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.

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.

Transfiere 2020

Transfiere 2020

Transfiere is the biggest professional and multi-sectoral forum for knowledge and technology transfer to take place in Spain. On 12-13 February, the Palace of Fairs and Congress in Málaga FYCMA witnessed the gathering of the most relevant players in the national and international Research & Development & Innovation ecosystem, at Transfiere 2020.

Being part of Transfiere 2020 allowed the 1,600 participants to build networks of contacts, synergies and knowledge sharing in fields as diverse as Artificial intelligence and digital transformation, Public Administration, Internationalisation opportunities, and Investment and Open innovation. 

At the LifeWatch ERIC stand, Giovanna Caputi, National Nodes Operations Manager, and Cristina Huertas-Olivares, International Initiatives and Projects Manager, interacted with delegates and disseminated information on the Infrastructure’s potential to facilitate interdisciplinary research in biodiversity and ecosystems.  

In parallel, working meetings were held on new Workflows & VRE developments at the University of Málaga-Picasso HPC, part of LifeWatch ERIC ICT-Core premises. Their coordinator, LifeWatch ERIC CTO Juan Miguel González-Aranda welcomed participants from LW ERIC international ICT Team, and introduced Professors Emilio López Zapata & José F. Aldana also considered reputed experts on HPC, Big Data & Artificial Intelligence at international level, who supported at technical level during the different sessions.

Felipe Romera, president of the Organising Committee of Transfiere 2020, was pleased that the two days of “much intensity” had provided a valuable meeting place for the Spanish innovation system and strategic sectors of the economy, both public and private.

You can read about Transfiere 2021 here.

Collaboration opportunities in the Arctic

LifeWatch ERIC participated in the second Board Meeting of the Conservation of Arctic Flora and Fauna (CAFF) at the invitation of the Swedish CAFF Chairmanship. The meeting, held on February 3-6, 2020 at the Gällivare Folkets Hus in Sweden, was attended by the LifeWatch ERIC e-infrastructure operation coordinator, Antonio José Sáenz-Albanés. 

CAFF is the biodiversity working group of the Arctic Council, established in 1996 as a high-level governmental forum to address issues faced by the Arctic governments and the indigenous people of the Arctic. LifeWatch ERIC is involved in the CAFF Arctic Migratory Birds Initiative (AMBI).

LifeWatch ERIC supports AMBI in many ways, hosting in its Spanish premises the offices of the Coordinator of the African Eurasian Flyway, which seeks to improve the conservation and management of shorebird sites along their migration paths from the Arctic down to Africa, and supporting AMBI objectives and its engagement within the African continent and in particular in Guinea-Bissau.

As the Board Meeting progressed however, it became clear that Arctic ecosystems are facing challenges that LifeWatch ERIC is already addressing elsewhere, such as Arctic Invasive Alien Species for example, thus opening up further possibilities to collaborate and add value to a wide range of issues.

In this context, when Antonio José Sáenz-Albanés gave a presentation on LifeWatch ERIC’s state-of-art of ICT developments in Data FAIRness and workflows, some still under construction and deployment, and commitments to dealing with environmental hot topics, it was warmly welcomed. 

The last day provided the opportunity to learn first-hand about the application of indigenous knowledge in managing biodiversity and ecosystem services by the Sámi people, also known as Saami or Lapps, who are native to northern parts of Norway, Sweden, Finland and the Kola peninsula of Russia.

LifeWatch ERIC Seminar to MSc Students

Training and education are among the core objectives of LifeWatch ERIC; the research infrastructure not only offers online learning opportunities thanks to its online platform and ICT tools, but also face-to-face courses and seminars to directly engage with academics, in particular University Students and early career researchers.

On 13 and 14 January 2020, LifeWatch ERIC Chief Executive Officer, Christos Arvanitidis, is in Thessaloniki and Crete giving, on behalf of the whole Executive Board of the infrastructure, a seminar addressed to master students on how LifeWatch ERIC, as a research infrastructure, can contribute to the study and conservation of transitional ecosystems.

European Researchers’ Night

September is a busy month in the LifeWatch ERIC calendar, not only for the many scientific congresses, but also because of the increased outreach to the general public, students and families in particular, to interest them in the science behind biodiversity and ecosystem research. Within the framework of the European Researchers’ Night, on 27 September 2019, events were staged in member countries to highlight the impact of research on our daily lives.

As a record 7.6 million people took to the streets in Climate Strike protests around the world, universities, laboratories and museums across Europe were opening their doors to promote how scientific researchers contribute to society by displaying their work in interactive and engaging ways, with the ultimate aim of motivating young people to embark on research careers of their own. 

The LifeWatch Greece team participated in a European Researchers’ Night in the Hellenic Centre for Marine Research, Heraklion. Hundreds of people attended and had the opportunity to learn about marine research and aquatic biodiversity in different thematic pavilions and hands-on activities, including Virtual Reality, interactive games and demonstrations.

In Lecce, Italy, professors Alberto Basset (LifeWatch ERIC) and Giuseppe Corriero (LifeWatch Italy) joined “A Pint with Science”, an open event in a popular bar, talking about ‘Biodiversity Emergency, Objective Sustainability’ to a responsive crowd of followers on Thursday. 

The following day, LifeWatch ERIC Service Centre at the University of Salento opened its premises to young people and families, to play dedicated serious games on biodiversity and make enquiries about the infrastructure and its activities. Listening to videos of key scientists explaining how ecological science builds an understanding of the issues we face globally, visitors were guided to learn more about the key challenges ahead in the field of biodiversity and ecosystem research 

In the midst of popular calls to deal with current climate issues, these outreach events showcase the diversity of research, bring researchers closer to the public, mobilise citizens, and increase general awareness and understanding of how important research and innovation are in addressing societal challenges.

International Summer School on “Data Management in Environmental and Earth Science Infrastructures”

Between 9 – 13 July, around 40 academics, researchers, PhD students, data managers and research infrastructure developers from all across Europe gathered in Lecce, to join the International Summer School on “Data Management in Environmental and Earth Science Infrastructures: theory and practice”, organised by the H2020 ENVRIplus project and the LifeWatch ERIC Service Centre.

In recent years, one of the major challenges in environmental and earth science has been managing and using continuously growing volumes of data collected across multiple disciplines, and educating both scientists and developers on how best to do so. Many different standards, approaches, and tools have now been developed to support the research data lifecycle, which need to be examined and, where appropriate, adopted by a wider community. In particular, modern semantic technologies provide a promising way to properly describe and interrelate different data sources in ways that reduce barriers to data discovery, integration, and exchange among environmental and ecological resources and the researchers who use them.

To address these challenges, ENVRIplus and the LifeWatch ERIC Service Centre organised a five-day summer school providing an unique insight into the contemporary debate on data management in the environmental and earth sciences. The programme, combining theory with hands-on sessions, explored themes as diverse as reference modelling and research metadata semantics, data processing and e-infrastructure, identification and citation, cataloguing and provenance, and closed presenting two use cases on data management in the context of LifeWatch Italy.

2018 International Summer School on “Data Management in Environmental and Earth Science Infrastructures”

Between the 9 –13 July, around 40 academics, researchers, PhD students, data managers and research infrastructure developers coming from all across Europe gathered in Lecce, to join the International Summer School on “Data Management in Environmental and Earth Science Infrastructures: theory and practice”, organised by the H2020 ENVRIplus and LifeWatch Service Centre.

In recent years, one of the major challenges in environmental and earth science has been managing and using continuously growing volumes of data collected across multiple disciplines, and educating both scientists and developers on how best to do so. Many different standards, approaches, and tools have now been developed to support the research data lifecycle, which need to be examined and, where appropriate, adopted by a wider community. In particular, modern semantic technologies provide a promising way to properly describe and interrelate different data sources in ways that reduce barriers to data discovery, integration, and exchange among environmental and ecological resources and the researchers who use them.

To address these challenges, ENVRIplus and the LifeWatch Service Centre organised a five-day summer school providing an unique insight into the contemporary debate on data management in the environmental and earth sciences. The programme, combining theory with hands-on sessions, explored themes as diverse as reference modelling and research metadata semantics, data processing and e-infrastructure, identification and citation, cataloguing and provenance, and closed presenting two use cases on data management in the context of LifeWatch Italy.

“Both ENVRIplus and the LifeWatch Service Centre have been working on these topics and have already organised dedicated workshops and training sessions in recent years.” say the organisers, Nicola Fiore (LifeWatch Service Centre) and Zhiming Zhao (ENVRIplus). “This year we decided to move forward and propose a full International Summer School; its participants were enthusiastic about the programme and so we are already at work on a 2019 edition”.

Ontology and Semantic Web for Biodiversity and Ecosystem Research

Workshop | Ontology & Semantic Web for Biodiversity & Ecosystem Research Lecce (Italy) | 11–14 July 2017

Many different standards, approaches, and semantic tools have been developed to improve data sharing and interoperability. Semantic technologies provide a promising way to properly describe and interrelate these different data sources in ways that reduce barriers to data discovery, integration, and exchange among biodiversity and ecosystem resources and researchers.

LifeWatch Italy and EUDAT want to tackle these challenges through their workshop Ontology & Semantic Web for Biodiversity & Ecosystem Research, a forum for the semantic web and linked open data communities, where professionals from Academia, Research Infrastructures, Industries and others interested in these topics are welcome to present theoretical and applied research work, share experiences and discuss the latest scientific results and technology innovations around semantic technologies and linked open data in the field of Biodiversity and Ecosystem Research.

In particular the event will revolve around four main themes:

  • Usages of semantic resources in Research Infrastructures (RIs)
  • Comparison among vocabulary governances
  • Alignment of vocabularies and ontologies
  • Services for semantics 
  • Semantic discoverability and interoperability

The workshop Ontology & Semantic Web for Biodiversity & Ecosystem Research will take place in Lecce, in the fascinating historical framework of Monastero degli Olivetani (University of Salento) from 11–14 July 2017.

International Summer School

Geocomputation using free and Open Source Software, Matera (Italy), 19-23 June 2017

The International Summer School, organised by Spatial Ecology (www.spatial-ecology.net), will be held at the University of Basilicata, in the magnificent town Matera, Italy, from 19 – 23 June.

A 5-day intense experience opening new horizons on the use of the vast potentials of Linux environment and the command line approach for data processing using Bash, AWK, Python, GRASS, QGIS, GDAL/OGR, R, PKtools, OpenForis. Trainers will guide newbies and experienced GIS users who have never used a command line terminal to a stage which will allow them to understand and apply very advanced open source data processing routines. The focus is to enhance a self-learning approach, allowing participants to progress and improve their skills in a continuously evolving technological environment.

More information and registration:

www.spatial-ecology.net

www.spatial-ecology.net/upcoming-events   

www.facebook.com/spatialecology > see events

twitter: @BigDataEcology

Workshop on Thesauri and Semantics

On 9 – 10 June 2016, LifeWatch Italy will hold its workshop “Thesauri & Semantics in the Ecological Domain“. The workshop will be held in Lecce (Italy), in the BIOforIU Multidisciplinary Laboratory of the University of Salento (BIOforIU), with the support of CNR IREA. The two days will be organised as follows:

Thursday, 09/06/2016

sharing good management practices of semantics in the context of ecology

Friday, 10/06/2016

discussing collaboration opportunities in the development and integration of thesauri/vocabularies.

To ensure the best organisation and quality of the workshop, we are starting to collect registrations which will be opened until 13 May. You can attend the workshop either as presenter or participant. Please also note that due to the very concentrated schedule of the workshop we might not be able to accept all proposals.

Alessandro Oggioni oggioni.a(at)irea.cnr.it

Ilaria Rosati ilaria.rosati(at)unisalento.it