriate because we could practice what we had just learned before.
The lessons were varied and dealt with a wide range of theoretical concepts and computational techniques. We started with the molecular dynamics , which helped me to refresh the main concepts of it. Then, with BioExcel Building Blocks, I discovered a tool for building workflows to prepare systems and run simulations, and it can be a great tool to use if you want to replicate the work of other scientists. The enhanced-sampling methods lesson showed the several techniques that one may use to study particular events such as allosteric processes. Integrative modeling of biomolecular complexes using HADDOCK showed us how docking might be a great tool in predicting binding if good strategy is applied. QM/MM simulations using CP2K software will be really profitable for me as I am planing to use it soon in studies of the interaction between proteins and metallic surfaces. The talk on AI for drug discovery showed how to improve the efficiency and effectiveness in this field. The last session about glycans revealed on how important might be the role of glycans attached to proteins and that we can not neglect them when working on our proteins.
The flashtalks and poster sessions were a magnificent opportunity to share with others your own work and to have discussions that inspired me and gave me new ideas on how to follow in my PhD research. Making these new connections was a very important achievement of the summer school. I also enjoyed the career session, where 4 scientists had the opportunity to explain their careers during and after finishing their PhD. Not only was it very useful to know first hand the careers that each one has done, but also for sharing the ups-and-downs, doubts and uncertainties that they have had (A¡and that much of us are experiencing). The message that I would take home is the phrase uttered by scientist Zara Sands during her talk: “Your vocation in life is where your greatest joy meets the world’s greatest need”.
After a full day of scientific immersion, there was also time to swim on the paradisiacal beaches of the Sardinian coast, play beach volleyball and visit the ancient city of Nora and the beautiful village of Pula. In addition, during this week, we were able to enjoy the delicious local food of the island such as pane carasau, malloreddus, fregola and the tasty and exquisite Mirto.
Debora Ness
King’s College London
Attending the BioExcel Summer School on biomolecular simulations 2022 in Sardina, Italy, has truly been one of the most inspiring, rewarding, and instructive experiences of my PhD so far. In this brief blogpost I will try to outline some of the reasons for this statement by giving a short experience report and summarising some of the highlights of the week.
Upon arrival, I immediately fell in love with the amazing resort and what it has to offer. After half a day of exploring the hotel facilities, including the bar (and the local beer Birra Ichnusa, which seems to have grown on many of us over the course of the week), the private beach and gorgeous swimming pool, we had an excellent welcome dinner at the restaurant of the resort. Conversations were light-hearted and it was the perfect opportunity to meet the other participants and the organisers before the course started the next morning.
The days were structured in a well-thought-out manner, with lectures covering theoretical aspects of a given topic and subsequent tutorials which enabled everyone to practice and implement newly acquired knowledge. The topics covered were diverse, ranging from Molecular Dynamics Basics to Machine Learning to advanced QM/MM simulations, but they were all presented in a very accessible way, i.e. there was something to take away from all sessions even with no/only minor previous knowledge of the topic. In between sessions, we all sat on the sunny terrace of the Science Centre Sardegna Ricerche, enjoyed Italian coffee, and a selection of tasty treats and varied lunch options.
On Wednesday in the afternoon, after a very inspiring poster session, we had a tour of the archaeological site of Nora, an ancient pre-Roman and Roman town on a nearby peninsula before we were spoiled with a seemingly infinite course meal (incl. wine!) at a lovely restaurant in Pula.
The fact that we all had to catch the shuttle bus at 8.30am every morning, which took us to the Science Centre, incentivised people to not skip the early morning sessions (as there was no later bus and it’s a 1.5-hours walk up the hill from the hotel to the Science Centre). Notably, after the abundance of food and wine we consumed during our night out in Pula, I witnessed a couple of very sleepy faces in the lecture hall the next morning. Yet, everyone was there. ☺
It has been a privilege to attend the daily high-quality lectures and workshops on a such broad range of topics at the well air-conditioned facilities of the local Science Centre Sardegna Ricerche, and the spontaneous afterwork volleyball sessions and fresh cocktails at the beach provided the perfect opportunity for all participants to exchange research ideas, make new friends, have fun, and unwind.
Maria Chiara Saija
J. Heyrovsky Institute of Physical Chemistry
If I had to describe my experience in one sentence, that would be “the sun kissed science”. BioExcel Summer School on Biomolecular Simulations 2022 is what every PhD student is dreaming of. The overall organisation was perfect in terms of schedule, transfers, accommodation and daily program. The technology park of Sardinia is a big infrastructure surrounded by forests and trees (don’t get me wrong, it was still +29!).
We were reaching the place by bus, every morning at 8.30 am; the daily sessions were really interesting and the coffee breaks between the lectures were precious opportunities to talk with people (both students and trainers) in a chill and informal atmosphere. During the lectures we covered the most popular simulation topics: MD, docking, enhanced sampling, QM/MM scheme and AI. The most valuable thing for me was that after every lecture there was the practical session. The trainers helped students and they provided step by step tutorials. Students had the opportunity to share their work via flash talks and poster session. Poster session is the perfect time to get ideas and valuable advice on your current project from the experts in the field.
The career session was also extremely useful for me, since I could listen to the working experiences of the youngest trainers. It’s very important, for the future, to explore different opportunities after PhD both in the academia field or not.
At the end of the daily classes, we were coming back to the hotel and that was the time to benefit from the sun and the sea. The hotel provided direct access to the beach, literally. Despite the full schedule, we found some time to enjoy life outside of the technology park. The local organisers, Attilio and Giuliano, organised a small trip to Nora in order to visit the ruins of the town. We also had an amazing dinner.
Personally speaking this experience enhanced my scientific background and my career perspectives; I loved the relaxed atmosphere that we created, I felt confident enough to talk to trainers and ask questions. The vibes among the students were totally positive, we shared a lot about our work (including technical tips), our lives and future projects.
I definitely recommend taking part in the school, if you have the opportunity.
