Workshop: Online Bioinformatic Platforms to Support Metabarcoding and Metagenomics Research and Applications

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:

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 Online Bioinformatic Platforms Workshop 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

Blue Growth in the Black Sea Region

Constanta, Romania, 9-10 March 2020. The International Conference on Blue Growth in the Black Sea Region will take place in Romania from 9 to 10 March, under the theme: ‘Ecosystem Services on River-Sea Macro-ecosystems’.

The first of its kind, the conference is organised by the Black Sea Economic Cooperation Organisation (BSEC), which came into existence as a model of multilateral political and economic initiative with the signing of the Istanbul Summit Declaration and the Bosphorus Statement by the Heads of State and Government of the countries in the region, on 25 June 1992.

Please refer to the website for more information.

NIS IJI Workflows Technical Meeting

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.

ScopeCompleting 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

Postponed: BEeS Conference

BEes

Ljubljana, Slovenia, 27-29 May 2020 was the original plan for the LifeWatch ERIC BEes Conference, which has been postponed because of the COVID-19 pandemic. It is not possible to organise an international conference and ensure the safety of participants in the current conditions, and we are following the guidance of national and global health advice.

Please do not to make any travel or accomodationn arrangements for this event. We thank all you potential participants for your patience and interest, but now is the time for us all to put our strengths together to fight this pandemic. New dates and conference details will be communicated as soon as possible.       

Smart Agrifood Summit

Málaga, Spain, 24-25 September 2020. Please note the changed dates! The Málaga Fair Trade and Congress Centre will host the Startup Europe Ecosystem for Open Innovation, the Smart Agrifood Summit. 

#Agrifood20, now in its third year, is an industry-leading event for the creation of innovative ecosystems digital transformation of the agri-food sector. 

Startup Europe is an EC initiative connecting startups, investors, accelerators, entrepreneurs, corporate networks, universities and the media through multiple networks. 

Click here to respond to this Call for Startups at the Smart Agrifood Summit. This is your chance to join the community and become amember of the ecosystem!

TiBE2020 Metabarcoding and Metagenomics

Online, 9-11 December 2020. The tenth edition of the Trends in Biodiversity and Evolution (TiBE) conference will be virtual this year and focus on Metabarcoding and Metagenomics. The meeting, held over three afternoons, will discuss exciting developments associated with the advent of ever more powerful DNA sequencing technologies, which are opening possibilities to explore the living world in ways that were unimaginable just a decade ago.

This annual event is organised by CIBIO-InBIO, the Research Centre in Biodiversity and Genetic Resources, connected through PORBIOTA with LifeWatch Portugal. It brings together senior researchers, post-graduate and graduate students working in the fields of biodiversity and evolutionary biology, to discuss cutting-edge findings in topics related to metabarcoding and metagenomic techniques, and their application in ecological and environmental research. The Conference is jointly organised by the CompBio and ApplEcol research groups. It will be hosted on an online platform that will facilitate networking opportunities and allow poster presentations. The program, including both plenary and short presentations from selected abstracts, is divided into three sessions:

• Molecular surveys of biodiversity and invasive species

• Next generation biomonitoring of aquatic and terrestrial ecosystems

• Understanding species in interactions in complex ecosystems.

Abstracts are invited either as 15-minute oral presentations, or as 2-minute poster videos. Please note that only registered participants will be accepted as presenting authors. The abstract submission deadline is 27 October, 2020.

Aquaculture Europe 2020

Aquaculture Europe 2020

Online, 12-15 April 2021.  Please note that Aquaculture Europe 2020  – The Blue and the Green – has been postponed until April 2021. The conference will still bring together stakeholders from many diverse disciplines to discuss and debate cross cutting issues such as new circular economies, life-long health and environmentally sustainable production.

There is now momentum in all aspects of food production towards a circular economy whereby waste is no longer regarded as a problem to be disposed of, but as a resource which can be reused, thereby closing the loop on aquaculture inputs and outputs and reducing environmental impact. 

Aquaculture is well placed to take the lead in the Blue – Green Bio-Economy, by demonstrating the efficacy of new technologies. And in terms of societal impact, recent research shows that aquaculture products, from seaweed to salmon, should be included as part of a balanced diet.

Click here for full details and registration to the Aquaculture Europe 2020 Conference.