LifeWatch ERIC in BiCIKL Kick-Off Meeting

BiCiKL

The kick-off meeting for the Biodiversity Community Integrated Knowledge Library (BiCIKL) took place last week on 27-28 May! LifeWatch ERIC is proud to be one of the fourteen official partners of this Horizon 2020 project,* contributing to the establishment of open science practices in the biodiversity domain as it follows its own mission to become a worldwide provider of content and services for this research community.

But what is BiCIKL?

BiCIKL is an EU-funded project coordinated by Pensoft that aims to unite key European and international research infrastructures across ten countries in their quest to facilitate open science and fair data practices in the biodiversity scientific community. Its four key products have been identified as: a community equipped with tools for searching and accessing FAIR (findable, accessible, interoperable, and reusable) interlinked data; an interlinked corpora of knowledge for biodiversity and related research domains; automated tools and workflows for data liberation and FAIRisation from literature; and semantic-based journal production workflows for publication and reuse of FAIR biodiversity data.

What exactly does it do?

BiCIKL plans to build a Biodiversity Knowledge Hub, providing access to data, associated tools and services at each stage and along the entire research cycle. Speaking technically, it will focus on harvesting, liberating, linking and reusing subarticle level data literature (specimens, material citations, samples, sequences, taxonomic names, taxonomic treatments, figures, tables, etc.), whether PDF- or XML-based. It will provide seamless linking and usage tracking of data along the line: specimens → sequences → species → analytics → publications → biodiversity knowledge graph → re-use.

What role does LifeWatch ERIC play?

LifeWatch ERIC, which already carries out specialised work in the areas of semantics and usage tracking, will be key in helping BiCIKL develop the methods, tools and workflows required for the realisation of BiCIKL goals. Its two main tasks will be to analyse the technical requirement of users and implement the Biodiversity Knowledge Hub (BiKH). It will participate in testing and streamlining interoperability and the alignment of findability, reuse and accessibility. Furthermore, LifeWatch ERIC will contribute to defining and implementing the necessary operational framework, as well as identifying BiKH components and translating the functional diagramme and operational framework into an educational cloud.


BiCIKL’s website is currently under construction, but you can follow its activities on Twitter.


*grant agreement No. 101007492, duration May 2021-2024

LifeWatch ERIC showcases: new technology for biodiversity researchers

The 20–21 May was an important milestone for the LifeWatch ERIC, as it hosted its long-anticipated e-Science for NIS workshop, albeit in a virtual form due to the ongoing pandemic. The workshop was organised with the support of ENVRI-FAIR, and was hugely successful, attracting over 220 registrations. The aim of the event was to showcase the results of five research endeavours, known as validation cases, into Non-indigenous and Alien Species (NIS) conducted over the last 18 months within the LifeWatch ERIC Internal Joint Initiative.

These validation cases led to the development of five separate workflows, created through the joint effort of scientists and ICT experts, both from LifeWatch ERIC Common Facilities and Distributed Centres, to accommodate the data and analytical processes generally required by the NIS scientific community. In turn, these workflows have been integrated into Tesseract technical composability layer, the new Virtual Research Environment (VRE) platform being developed by LifeWatch ERIC. Both the innovative advances in technology and the associated scientific reports sparked engaged and enthusiastic discussion over the two days. In fact, the workshop proved to be particularly appreciated by attendees, with 85% rating it as “very good” or “excellent”, as well as the web-services presented also considered “very good” or “excellent” by 78% of participants.

LifeWatch ERIC is at the service of the biodiversity and ecosystem research community, and is constantly seeking to create opportunities for mutual exchange. For this reason, the presentations of the validation cases were complemented by a series of round tables, featuring academics and experts from a wide range of fields. The speakers debated the ecological, economic and social impact of NIS, and the need to work across disciplines, combining social and natural sciences. The final consensus was that greater coordination of data collections is required in order to integrate existing data from different sources, and find ways to enable access to such collections.

Non-indigenous Invasive Species have enormous impacts on ecosystem services, human health and on the economy. This is why LifeWatch ERIC was proud to present the results of the validation cases providing powerful and flexible workflows capable of integrating more data and services than has yet been possible. The workflows will be available in the LifeWatch ERIC Tesseract VRE, which among its many innovative functions, enable the import of data from different sources, their exploration in maps for validation, and the use of standard tools to connect data analytics through its HPC and cloud-related technologies. Tesseract is also built around the unique LifeWatch ERIC tool known as LifeBlock, which uses Blockchain technology to ensure the integrity of all data inputs and full recognition for contributors. The VRE is not only an innovative tool that can be customised to other bioregions, but it will continue to evolve in the light of future feedback from scientists. In the long run, the use of Tesseract will contribute to boosting social awareness about biodiversity and help policymakers concerned about habitat conservation to implement sound science-based decisions.

LifeWatch ERIC would like to take this opportunity to acknowledge the superb efforts of all the team members involved, and to thank ENVRI-FAIR Science Cluster for its support during the workshop, as well as all the wonderful speakers and participants who actively contributed to make this 2-day workshop a success and with whom LifeWatch ERIC hopes to continue working in the future.

The recording of the workshop will shortly be made available, in the meantime, you can find the workshop presentations here.

e-Science for NIS Research Workshop

NIS WORKSHOP

On 20–21 May 2021, LifeWatch ERIC will be hosting the online workshop “e-Science for NIS Research”, with the support of the ENVRI-FAIR Project. The workshop will showcase the results of four validation cases into Non-indigenous and Invasive Species (NIS) conducted over the last 18 months within the LifeWatch ERIC Internal Joint Initiative. Registration is compulsory and free of charge.

The first day will be dedicated to the marine domain, with sessions focusing on the long-term monitoring of hard-bottom marine communities and marine/transitional NIS occurrence and trophic niches dynamics. LifeWatch ERIC and Distributed Centre staff will also be presenting workflows using photographic, metabarcoding and stable isotope tools to extract and analyse data of different typologies from varying sources.

The second day will be devoted to the terrestrial domain, with a particular focus on the detection and monitoring of invaders through remote sensing and habitat vulnerability to NIS and impact on biotopes. Presenters will also showcase workflows involving the use of satellite and occurrence data, combining different statistical and machine-learning algorithms to map the distribution of invaders and identify which habitats are most at risk.

The workshop programme will be enriched with several round tables, covering hot topics within the biodiversity and ecosystem research community such as cooperation between Research Infrastructures, the impact of NIS on marine ecosystems as well as their impact on economy and society, disruptive technologies for NIS research and how open science and open access can benefit researchers.

As a follow-up to the workshop, a hands-on training session on the use of the four workflows and Virtual Research Environments (VRE) will be held on 4 June, subject to sufficient interest. The full programme and any relevant updates can be found here. 

VLIZ recruiting marine researcher

Gloved researcher handling fish at VLIZ Marine Observation Centre

The Flanders Marine Institute (VLIZ) is looking to hire a researcher to join its Marine Observation Centre with immediate start.

The ideal candidate would have a PhD in marine sciences (or equivalent) to further LifeWatch Belgium‘s work in fish tracking research.

Valued qualities also include being able to work both independently and in a team, as well as strong organisational skills and an enthusiasm for collaborative international research, particularly offshore fieldwork. Applications for this two-year contract will be accepted up to and including 7 May 2021.

For more information on this vacancy, please click here.

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.

Spatial modelling in Portugal

Spatial Modelling

study from 2012 to 2019 in the Sabor river in northeast Portugal focused on stream fish affected by hydropower development. Trajectory analysis was used to quantify the directionality and velocity of community change across 30 sites, and geometric modelling provided a simple framework to understand where and why temporal community dynamics vary across dendritic stream networks.

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