Towards the ENVRI Community International Summer School: Webinars on Designing and Developing Data Services for End Users

Data Services for End Users Webinars

In the run-up to the ENVRI Community International Summer School in July, LifeWatch ERIC and ENVRI-FAIR will be organising two webinars on “Designing and Developing Data Services for End Users”. Participation in the webinars can be in preparation for the School or as stand-alone sessions, for those who cannot attend the School, or those who are still considering registering. For more information on the ENVRI Community International Summer School “Road to a FAIR ENVRI-Hub: Designing and Developing Data Services for End Users”, please visit the dedicated minisite.

The webinars are particularly aimed at IT architects, Research Infrastructure (RI) service developers and user support staff, and RI staff working on user interaction and community/network building. Links to the sessions will be provided upon registration.

Webinar #1: Service validation & evaluation: making sure your services are up to the task

Date
Friday 17 June, 10:00-11:30 CEST

Where
Zoom (link to be provided upon registration)

Programme

  • Validating services & assessing their TRL – Mark van de Sanden (SURF)
  • Service evaluation: why & how – Yin Chen (EGI)
  • Evaluating ENVRI services: experiences from the ENVRIplus – Maggie Hellström (ICOS)
  • Q&A and general discussion – plenary

Webinar #2: Service documentation & tutorials: rolling out the red carpet for end users

Date
Thursday 23 June, 10:00-11:30 CEST

Where
Zoom (link to be provided upon registration)

Programme

  • Writing effective service documentation for EUDAT services – Rob Carillo (EUDAT)
  • Service tutorial design: experiences from EOSC Synergy – Helen Clare (JISC)
  • Using Jupyter Notebooks to introduce services to “new” end users – ENVRI-FAIR expert (TBA)
  • Q&A and general discussion – plenary

You can sign up for one or both webinars using the form linked below:

Click here to access the form.

Rolling Out Season 2 of the LifeWatch ERIC Podcast “A Window on Science”

LifeWatch ERIC Podcast

While the first LifeWatch ERIC podcast season focused on the Internal Joint Initiative, the construction of that Virtual Research Environment, this second season draws on the experiences of the scientists and ICT specialists involved in the five validation cases used to develop said Virtual Research Environment. Five investigations into the impact of Non-indigenous and Invasive Species on a range of environments suffering from climate change and anthropogenic pressures.

Over the next three months, therefore, you will hear from the terrestrial and marine researchers, ICT technicians and software engineers, molecular geneticists and data managers who worked together in trans-disciplinary teams to construct and test five workflows – pipelines of data sourcing and processing – to make that research possible at scales never achieved before. The LifeWatch ERIC podcast season 2 “A Window on Science” features:

  • Wednesday 11 May: The Atlantic Blue Crab
  • Wednesday 25 May: ARMS. Hard-bottom communities
  • Wednesday 8 June: Metabarcoding
  • Wednesday 22 June: Ailanthus, and
  • Wednesday 6 July: Biotope.

Don’t forget that these LifeWatch ERIC podcasts, as well as being embedded in our website portal (find all of Season 1 here and the live episodes of Season 2 here), are also available on Spotify, Google Podcasts, Apple Podcasts, and Amazon Music.

Doctoral Thesis Defence on AI, Biodiversity and Sustainable Ecosystem Management 

AI biodiversity

On 27 April 2022, a presentation of a doctoral thesis by doctoral candidate Francisco Pérez-Hernández, entitled “Pre- and Post-Processing Strategies in Deep Learning for Multi-class Problems in the Field of Security and Biodiversity” took place at the “Escuela Técnica Superior de Ingeniería Informática” (ETSII) of the University of Granada. This thesis is one of the results of the Thematic Centre on Artificial Intelligence (AI) and Deep Learning, and High Mountains Ecosystems, under the umbrella of the so-called LifeWatch ERIC SMART ECOMOUNTAINS Andalusia ERDF project, hosted by the University of Granada as one of the distributed facilities engaging with LifeWatch ERIC.

This is an outstanding milestone in the application of state-of-art AI and Deep Learning techniques in, e.g., advanced satellite image processing for the study of biodiversity and ecosystems, to be made available to the scientific community and environmental decision makers in the form of a LifeWatch ERIC Virtual Research Environment.

Among those attending the defence were the doctoral tutors, supervisors and member of the evaluation committee: Juan Miguel González-Aranda, LifeWatch ERIC CTO, Enrique Herrera Viedma, Vice-Rector for Research and Transfer of the University of Granada; Siham Tabik, Professor of the Department of Computer Science and Artificial Intelligence; Francisco Herrera Triguero, Professor at the Department of Computer Science and Artificial Intelligence at the University of Granada; Domingo Alcaraz Segura Professor at the University of Granada; Juan Mario Haut Hurtado, Professor at the University of Extremadura,  and Gloria Ortega López, Professor at the University of Almería. 

LifeWatch Slovenia Publishes New Research Paper

LifeWatch Slovenia Research

Researchers affiliated with LifeWatch Slovenia have published the research paper: “Karst Groundwater Dependent Ecosystems—Typology, Vulnerability and Protection” (Nataša Ravbar, Tanja Pipan). You can read the abstract below and click on the link to access it in full.

Karst Groundwater Dependent Ecosystems—Typology, Vulnerability and Protection

Nataša Ravbar, Tanja Pipan

Karst groundwater dependent ecosystems (KGDEs) represent an important asset worldwide due to their ecological and socioeconomic values. In the contribution the main KGDEs of the Dinaric karst in Slovenia are presented. The main hydrological processes (i.e., extent, duration and frequency of groundwater inflow), the main biota and indicator communities, and the factors limiting the evolution of species (e.g., darkness) were identified. An overview of rare, endemic and charismatic species was also shown including Proteus anguinus, Marifugia cavatica, Monolistra racovitzae racovitzae and others. Due to its location in an area of very high geographical diversity and between different climate types, the Slovenian Dinaric karst is one of the hotspots of subterranean biodiversity on a global scale. The interaction between orographic, climatic, hydrological and edaphic conditions, as well as the fact that the area served as a hub for different species and as a refuge during the ice ages, are crucial for the very high biodiversity in this area. Due to deforestation in prehistoric times, man has even contributed to the diversification of the flora by creating space for the appearance or spread of habitats that are now considered natural (e.g., dry grasslands). An important factor in maintaining a particularly rich diversity of karst flora and fauna is also the low human impact and the very well preserved landscape in its natural state. KGDE sites in Slovenia with the greatest known species diversity are the Postojna -Planina and Škocjanske Jame cave systems, Cerkniško and Planinsko Polje, and the intermittent lakes of Pivka. Characterization of KGDEs is a prerequisite for a better understanding of the processes that control them, their biological function, and their vulnerability. The ecohydrological characterization of KGDEs of Slovenian Dinaric karst can serve as a pilot study for other karst regions with high biodiversity.

Photo credit: B Kogovšek, N Ravbar, Adobe Stock.

ENVRI Community International Summer School is back in person!

ISS2022_news

We are delighted to announce the 2022 edition of the ENVRI Community International Summer School. And this summer, we are back in person! 

The Summer School, now at its fifth edition, is organised by ENVRI-FAIR and LifeWatch ERIC and will take place in Lecce, Italy, from 10–15 July. This edition’s title is “Road to a FAIR ENVRI-Hub: Designing and Developing Data Services for End Users”, and it will cover topics such as user interfaces, packaging of services, reusability and validation of services, and building and supporting networks through the lens of the ENVRI-Hub approach. 

This School is therefore mainly aimed at IT architects, Research Infrastructure (RI) service developers and user support staff, and RI staff working on user interaction and community/network building.

The Summer School will welcome participants on the afternoon of Sunday 10 July with an opening event, while the actual School programme will last from Monday to Friday afternoon, closing with a certificate ceremony. Two online webinars are also planned to take place in the third and fourth week of June on specific use cases, in preparation for the School or to attend as stand-alone sessions.

The outline of the School programme is as follows:

  1. Introducing the ENVRI-Hub (concept and architecture)
  2. Learning to know your end users and their expectations: requirements elicitation
  3. Create high quality documentation and usage examples to support service end users
  4. Developing Services and Fostering Reusability/Interoperability among them
  5. Validating and evaluating your services
  6. Participants’ Presentations, School Evaluation and Certificates

Successful applicants to “Road to a FAIR ENVRI-Hub: Designing and Developing Data Services for End Users” will be offered full board in the beautiful baroque city of Lecce in Southern Italy, and will be invited to “extracurricular” activities such as restaurant dinners and excursions in the surrounding area. 

Interested persons are invited to apply by 30 May by filling in the sign-up form here. Follow LifeWatch ERIC and ENVRI Community updates!

You can access the dedicated minisite with more detailed information on the School here.

WoRMS Video Tutorials available on LifeWatch ERIC Training Platform

WoRMS Tutorial

Last year, the WoRMS Data Management Team (DMT), which is supported by LifeWatch Belgium, created instruction videos for the WoRMS editors, to assist them in their online editing activities. Now, the WoRMS DMT has released a series of short tutorial videos specifically aimed at its users, which have also been made available on the LifeWatch ERIC Training Platform.

Are you sometimes a bit at a loss on how you can find species-related information through the WoRMS website? Maybe you are just curious on how you can efficiently search through the available distributions, specimens or literature in WoRMS? Or you want to match your own species list to WoRMS? Well, this series of 6 short tutorial videos – all under 10 minutes – will guide you through all these ‘how to…’ topics:

  • How to search for taxa in WoRMS, through the quick, simple, and advanced search interfaces
  • How to search for literature in WoRMS
  • How to search for distributions in WoRMS
  • How to search for specimens in WoRMS
  • How to upload images and videos through the WoRMS photo gallery (both without and with login)
  • How to match your taxa to WoRMS using the taxon match tool

Click here to access the videos on our Training Platform.

The creation of these tutorial videos fits under the WoRMS endorsed project within the UN Ocean Decade, where WoRMS continues to support not only scientists, but everyone who makes use of species names, including policy, industry and the public at large.

This news item has been adapted from a post on LifeWatch Belgium.

The Next-Generation Research Infrastructure

A Window on Science S1

As promised in the trailer we released a few weeks ago, Season 1, Episode 1 of our brand new podcast ‘A Window on Science’ is now live!

The first season of the LifeWatch ERIC podcast series ‘A Window on Science’ outlines the  steps forward that the European e-Science infrastructure for biodiversity and ecosystem research has made in the last two years, developing cutting-edge services for researchers. Our CEO, Christos Arvanitidis, opens the series, walking us through terminology that may seem challenging to non-scientific audiences: Research Infrastructures, the Joint Internal Initiative, and virtual servers. The conversation places LifeWatch ERIC clearly in the context of the European Research Area and outlines not only the progress already made, but strategic plans for the next five years – becoming ‘the next-generation Biodiversity and Ecosystem Research Infrastructure’.

If you’re interested in the topics covered in this podcast, and want to find out more, we invite you to visit our dedicated minisite on the Internal Joint Initiative, or to flick through our ‘Alien Alert!’ magazine.

The Window on Science podcasts are available on our website and on the following platforms:

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.

Big Seashell Survey 2022 shows remarkable differences between Belgium and the Netherlands

Big Seashell Survey

On Saturday 19 March 2022, circa 750 citizens collected over 38,000 shells on Belgian beaches for the Big Seashell Survey 2022, with a top-5 in line with the results of the 2021 edition. For the first time, the Netherlands joined this LifeWatch Belgium citizen science initiative and collected another 22,000 shells, showing remarkable differences between the countries.

The Flanders Marine Institute (VLIZ) and its partners (EOS wetenschap, Natuurpunt, Provincie West-Vlaanderen, Strandwerkgroep, Kusterfgoed, the ten coastal municipalities) joined forces for the fifth edition of the Big Seashell Survey, a well-established LifeWatch Belgium citizen science initiative.

On Saturday 19 March, under the bright sunshine, 750 citizens collected, counted and identified 38,000 beach shells, with the help of more than eighty mollusk experts. For the first time, the Netherlands – Naturalis, NMV, Stichting Anemoon, Stichting De Noordzee and the Strandwerkgemeenschap – stepped in and collected another 22,000 shells on seven beaches in the Dutch province of Zuid-Holland and on one Texel beach. In the countries, 60 different species have been registered, with two out of three species shared by Belgium and the Netherlands. Non-indigenous species (NIS) accounted for 10% of all specimens and species.

In addition, scientists discovered remarkable differences between the two countries. Belgium recorded a top-5 comparable to the result of the 2021 edition (Baltic tellin 37%, Cut trough shell 22%, Edible cockle 18%, Blue mussel 9% and Atlantic razor clam 5%), whereas on Dutch beaches there was a clear dominance of Spisula shells, with 49% Cut trough shells, 9% Elliptical trough shells and 6% Thick trough shells. Here, Atlantic razor clams (9%) and the Edible cockle (8%) completed the top-5. One explanation for the high number of Cut trough shells on Dutch beaches could be the slightly different hydrographic conditions with more exposure, in favour of this shell.

Another difference appears to relate to the vicinity of the Scheldt estuary”, says Jan Seys (VLIZ). “The mouth of this estuary, next to the eastern part of the Belgian coast, contains more silt and clay then the sandier Zuid-Holland and Flemish west coasts, and it has quite some peat banks in and on top of the sea-bottom. This silty environment is perfect for the Baltic tellin; the peat banks can house American and white piddocks”. On the Dutch coast, the Baltic tellin ended up in eighth position, accounting for only 2% of all shells. And in the Netherlands, Barnea candida did not end up in the top-10, whereas piddocks at the eastern part of the Belgian coast were much more common (9% of all shells).”

This news story was originally posted on LifeWatch Belgium.

Ten remarkable new marine species from 2021

Top Ten WoRMS

As in previous years, the World Register of Marine Species (WoRMS), an initiave hosted by VLIZ, LifeWatch Belgium‘s focal point, has released its annual list of its top-ten marine species described by researchers during the past year, marking World Taxonomist Appreciation Day on 19 March!

If you were unaware of this celebration of all the work that taxonomists do, you can find more herehere, and here.

The 2021 top-ten list is just a small highlight of over 2,000 fascinating new marine species discovered every year (there were 2,241 marine species described in 2021 and added to WoRMS, including 263 fossil species).

Full list:
How were the species chosen?

A call for nominations was announced in December 2021, sent to all editors of WoRMS and editors of major taxonomy journals, and posted openly on the WoRMS website and social media so anyone had the opportunity to nominate their favourite marine species. Nominated species had to have been described in 2021, and come from the marine environment (including fossil taxa). A small committee (including both taxonomists and data managers) was brought together to decide upon the final candidates. The list is in no hierarchical order.

The final decisions reflect the immense diversity of animal groups in the marine environment (including fish, crustaceans, molluscs, corals, sponges, jellies and worms) and highlight some of the challenges facing the marine environment today. The final candidates also feature some particularly astonishing marine creatures, notable for their interest to both science and the public.

Each of these marine animals has a story. This year the chosen species range from the extremely tiny and often overlooked, to a new species of whale! Among the featured is the tiny Japanese Twitter Mite, discovered on social media, the Quarantine Shrimp, described during the COVID-19 lockdown, a new species of mysid hiding in plain sight, the massive Yokozuna Slickhead, honouring high ranking sumo wrestlers, and the astonishing Jurassic Pig-Nose Brittle Star!

About the WoRMS top-ten list of Marine Species

After 250 years of describing, naming and cataloguing the species we share our planet with, we are still some way off from achieving a complete census. However, we do know that at least 240,000 marine species have been described because their names are managed in WoRMS, by almost 300 scientists located all over the world.  

WoRMS’ previous lists of the top-ten marine species described for the decade 2007–2017, for 2017, 2018, 2019 and 2020 can be found here:

This news item was adapted from a post on LifeWatch Belgium.