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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

During 13.09-17.09.2021, I took part on Data Steward School, a course created by Visnea company and carried out in close cooperation with the ICM UW (Interdysciplinary Centre for Mathematical and Computational Modelling, University of Warsaw) organization and GO-FAIR Initiative. GO-FAIR sets the standards for scientific data management and implements them all over the world. Visnea sp.z o.o. is the official partner of GO-FAIR Initiative in Poland. The Data Steward School training program covered among others: data stewardship, trends in data management in research, open access and creative commons or data protection topics. We have learned a lot about open data policy in research. We had a possibility to visit ICM UW and it’s impressive server room.

Second part of the course took place during 18.10-20.10.2021. That time we talked about security of research data, personal data protection, anonimisation and pseudonimisation of data, ethical issues in research, data repositories and we could consult data management plans that we prepared for this course’s purpose. We discussed also topics like: data quality, reliability of scientific data, data journals and possibilities of data citations but also data sharing and long term storage of data.

The last part of the course took place during 17.11-19.11.2021. The schedule of this part included intellectual property and data protection in case of cooperation between research units and industrial entities, copyrights, data protection issues in international research cooperation, FAIR Data rules and tools for FAIRification.

The whole course was very demanding and gave a lot of useful and important information and skills concerning open research and open data issues. The whole training allowed for gaining of new professional qualifications and unique competences in the field of scientific data management. It was also a great chance to meet colleagues from many different disciplines, which gave an opportunity to exchange our points of view and experiences in terms of open research data.

Later on, during the 5th Pomeranian Open Science Conference in December, a short meeting was held for all graduates of the Data Steward School training program. It was an opportunity to meet again with some of colleagues and take part in discussions among members of the Polish Working Group Data Stewardship Competence Centers PL (DSCC-PL).

Małgorzata Kurkowiak

Staff of the ICCVS Research Support Team – dr Wioleta Domańska-Babul, Magdalena Dziki, Joanna Grzegórska, Anna Krajewska, and myself – spent four training days at the University of Malta (UM) during 1-4 Nov 2021. We met colleagues from various UM units to exchange information and gain knowledge on processes and solutions related to our daily work.

We visited laboratories and met research staff at the Faculty of Health Sciences, Dpt. Applied Biomedical Science. At the Research Support Service Directorate we discussed the support for proposal preparation for European programmes. We were also introduced to how the process of introducing Standard Operating Procedures (SOPs) as well as the research equipment inventory was organized and how the laboratory support unit works to support the faculties. At the UM Project Support Office the colleagues explained the way financial pre-award and post-award financial management of projects and presented the features of the electronic system for project administration. At the Knowledge Transfer Office we learnt about current applied projects in vaccine science. We also met the SEA EU project representatives and discussed the opportunities of next actions within the projects SEA-EU and reSEArch EU, but also other new upcoming activities such as the initiation of a joint PhD student network. We also presented UG’s current activities in the area of promotion of equality and diversity as well as exchanged views about the process of introducing Gender Equality Plans at both universities. Last but not least, we also explored the amazing attractions that Malta offers, such as sights in Mdina and Valetta, and visited the beautiful island Gozo – time used as enjoyable and effective team building activity for our team.

University of Malta and University of Gdańsk are partners in the SEA-EU Alliance, a strategic network of six partner universities established within the European Universities Initiative. In 2020 ICCVS has entered a memorandum of understanding with University of Malta to cooperate in research on cancer immunotherapy and the activities have already been started by dr David Saliba from UM with ICCVS UG researchers prof. Hupp, dr Małgorzata Lisowska, and Zuzanna Trybała. 

Izabela Raszczyk

This year, for the first time  ICCVS staff and PhD students participated in a dedicated Intercultural & Diversity Management Workshop. The workshop was led by prof. Natasza Kosakowska-Berezecka and dr Magdalena Żadkowska from the University of Gdańsk, who have a broad coaching experience in this field.

The activity is part of the Human Resources Strategy for Researcher (HRS4R) of the University of Gdańsk that has received the Award HR Excellence in Research in 2016. ICCVS contributed to the recent periodic update of the Action Plan and prepared in 2021 its input after a need analysis at ICCVS (focus group meeting).

The workshop took place in the beautiful  Sobieszewo Island situated on the Baltic Sea, between the Gdańsk Bay and the delta of the Vistula river.

The first part of the workshop was dedicated to learn more about working in an intercultural environment and benefitting from diverse teams. The following questions and issues were tackled:

• Why do we need intercultural competences? – benefits of multiculturalism for individuals and organizations
• Stages of development of cultural sensitivity – how to develop sensitivity to differences?
• Intercultural differences – Poland vs. countries of origin

The second part of the workshop was focused on jointly proposing a series of activities strengthening our intercultural community, inclusiveness, diversity and internationalization to be conducted at ICCVS during the upcoming academic year.

Magdalena Dziki

In early July of 2019, multiple members of the ICCVS assisted to the Mass Spectrometry Summer School (MSBM) in Dubrovnik, Croatia. This event focused on learning all about the different mass spectrometry techniques and the evaluation of the knowledge in this field by different tests and exams.

The conference opened with a friendly talk by David Goodlett and followed with other interesting activities to learn our own personality and meet the people that assisted the event. Beside the different lectures and didactic activities, all the members of the ICCVS presented their work on a poster session, were they also learn more about the current uses of mass spectrometry in different fields of research.

During the conference Javier Alfaro was invited to do a lecture and two workshops, where he showed the computational strategies to follow in mass spectrometry analysis.

But not everything in the MSBM was about learning. Multiple companies that funded the event assisted to the summer school to show their last technologies in mass spectrometry and kindly networked with both students and professors. In the same way, the summer school offered free time to enjoy the magnificent weather of Dubrovnik in summer and organized a boat trip to one of the closest islands to the city and a beautiful banquet dinner as closing event.

The Mass Spectrometry Summer School offers a perfect event to learn about mass spectrometry techniques and how they work and also the perfect place to network with people that are on the edge of this field. It also create a balanced environment to both learn and enjoy at the same time.

Marcos Yébenes Mayordomo

The 1^st Nanobody Symposium was held in Bonn, Germany and had more than 200 scientist and exhibitors in attendance. The 2-day symposium began with a welcome session by the organisers; current rising star in nanobodies Dr Florian Schmidt and the manager of the Core Facility of Nanobodies at the University of Bonn, Paul-Albert König. The first talk was presented by Prof. Serge Muyldermans, one of the founding scientist responsible for the development of camelid antibodies and a pioneer in the field of their derivatives, nanobodies. His talk took us through how his lab first discovered, validated and used Camelid antibodies and nanobodies. Prof. Muyldermans also discussed a number of collaborations over a variety of fields that demonstrated the rapidly expanding range of uses for nanobodies . His anecdotes were informative, engaging and highlighted the growing pains of this emerging class of proteins. After the opening talk, the sessions were divided into 5 sections focussed on different aspects of nanobody biology; 1^st focused on the diagnostic and therapeutic uses of nanobodies in the clinic, 2^nd on the technology of generating and developing nanobodies with target specific applications, 3^rd on the use of nanobodies in structural biology, 4^th on nanobodies in imaging and finally the last session on using nanobodies as tools in cell biology research.

As well as industry experts in nanobodies such as Prof Hidde Ploegh -one of the plenary speakers at the conference- and Prof Ulrich Rothbauer. There were several young scientists who really made an impression including final year PhD students Helen Farrants and Ruiyao Cai who showed really interesting and original results in the field of cell biology and whole-body imaging respectively. They showed how nanobodies can be controlled using small molecules intracellularly and that they can be used in whole body imaging of the vascular and neuronal network of rats. A number of talks provided a more technical look at both nanobody generation and structural biology applications, Markus Seeger and Jan Steyaert were the high points in this section. These talks provided me with a lot of technical points to consider in my own project and should contribute to helping me navigate the challenges associated with the laboratory based part of my project. Following all the talks a question and answer session was held. As well as taking part in asking questions I found the types of questions asked and the answers clarified and underlined the quality of the work of the presenters as well as showing potential faults/issues. The talks also had socio-political aspects with debates about free access to materials, methods, the generation of databases and intellectual property proved popular topics throughout the symposium and were carried forward into the workshops and breaks.

The Symposium included workshops on both days. I attended the Nanobodies as Tools and the nanobody libraries workshop. The set up for both was a Q&A/ discussion chaired by industry experts. The attendance included experienced post docs and like me, students new to the field. From the workshops, practical lab and data based tips for generating, handling and developing nanobodies were exchanged and have really changed the methods I have used for some of the experimental work.

At the Symposium, I was one of over 60 people to present a poster. With viewing session held throughout the symposium, I was able to both engage with other attendees and discuss their work and also present my research to the wider audience. The interest at my poster was very encouraging and provided a positive experience at an international conference on both an academic and social side.

Overall, the symposium was a great source of new scientific information from both a practical and knowledge perspectives and has helped shape my research plan and the methodologies I will use. Attending this International symposium certainly provided me with the opportunity to build a new scientific research network for my future career. I am grateful to t he James Rennie Bequest, ICCVS and FNP for providing me with funds to attend this symposium.

Tsabieh Bilal

International Synthetic and Systems Biology Summer School (SSBSS) was held in Scuola Normale Superiore – Pisa, Tuscany, Italy (22-26 June). The summer school included 40 hours of lectures from the pioneers in the field including Jason Chin (MRC, Cambridge), Adam Arkin (UC Berkeley, USA), Ron Weiss (MIT, USA), Karen Polizzi (Imperial College London) and Virginia Cornish (Columbia University, USA). Each speaker first introduced the basic concepts related to their expertise; and then described the developments in the field. It was a great opportunity to learn about the recent advances in synthetic biology.

Although I was the only one from  ICCVS participating to the summer school this year, I believe that more members from our team will attend in the following years. The summer school was quite interdisciplinary, and it was related to many subjects such as cancer, immunology and mathematical modelling. Besides the lectures, poster sessions created the ideal environment to have scientific discussions with peers (mostly masters, PhDs or postdocs) and lecturers.

In addition to the scientific fulfillment, I also had a lot of fun at the summer school. We managed to visit Florence and Cinque Terre with my friends – whom I met there – in our spare time. We had tons of good food, coffee and memories. I would definitely suggest going to this summer school. Only thing is, mosquitos in Italy have no mercy, so make sure you bring tons of mosquito repellent!

Elif Gediz Kocaoglan