Introducing the EBES Master’s Diary

EBES Master's

In the Spring Term of 2022, LifeWatch ERIC will be funding a three-month internship abroad for three students, Martina, Marco and Ludovico, of the e-Biodiversity and Ecosystem Sciences Master’s degree (EBES) at the University of Salento, which is supported by LifeWatch ERIC.

Thanks to this dedicated LifeWatch ERIC internship programme, the students will be going to the Ionian University in Corfu, where they will be given the chance to apply the skills they have developed during their studies, carrying out research for their dissertations and gaining experience in the university labs. Individually, Martina, Marco and Ludovico will be focusing on using text mining to extract information on spatial and ecological traits of freshwater fishes, using a modelling approach to investigate the reasons a species population stays heterogenous, and building user-friendly citizen science applications with the aim of monitoring natural ecosystems. You can follow all three of the students’ journeys throughout their experience in Corfu by watching their Master’s Diary, which they will be updating periodically – subscribe to our YouTube channel to ensure you never miss an update! 

The EBES Master’s Degree e-Biodiversity and Ecosystem Sciences (EBES) is the newest curriculum available within the Master of Coastal and Marine Biodiversity and Ecology degree, designed to provide trans-disciplinary knowledge and skill sets for a new generation of ecologists proficient in data science, modelling and eco-informatics. It is a two-year programme at the University of Salento, entirely taught in English, allowing students to gain highly specialised instruction on biological and ecological sciences,ecological modelling and ecological informatics technologies. The course was created as current global challenges call for a deeper understanding of ecological phenomena at various levels of scale, to identify patterns and underlying mechanisms of biodiversity organisation and ecosystem functioning, and design scenarios of future change. 

For more information about the EBES Master’s Degree, please see the dedicated webpage of the University of Salento, or download the PDF here.

International Women’s Day 2022: Despoina Vokou 

Despoina Vokou

For International Women’s Day 2022, we at LifeWatch ERIC are putting eight scientists in the spotlight. Each of the LifeWatch ERIC member states has proposed a figure who has broken boundaries over the course of her lifetime, and is an inspiration to younger generations looking to pursue a career in STEM.

As we explored in the podcast we recorded for The International Day of Women and Girls in Science, women are still underrepresented in various scientific fields, such as engineering, computer science and AI. Additionally, scientific research in general is not only unbalanced in terms of composition (33% female) but also in terms of hierarchy, with only 12% of national science academy members being women, who are disproportionately overlooked when it comes to promotion and grants.

The women at the centre of our campaign are very diverse, hailing from a range of countries and time periods, but they all have one thing in common: overcoming the odds in order to contribute to scientific improvement. We want to draw attention to just a fraction of the women who have defied the cultural barriers pitted against them to bring good to the world, and bring recognition where they might have been overlooked. 

Despoina Vokou is a Professor of Ecology in the Aristotle University of Thessaloniki, Greece, where she previously held the roles of Head of the School of Biology and Deputy Dean of the School of Science. She obtained her bachelor’s degree from School of Pharmacy, National and Kapodistrian of the University of Athens, followed by a PhD from the School of Biology at the Aristotle University of Thessaloniki. Her research interests include aerobiology, mycology and plant ecology, Mediterranean ecosystems, biodiversity conservation and management of protected areas. She has published over 110 scientific publications with an h-index of 36. 

Vokou’s expertise in her field has received much recognition, having also been heavily involved in the direction of WWF Greece over the last 30 years; she was invited to represent Greece at the 10th Μeeting of the Conference of the Parties to the Convention on Biological Diversity (CBD COP 10) in Japan, and was president of the Natura 2000 national Committee, as well as being called up as an expert on international environmental issues/WPIEI-Biodiversity for the 2014 Greek Presidency of the EU Council.

The National Bank of Greece invited her to review its report on ‘The environmental, economic and social impacts of climate change in Greece’, and the 5th Assessment of the Intergovernmental Panel on Climate Change (IPCC) invited her to review chapters of its famous report  ‘Climate Change Impacts, Adaptation and Vulnerability’. In addition to being a Member of the Council of European Ecological Federation (EEF) for nearly a decade, Vokou is also a founding member of the Hellenic Ecological Society (HELECOS), which she presided over for several years.

LWGreece Research Infrastructure Data Services

Research Infrastructure Data Services

The Hellenic Centre for Marine Research (HCMR) is working on the enhancement of the LifeWatchGreece Research Infrastructure (LWGreece RI) Data Services. The purpose of these activities is to provide end-users with a user-friendly service, enabling them to search and access (meta)data from two sources, Micro-CT vLab and IPT MedOBIS.

The activities are divided into three major categories:

(a) design and implementation of facilities for harvesting data

(b) data modelling and semantic data transformation activities, and

(c) updates and enhancements of the Data Services of the LWGreece RI.

More details of these activities are given below:

A set of supporting services and tools have been designed and implemented, able to harvest resources from two databases: (a) the IPT MedOBIS database and (b) the Micro-CT vLab database. A harvesting mechanism has been implemented that exports information from the above-mentioned sources, which are subsequently transformed and added to LWGreece repositories (see point below). 

After harvesting data from the sources described above, they needed to be homogenised before depositing them in the repositories of the LWGreece infrastructure. To this end, a set of mappings was implemented, using X3ML Specification Language,[1] that describes the transition of the harvested resources from their original schemata, to a common target top-level ontology MarineTLO.[2] The result was a set of ontological-based descriptions regarding MarineTLO that were inserted into the LWGreece semantic repositories.

Several endpoints of the Data Services were updated, so that they can properly retrieve information from LWGreece semantic repositories. In addition, we have enhanced the services based on the findings and the updated modelling that emerged from the two new sources that were used (i.e., IPT MedOBIS, micro-CT vLab). 

It is worth mentioning that the Data Services (along with all the other available vLabs) is now available through the Metadata Catalogue of LifeWatch ERIC. Allowing this central catalogue to be machine-interoperable is necessary for the population of the catalogue, and implements the FAIR principles and EOSC-interoperability, promoted through ENVRI-FAIR WP9 and WP11.


[1] Marketakis, Y., Minadakis, N., Kondylakis, H., Konsolaki, K., Samaritakis, G., Theodoridou, M., Flouris, G. and Doerr, M., 2017. X3ML mapping framework for information integration in cultural heritage and beyond. International Journal on Digital Libraries, 18(4), pp. 301-319.

[2] Tzitzikas, Y., Allocca, C., Bekiari, C., Marketakis, Y., Fafalios, P., Doerr, M., Minadakis, N., Patkos, T. and Candela, L., 2016. Unifying heterogeneous and distributed information about marine species through the top level ontology MarineTLO. Program, 50(1), pp. 16-40.

Explainers: the Micro-CT vLab

Micro-CT vLab

The Micro-CT vLab is a virtual laboratory which is hosted in the Hellenic Centre for Marine Research (HCMR) and was initially established during the ESFRI LifeWatchGreece Research Infrastructure. This virtual lab offers users access to virtual galleries of various samples which can be displayed and downloaded through a web application. This tool has been updated over the Elixir-GR, BIOIMAGING-GR and Synthesys+ projects with the addition of several new features. Firstly, the Micro-CT vLab has now been upgraded to Drupal version 9. A series of micro-CT datasets from medical to biological studies can be uploaded in order to be stored and disseminated.

Furthermore, the Micro-CT vLab has now a REST API for creating new content. Through the API, the user has the ability to access micro-CT API endpoints, which can retrieve information about various micro-CT scans, species and metadata information related with the micro-CT datasets. A metadata catalogue has been also created in order to dynamically display the complete metadata available for each dataset which are published in the micro-CT. Finally, following registration, the user now has the ability to upload the original micro-CT datasets and the related metadata through a user-friendly form.

You can watch a short demonstration video of the Micro-CT vLab below.

LifeWatch ERIC CEO at the Ionian University

Ionian University

On 23–24 November 2021, LifeWatch ERIC CEO, Christos Arvanitidis, travelled to the Ionian University in Zakynthos (Greece) to deliver three lectures to Bachelor’s degree students at the University’s Department of the Environment.

Dr Arvanitidis gave three in-person lectures; the first presented the research infrastructure LifeWatch ERIC and its unique position at the service of the biodiversity and ecosystem research community, the second covered examples on the international, European and national legal framework of the sea, whilst the third demonstrated  how LifeWatch ERIC can help scientists working on lagoonal biodiversity and ecosystem dynamics. Dr Arvanitidis himself is a marine scientist and Research Director at the Hellenic Centre for Marine Research, where he helped to form the national node LifeWatchGreece before becoming LifeWatch ERIC CEO.

LifeWatch ERIC already has strong ties with the Ionian University, which will soon be offering the same LifeWatch ERIC-developed e-Biodiversity and Ecosystem Sciences (EBES) MSc programme already available at the University of Salento (host of LifeWatch Italy). Once activated there, the course will give enrolled students the opportunity to obtain a “Joint Degree” with an exchange programme between the two countries.

You can view the EBES Master’s brochure here.

LifeWatch ERIC CEO and CTO Inspire at ‘Inspirational Event 2021’

Inspirational Event

Inspirational Event 2021, powered by Advance Services, took place at Heraklion (Crete) on 15 and 16 November. Its purpose was to bring together successful and distinguished professionals to give half-hour talks, passing on their knowledge, experiences and advice to an audience consisting of executives and entrepreneurs of the local community.

Alongside LifeWatch ERIC Executive Board members, Dr Juan Miguel Gonzalez-Aranda (LifeWatch ERIC CTO & Head of its ICT-Core) and Dr Christos Arvanitidis (LifeWatch ERIC CEO), spoke Dr George Bruseker (Takin Solutions CEO), Dr George Caridakis (Professor at the Aegean University), Mr Yannis Lidakis (Harvard University Representative & SkyExpress Commercial Director) and Dr Armando Stellato (Professor at the University of Rome). The event was chaired by Nikos Minadakis, CEO of Advance Services, which provides Technical & Operations Consultancy to LifeWatch ERIC.

The audience was thrilled with the professional experiences, tips, suggestions and ideas of the speakers, and actively participated with comments and questions. A total of fifty people who had received invitations said they would gladly attend the event each year and were looking forward to returning. The executives of Advance Services expressed their enthusiasm in repeating the event, next time with even more speakers, listeners and a wider range of topics.

Biomonitoring of aquatic ecosystems using genetic methods

Hand holding vial containing clear liquid

The second part of a DNAqua-Net workshop on “Biomonitoring of aquatic ecosystems using genetic methods”, was hosted virtually by the Cyprus University of Technology and the Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC) of the Hellenic Centre for Marine Research on Friday 12 March 2021. It presented to experts, and to the general public, the exciting potential of new, promising and rapidly developing genetic methods for assessing biodiversity, and their use as monitoring tools.

Throughout their lifetime, all organisms release DNA into the environment (environmental DNA or eDNA). New genetic methods, such as DNA metabarcoding, detect this eDNA that is released into the environment and can partially identify and quantify the existence of various organisms without necessarily collecting whole organisms. In aquatic ecosystems, for example, living species can be detected by filtering only a few litres of water and submitting them to genetic analysis.

In an age of great ecological challenges, eDNA methods will find applications in monitoring changes in biodiversity caused by factors such as ecosystem degradation and climate change, in the early detection of alien/invasive species, and in the identification of rare and endangered species. They therefore have the potential to substantially improve the procedures for assessing and monitoring the ecological status of aquatic ecosystems, in particular as part of national and European directives, such as the Water Framework Directive and the Marine Strategy Framework Directive.

The workshop provided in-depth information on the great potential of DNA and eDNA-based methods to experts involved in the practical implementation of these European Directives, and highlighted the status quo of the reference databases. The presentations by IMBBC and CUT were followed by a discussion which emphasised the need for collaborative action between stakeholders (scientists in the fields of genetics, ecology and bioinformatics, policy makers, management bodies, NGOs, etc.) in order to standardise the methods used at national level so as to be able to engage in formal bio-monitoring actions on the ecological quality of aquatic ecosystems right across Europe.

World Conference on Marine Biodiversity 2020

The World Conference on Marine Biodiversity 2020 was successfully presented online between Sunday 13 – Wednesday 15 December 2020, by the University of Auckland, New Zealand. A state-of-the-art virtual conference platform, that facilitated interactive plenary sessions, live panel discussions, filmed presentations, e-posters, a meeting hub and virtual exhibition areas, attracted over 400 participants.  

LifeWatch ERIC was privileged to be able to support the international event as platinum sponsor. Chief Executive Officer Christos Arvanitidis, in a pre-recorded video message broadcast at the start of proceedings, warmly welcomed the participants, wishing them good luck and a great remote conference, inviting them to support the United Nations decade of ocean science for sustainable development and to become part of the LifeWatch ERIC global community.

The CEO’s emphasis on open access data, reproducible analytics and mobilised communities was reinforced by a dedicated webpage offering details of those LifeWatch ERIC products of greatest interest to marine biologists, with the Metadata Catalogue in prime position. National Nodes contributed materials on Micro-CTvLab, RvLab and MedOBIS (Greece), the LifeWatch Species Information Backbone, the Marine Observatory and three Antarctic services (Belgium), and EcoPortal (Italy).

LifeWatch ERIC staff from these member countries were also on hand at the virtual stand during the coffee breaks to maximise human interaction, in spite of the 12-hour time zone difference. The booth created considerable interest, with over 200 visitors overall and 85 downloads of brochures and other links. 

5th LifeWatch ERIC General Assembly

5th General Assembly

The Dirk Bouts Building in the Flemish Administrative Centre (VAC) in Leuven, Belgium, was the scene for the 5th LifeWatch ERIC General Assembly, from 11–12 December 2019, chaired by Gert Verreet. Composed of the representatives from all full Member States and observers, the purpose of General Assembly Meetings, the highest governing body of LifeWatch ERIC, is to set the overall direction and to supervise the development and operation of LifeWatch ERIC. 

At the heart of this 5th General Assembly lies the prototype of the LifeWatch ERIC Platform, an integrated initiative of LifeWatch ERIC Common Facilities presented by the CTO, Dr Juan Miguel González-Aranda. Thanks to its application layers and user-friendly interfaces, the prototype will enable the integration of all the resources, including web services developed by National Nodes over the years, as well as those resulting from Common Facilities and Joint Initiatives, like the recent investigation undertaken by the infrastructure members on the current and future challenges of NIS in Europe, into Virtual Research Environments (VREs). The prototype was adopted by the General Assembly, officially marking the beginning of the deployment and operational phase, with its implementation expected to continue until the end of next year.

With many other important issues on the agenda, this rich two-day meeting moved from a review of LifeWatch ERIC activities in 2019 to forward planning for 2020 and delivering general frameworks for implementation. Among these, the Assembly approved the general framework for Service Level Agreements (SLAs) to be used as the basis for a roll-out to national nodes in the course of the year, and an engagement policy to reinforce our dialogue with – and capacity to reach out to – external stakeholders. By finalising the rules and procedures for subsidiary bodies, and having established the selection committee to complete the recruitment of one of the most strategic positions, the Chief Financial Officer, LifeWatch ERIC will be in good shape to hit the ground running in 2020.

2nd Dahlem-Type Workshop

2nd Dahlem-Type Workshop

The LifeWatch ERIC Internal Joint Initiative was launched in October 2019 to design and construct a Virtual Research Environment capable of processing and modelling available data on one of the planet’s most burning biodiversity issues, the proliferation of Non-indigenous and Invasive Species (NIS), in order to help mitigate their impacts. 

Development of a new Virtual Research Environment (VRE) is essential to further integrate the tools and services available in the LifeWatch ERIC web portal. The process will allow stakeholders greater ability to develop their research activities within the e-Science Infrastructure, whilst also clearly demonstrating the added value that LifeWatch ERIC’s advanced technologies can bring not only to the biodiversity and ecosystem scientific community, but to policymaking and human wellbeing around the globe. 

The conceptual paper and workflow-timeline developed at the 1st Dahlem-type workshop in Seville, Spain, 14-18 October, formed the basis of this 2nd Dahlem-type Workshop, organised in Rome, Italy, from 2-6 December, this time coordinated by the LifeWatch ERIC CTO, Juan Miguel González-Aranda. This 2nd Dahlem-type workshop delivered the first prototype of the new LifeWatch ERIC Non-indigenous and Invasive Species Virtual Research Environment. The collaborative construction and deployment approach and the intense interaction between ICT and NIS experts made it possible to achieve definition of the requirements and needs of the scientific community and of the main architecture layers (application, e-Services composition, e-infrastructure integration, and resources) that underpin the VRE.