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At the beginning of October 2022 two ICCVS scientists, Zuzanna Trybała and Łukasz Arcimowicz spent two weeks with the team of professor Bořivoj Vojtěšek at the Regional Centre for Applied Molecular Oncology (RECAMO) at Masaryk Memorial Cancer Institute in Brno. They had a unique opportunity to learn the process of protein production in the mammalian expression system utilizing the ExpiCHO system. The antibodies obtained at RECAMO will be useful in future projects led by Dr Małgorzata Lisowska at ICCVS in the field of antibody design. Our scientists found the method very practical and are excited about implementing it at our Centre.

ICCVS employees were impressed by RECAMO with modern laboratories, high-end equipment and world-leading research. They received a warm welcome and guidance from RECAMO researchers: dr Martin Krkoška, dr Zuzka Tylichová, dr Pavlina Zatloukalová, dr Radovan Krejčíř, Soňa Babčanová and others. Our scientists had many inspiring discussions and conversations about differences and similarities between our countries, science, and future possibilites that led to valuable friendships.

During their stay, our scientists visited also another research centre based in Brno that collaborates with the ICCVS – CEITEC and professor Mary O’Connell’s group where they had the pleasure join dr Pavla Musilová and dr Janka Melicherová in their daily experiments. It was a valuable experience seeing state-of-the-art laboratories and visiting the Masaryk University campus.

The city of Brno surprised our researchers and turned out to be a vivid city, full of breathtaking landmarks and tourist attractions, not to mention the delicious smažený sýr! It is a beautiful city that in many ways may be even considered better then Prague! The trip was made possible thanks to NAWA Prom and ERASMUS+ programmes.

From the left: Zuzanna Trybała, Martin Krkoska, Łukasz Arcimowicz and Zuzka Tylichova at RECAMO	Martin and Vaclav in their office
Janka, Pavla, Zuzanna and Łukasz at CEITEC	Zuzanna and Łukasz during their daily work at RECAMO
Zuzanna during her daily work at RECAMO	Łukasz and Zuzanna sightseeing Brno

Georges Bedran performed a 5-month internship at the University of Michigan in prof. Alexey Nesvizhskii’s lab. Using the state-of-the-art tools developed by the Nesvizhskii lab and the computational knowledge in immuno-oncology at ICCVS, Georges explored novel sources of tumour specific antigens (TSAs). This work will fill a specific gap in the literature and provide a well trusted resource for future studies aiming to understand immune-evasion or develop a new category of antigens.

Georges Bedran

The workshop was conducted at the University of Split, Croatia, between 4-6 July. We were two – dr Sachin Kote and prof. Adam Jagiełło-Rusiłowski – representatives from the University of Gdansk (UG). The workshop was led by a renowned, experienced international expert from the University of Edinburgh (UoE) in speculative and creative design, applied in the research context. The workshop was coordinated and facilitated by assistant professor Ivica Mitrovic, Art Academy, and Nikola Balic, Head of Science and Innovation, University of Split (US).

Dr Sachin Kote from the ICCVS (UG) has given valuable insight as a wet laboratory scientist who provided the vision to develop an “artifact” whose form and function of a possible future research lab in 2040. With other group members, dr Kote presented a vision of a speculative research future. The vision called HEER (Her Eternal Ephemeral Resources) imagined the life of a scientist in 2040 as a love story between Artificial Intelligence (AI) and a scientist. Conversational problem solving enabled by data hoarding and secondary research opportunities could be one of the plausible futures.

Besides the workshop, dr Kote visited prof. Janos Terzic from the School of Medicine (US), for the scientific collaboration between Poland and Croatia.

Application of Ashwin Kallor a PhD student form computational biology group at ICCVS was selected in a competitive recruitment process to participate in the International High Performance Computing Summer School 2022. Below Ashwin’s reminiscences about the event.

The International High Performance Computing Summer School (IHPCSS) was held this year at Athens, Greece between 20 and 26 June. This is an annual event which is hosted jointly by the Partnership for Advanced Computing in Europe (PRACE), XSEDE (USA), SciNet (Canada) and RIKEN Center for Advanced Computing (Japan) where participating students are provided training on various topics related to high performance computing, ranging from parallelization to big data techniques. Hands-on classroom lectures are supplemented with learning materials and take-home exercises to impart a holistic and rigorous grounding in the underlying concepts of HPC while exposing the students to real-world applications through examples derived from engineering, astrophysics and the biomedical sciences. The participants are also given an opportunity to present their doctoral/post-doctoral research during a two day electronic poster session and connect with academicians/industry professionals during a career fair held during the latter half of the program. Beyond didactics, each student is assigned a specific mentor, who is expected to provide the student with professional, academic and even personal guidance on various issues faced by them.

The summer school was an enriching experience. Through the classroom sessions, I was able to learn new techniques in parallelization and big data processing such as OpenMP and PySpark, both of which are expected to be implemented in my computational workflows in due course. Outside the classroom, I was able to present the work conducted by the computational biology group at ICCVS during the e-poster session with a poster titled “Utilizing high performance computing for cancer vaccine discovery”. Meeting students, academicians and industry professionals from around the world was eye-opening since we were able to exchange ideas around HPC-related techniques and discuss our work. The networking sessions were further enhanced through the career and resume/interview sessions, where industry professionals and academicians provided advice on how to approach job interviews, how to frame and develop resumes and also the skill-sets required for each industry. In this regard, it is fitting to acknowledge the contribution of my mentor, Dr Pawel Janowski, who, through his constant support and encouragement, ensured that my time at the summer school was stimulating, both at the intellectual and personal level. Of course, the summer school was not entirely work and career-oriented as trips to a musical performance at the ancient Odeon theatre, the Athenian Acropolis and the Lycabettus Hill provided much-needed recreation during a week of intensive learning.

I take this opportunity to acknowledge Dr Natalia Marek-Trzonkowska and Dr Javier Alfaro, without whose assistance and encouragement this trip would not have been possible.

Ashwin Kallor

During 28 June – 4 July I spent the training days at the University of Pisa.

I visited the laboratory of Prof. Chiara Gabelli and Prof. Vittoria Raffa where I learnt how to perform a gene editing protocol based on CRISPR-Cas9 technique, applied to human cancer cells as well as to the teleost zebrafish.

I prepared ribonucleoprotein complexes (RNP). I performed transfection of RNP and after I analyzed cell internalization of RNP using immunofluorescence. I learnt basic technique employing zebrafish including adults fish crossing, embryo collection, microinjection of RNP in embryos in 1-cell stage. In addition, I performed genomic DNA extraction from embryo and I gained basic knowledge in data analysis of High Resolution Melting technique. I received a valuable training on the new and very potent techniques.

Visiting the University of Pisa and being welcomed by the very hospitable people working there was a wonderful experience for me. In the broader perspective, the mobility can initiate the establishment of the research collaboration and staff exchange between University of Gdańsk and University of Pisa.

Alicja Dziadosz

Our employee, M.Sc. Eng. Balbina Surma, participated in the 23^rd STP VALENCIA: LANGUAGES & IT TRAINING FOR UNIVERSITY STAFF. The event took place at the beginning of June 2022 at the Universitat Polite.

Over 120 participants from different parts of the world and various fields of science attended this event. It was a great opportunity to exchange experiences and interdisciplinary approaches for further development.

The supervisor of IT group, Eduardo Blasco Talavan, shared his knowledge on the use of database management system tools such as MS Access.

During the training importance of  cybersecurity was highlighted. The  participants also learned the secrets of the art of presentation with Prezi software, which enables multi-level content visualization.

During the intensive course, participants also had the opportunity to become acquainted with the art, culture and traditions of Valencia.

Balbina Surma

The 1st Progress and Assembly meeting of KATY (Knowledge At the Tip of Your fingers: Clinical Knowledge for Humanity) was held on 24th/25th May, 2022 in Rome.

The KATY project is about developing an AI enabled prognostic platform in cancer focused on Renal Cancer as an application.

Work Package “Large Scale Pilot and Validation” of the project is led by dr Javier Alfaro, a PI of Computational Science Group at the ICCVS and co-led by dr Emilia Daghir-Wojtkowiak.  Working on a proof-of-concept application of the KATY platform on a renal cancer dataset, they coordinate scientific activity of people of different backgrounds and professions to make a patient-centric interface available through the KATY platform.

The 1st Progress and Assembly Meeting provided an opportunity to report scientific highlights (20 partners out of 11 countries gathering people of different background), focused on:

1) Clinical Scenarios and Pilots (clinicians, biologists, bioinformaticians)

2) Data engineering through the development of a DataLake and Distributed Knowledge Graph (data scientists, mathematicians, biologists),

3) Predictive modelling using Artificial Intelligence (data scientists, mathematicians, informaticians, computer infrastructure experts),

4) Making models accessible through the KATY platform (front-end and back-end developers, bioinformaticians).

During the Meeting, Javier Alfaro, Emilia Daghir-Wojtkowiak and Ashwin Kallor were reporting the on-going work focused on various aspects of clinical scenarios, proteomics and immunopeptidomics.

It is worth adding that the KATY consortium is a very interactive environment and during the Meeting, many questions, untouched issues/problems have been addressed and solved by mutual discussion. All participants finally had the opportunity to meet not only on-line but face-to-face in the heart of Rome and each person had a chance to eat his self-made pizza!

Emilia Daghir-Wojtkowiak

ICCVS is the center for many international researchers and multidisciplinary research to contribute to cancer vaccine therapy. Besides the research, ICCVS encourages sports activities because these develop skills like teamwork, leadership, patience, discipline, learning from failure, sportsmanship, etc. Therefore, we are happy to share that our deputy team leader, dr Sachin Kote, has been selected as the player from ICCVS and represented us in the University of Gdansk badminton team of the Academic Sport Association (Akademicki Związek Sportowy – AZS) in the national championship, held on March 25-27, 2022 in Gdynia, Poland.

AZS is the largest sports association in Poland and has a rich history. It has become the most numerous student organization operating at Polish universities. Playing any sports is the key to a healthy and balanced life, particularly the researcher/scientist life. Therefore, it is mandatory to play sports regularly, and these skills are equally important – says dr Kote. The UG badminton court is located at University of Gdańsk premises in Kładki street in Gdańsk. Prof. Tomasz is one of the finest coaches I have ever seen since I started to play badminton. We encourage all ICCVS and other UG department members to take advantage of the badminton facilities provided by the UG campus – adds dr Kote.

Sachin Kote

In the last week of March three ICCVS scientists: Alicja Dziadosz, Alicja Sznarkowska and Zuzanna Trybała visited the laboratory of Professor David Saliba at University of Malta. The visit was a part of the continued collaboration between ICCVS and UoM. Our scientists had a valuable opportunity to meet and discuss common research areas with researchers from UoM. A vital part of the visit was the continuation of training researchers from Professor Saliba’s laboratory in phage library techniques which started in September 2021 when Prof. Saliba visited ICCVS.

Our scientists also participated in a demonstration of the lipid bilayer formulation which is a technique that can be beneficial in many future experiments.

Visiting and exploring beautiful Malta and being welcomed by the very hospitable and kind people from the University was a wonderful experience for our scientists. During the numerous meetings, interesting presentations, and thought-provoking discussions they had a great chance to exchange ideas and establish new partnerships.

Zuzanna Trybała & Alicja Dziadosz

The Open Research Data Staff week took place at the University of Malta, Valletta Campus during 24-26 of January 2022. The programme was scheduled for Open Research Data Officers and Open Science Ambassadors in order to discuss and review best practices in open science field and to recommend further steps. I had a pleasure to join the group of Open Science Ambassadors. It was a chance to meet other researchers from different disciplines focused on open research and open data policy. We spent the time on inspiring and interesting discussions of opportunities but also challenges related to open data and open science. We could share our personal experience with open science in practise and open science initiatives on our universities. We also had an exceptional opportunity to visit the National Aquarium, Qawra which gave us an unique possibility to talk with science educators on site.

Apart from the Open Science events, we also had the time to explore beautiful views and places on Malta.

The Open Research Data Staff week was organised under the reSEArch-EU Project (reinforcing SustainablE Actions, resilience, cooperation and harmonisation across and by the SEA-EU Alliance), which is an initiative of the SEA-EU (European University of the Seas). SEA-EU is an alliance of six coastal European universities which share research interests and a commitment to integrate their infrastructures and harmonize their functioning to thrive and adapt to today’s changing world.

Małgorzata Kurkowiak