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

LifeWatch ERIC needs to boost its construction and to engage users in developing their research activities into the Virtual Research Environments of the e-Science Infrastructures, by clearly demonstrating and documenting the added value these new technologies bring to address challenging hot topics.

LifeWatch ERIC has started an Internal Joint Initiative with the exact aim of addressing these needs and reinforcing the positioning of LifeWatch ERIC within the biodiversity and ecosystem scientific community. As a subject for the demonstration case, LifeWatch ERIC has selected non-indigenous and invasive species (NIS).

If you are interested in the IJI and want to join us on the validation cases, just drop us an e-mail service.centre[at]lifewatch.eu.

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