Researchers grab chance to experiment with LifeWatch ERIC tools at Hands-on Session

Screenshot of Hands-on Session featuring smiling participants

On Friday 4 June 2021, as a follow-up to the successful e-Science for NIS Research Workshop on 20-21 May, LifeWatch ERIC gave researchers the opportunity to try out LifeWatch ERIC-developed software at a Hands-on Session. It marked the debut of key tools built by LifeWatch ERIC as part of its Internal Joint Initiative (IJI) in its quest to facilitate open access data in the domains of biodiversity and ecosystem research.

All training resources, including presentations, demos and manuals are available through the LifeWatch ERIC Training Platform. (Please note, those who missed out on the Session can find the relevant materials simply by following the link to the training programme and creating an account).

After an introduction from CTO and ICT-Core Director Juan Miguel González-Aranda, together with Service Director Alberto Basset, the floor was given to technical staff, Lucia Vaira, Xeni Kechagioglou, Antoni Huguet Vives, Nikos Miandakis and Antonio José Saénz Albanés, to explain and demonstrate the Metadata Catalogue and the Tesseract VRE, which was illustrated using the Crustaceans Workflow (presented at the Workshop on 20 May). After the presentations and demonstrations, participants were given the opportunity to try the services and workflows for themselves, interacting with the trainers who provided guidance and feedback.

The session was brought to a close with input from Juan Miguel González-Aranda, who reiterated the importance of continued feedback and exchange with the scientific community in order for LifeWatch ERIC to refine and improve its services. CEO Christos Arvanitidis then thanked everyone who took part, noting that the Session was just the beginning of the results LifeWatch ERIC has to showcase after its first five years of hard work alongside dedicated collaborators. He also highlighted that LifeWatch ERIC is leading an important Work Package as part of the EOSC Future project, and how the efforts of everyone involved will ensure that LifeWatch ERIC services can be deployed on the EOSC platform, benefiting a wider audience than ever before.

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. 

Workshop: Online Bioinformatic Platforms to support Metabarcoding and Metagenomics research and Applications

The pan-European Workshop, held in Porto from 26 – 28 February, in the Research Centre in Biodiversity and Genetic Resources (CIBIO-InBIO) at the Vairão campus of the University of Porto, Portugal, boasted a very specific title: ‘Online Bioinformatic Platforms to Support Metabarcoding and Metagenomics Research and Applications’.

The workshop witnessed more than 30 participants from nine European countries (Belgium, Estonia, Germany, Greece, Italy, Norway, Portugal, Slovenia, Spain, Switzerland) with different expertise and backgrounds, ranging from metagenomics and metabarcoding, to ecology and ICT.

The workshop was jointly organised with PORBIOTA/LifeWatch Portugal, DNAqua-Net (dedicated to the protection, preservation and restoration of aquatic ecosystems and their functions) and the EnvMetaGen project at InBIO (Research Network in Biodiversity and Evolutionary Biology). LifeWatch ERIC supported its organisation as part of its Internal Joint Initiative on Non-indigenous and Invasive Species. The workshop explored the architecture and function of an online bioinformatics platform capable to address as many needs of the scientific community as possible, such as:

1) Checking existing distributed Bioinformatics e-Resources within the LifeWatch ERIC communities of practice,

2) Reaching a common understanding of users’ requirements and needs in Virtual Research Environments, and

3) Proposing an efficient and realistic and engaging mechanism from an ICT perspective, capable of federating those e-Resources within the LifeWatch ERIC VREs.

Examples of evidence-based research were provided by the European Open Science Cloud (EOSC), MIRRI (Microbial Research Resource Infrastructure), ELIXIR (which unites Europe’s leading life science organisations in managing and safeguarding the ever-growing volumes of data generated), other Research Infrastructures and Bioinformatics initiatives.

The outcome of the three days was a plan with well-identified next steps towards the co-construction of the bioinformatic platform.

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. 

1st Dahlem-type Workshop

LifeWatch ERIC just launched an Internal Joint Initiative (IJI) focusing on the topic of Non-indigenous and Invasive Species (NIS) with the aim of developing new dedicated Virtual Research Environments. The IJI kicked off with the organisation of the LifeWatch ERIC 1st Dahlem-type Workshop: Current and future challenges of NIS in Europe, which took place from 14th to 18th October, in the Casa de la Ciencia, and the V. De Madariaga Foundation, in Seville, Spain. 

The choice of the Dahlem-type1 workshop stems from the desire of the infrastructure to use the most participative interdisciplinary approach in the search for new perspectives to drive the international research agenda on NIS and to involve relevant communities in the development of validation cases. For this reason, experts from different domains – from scientists working in the field of NIS, to ICT specialists and bio-informaticians – gathered in Seville to select the most promising research and management questions, identify the resources and tools available and specify those to be developed.

As a first step, participants identified and clustered the main issues related to NIS and discussed two macro topics, 1) risks and impacts of NIS, and 2) long-term responses of both the NIS and the native communities after invasion. Participants agreed on the development of a general framework to describe and estimate both risks and impacts of NIS (Topic one) and responses from the perspective of both NIS and native communities (Topic two) in the context of climate change. Several validation cases were proposed for each topic to apply this new framework.

On topic one, the suggested validation cases focus on the EU-scale assessment of ecosystem and habitat-type vulnerability to NIS in the context of climate change, including an assessment of sink source dynamics for specific, model, ecosystem types such as harbour ecosystems. On topic two, the chosen validation cases are based on the availability of long-term data series on a number of relevant invaders: (1) Caulerpa taxifolia and racemose; (2) Callinectes sapidus & other Crustaceans; (3) freshwater fishes at a global scale; (4) Mnemiopsis; (5) Rugulopteryx; (6) Ailanthus invasion and response monitoring with satellite images; (7) Metagenomics for invasive species; and (8) early detection of NIS with the metagenomic approach. An additional validation case was also proposed for later collaboration dealing with the risk for human health of NIS as vectors of pathogens.

The  LifeWatch ERIC ICT team’s contribution was to highlight those data resources and services required for the development of the validation cases and to suggest the implementation of an innovative approach, LifeBlock, a LifeWatch ERIC service that for the first time ever applies blockchain technology to biodiversity science. 

As an immediate result of this collaboration, scientists and ICT experts jointly outlined a conceptual paper and designed a workflow that will serve as an organised timeline along which different e-tools have to be developed to help address relevant issues related to NIS for scientists, managers, decision-makers and society.

The next Dahlem-type workshop will take place in Rome from 2nd to 6th December 2019, this time driven and coordinated by the ICT community, to produce a second technical paper and pave the way towards developing the required Virtual Research Environments.

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1 A Dahlem-type Workshop is defined as a quest for knowledge through an interdisciplinary communication process aimed at expanding the boundaries of current knowledge, addressing high-priority problems, identifying gaps in knowledge, posing questions aimed at directing future inquiries, and suggesting innovative approaches for solutions. 

LifeWatch ERIC Internal Joint Initiative

Non-indigenous and Invasive species (NIS) are considered a major threat to biodiversity around the globe: they can impact ecosystems in many ways by outcompeting or predating on native species. Who has not heard of the Burmese pythons in Florida that eat alligators? The negative impact of imported rats and cats that have decimated island fauna populations? However, the long-term impacts of NIS on ecosystem integrity are poorly explored, and policy-makers are often left without sufficient information to make wise management decisions.

In the belief that the first steps in tackling biodiversity loss must be to improve our knowledge by developing better inter-disciplinary paradigms, LifeWatch ERIC is launching an exciting new Internal Joint Initiative (IJI), involving the scientific communities of National Nodes and other European Research Infrastructures, that will thoroughly describe the issues involved in ecosystem and habitat type vulnerability, and produce future scenarios under changing vectors to help decision-makers combat the impacts of climate change. 

The LifeWatch ERIC Internal Joint Initiative will combine data, semantic resources, data management services, and data analysis and modelling from its seven member countries – Belgium, Greece, Italy, the Netherlands, Portugal, Slovenia and Spain – to bring together national assets on a scale never attempted before. This integration of Common Facilities and National Nodes will provide the comprehensive and synthetic knowledge so much needed by institutions and administrators.

By deploying and publishing on the LifeWatch ERIC web portal the federated resources and e-Tools and e-Resources, the Internal Joint Initiative will also define the requirements and architecture of the LifeWatch ERIC virtual research environments, and provide a clear demonstration of the Infrastructure’s added value for researchers in addressing specific biodiversity and ecosystem management issues. 

Non-indigenous and Invasive Species are a global problem. They are distributed among most plant and animal taxa, and present a number of key issues that remain challenging for both researchers and policy-makers. The knowledge produced by the Internal Joint Initiative will thus be of global significance. It is to be hoped that this demonstration case will be seen to have scientific and socio-economic implications for many different fields of investigation over the coming decades.