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Ostend, 16-17/03/2020  *Meeting has been moved online due to Covid-19 pandemic, new arrengements were communicated to participants.

Registration is free of charge and compulsory, please click here.

Scope Completing final scientific & users’ requirements to advance in the ICT developments for Workflows on Non indigenous-Invasive (Alien) Species -NIS- of the Internal Joint Initiative (IJI).

The purpose of this 2-day meeting is:

1) To go over IJI Workflow #1 ARMS+ ASSEMBLE final version review & approval.

2) To discuss other issues: Tesseracto_VRE & rest of workflows (#2 to #6) developments progress, etc.

When

16-17/03/2020

Where

Flanders Marine Institute (VLIZ)
Spuikom & De Noordzee conference rooms – InnovOcean site (entrance: warehouse 61)
Wanderlaarkaai 7
8400 Ostend
Belgium

How to reach us? Click here

Agenda

Coming soon!

More info

https://www.lifewatch.eu/web/guest/iji-workflows-technical-meeting

*Meeting has been moved online due to Covid-19 pandemic, new arrengements were communicated to participants.
Registration is free of charge and compulsory, please scroll down to fill in the form.

Scope

The purpose of this 2-day meeting is:

1. To go over IJI Workflow #1 ARMS+ ASSEMBLE final version review & approval.
2. To discuss other issues: Tesseracto_VRE & rest of workflows (#2 to #6) developments progress, etc.
3. Explore synrgies with ongoing projects.

When

16-17/03/2020

Flanders Marine Institute (VLIZ)
Spuikom & De Noordzee conference rooms – InnovOcean site (entrance: warehouse 61)
Wanderlaarkaai 7
8400 Ostend
Belgium

Where

How to reach us? Click here

Agenda

Coming soon!

Registration is closed.

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 organization of the LifeWatch ERIC First 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 2^nd to 6^th 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.

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.

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 policy-making and human wellbeing around the globe.

The conceptual paper and workflow-timeline developed at the first Dahlem-type workshop in Seville, Spain, 14-18 October, formed the basis of this second Dahlem-type Workshop, organised in Rome, Italy, from 2-6 December, this time coordinated by the LifeWatch ERIC CTO, Juan Miguel González-Aranda. This second 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.

Porto, Portugal, 26-28 February 2020. The pan-European Workshop, held 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:

• Checking existing distributed Bioinformatics e-Resources within the LifeWatch ERIC communities of practice,
• Reaching a common understanding of users’ requirements and needs in Virtual Research Environments, and
• 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.

Presentations:

Christos Arvanitidis | LifeWatch ERIC – mission and recent developments. Download PDF

Rocío Bautista | Bioinformatic analysis at SCBI. Download PDF

Pedro Beja | Next generation sequencing: Opportunities and challenges of a disruptive techmology for biodiversity assessment and monitoring. Download PDF

Bopco & JEMU | The Barcoding Facility for Organisms and Tissues of Policy Concern & The Joint Experimental Molecular Unit. Download PDF

CIBIO | Research Centre in Biodiversity and Genetic Resources. Download PDF

CNR-IBIOM | Infrastructure, data and analysis resources. Download PDF

Day 2 Session 3 | What should be the characteristics of online bioinformatics platforms in LifeWatch ERIC? Download PDF

Mafalda Galhardo | Metabarcoding and data processing pipelines. Download PDF

Juan Miguel González-Aranda | Towards the establishment of a LifeWatch ERIC bioinformatics platform. Download PDF

Tine Grebenc & Nataša Šibanc | Slovenian Forestry Institute. Download PDF

Matjaž Gregorič | Spider webs as a source of eDNA. Download PDF

Marta Goberna | Spanish Institute for Agricultural Research, Department of Environment and Agronomy. Download PDF

Pascal Hablützel | VLIZ’s ambition for online bioformatic platforms to support metabarcoding and metagenomics research. Download PDF

Florian Leese | DNA-based aquatic bioassessment in Europe and beyond: Chances and challenges. Download PDF

Jennifer Leonard | Conservation and Evolutionary Genetics Group, Doñana. Download PDF

Florian Mauffrey | Development of a molecular diatoms index for water quality assessment of Swiss rivers. Download PDF

Niklas Noll | Going through a metabarcoding workflow – pointing out problems and proposing solutions for a bioinformatics platform. Download PDF

Alberto Pallavicini | Units of the Department of Life Sciences, University of Trieste. Download PDF

Christina Pavloudi & Haris Zafeiropoulos | LifeWatchGreece Hellenic Centre for Marine Research. Download PDF

Sergei Põlme | UNITE: Curated and evolving databases for molecular identification and for communicating fungal species. Download PDF