TiBE2020 Metabarcoding and Metagenomics

Trends in Biodiversity and Evolution

9-11 December 2020, online. 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 Trends inn Biodiversity and Evolution 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 TiBE2020 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 programme, 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. Abstract submission deadline is 27 October, 2020. Click here to download the abstract submission template. 

AERAP virtual conference “A New Era for Africa-EU Science and Innovation Partnerships”

The Africa European Radio Astronomy Platform (AERAP) held a virtual conference on 9-10 September 2020, entitled “A New Era for Africa-EU Science and Innovation Partnerships”. Scientists, innovators, network policymakers and other stakeholders came together to advance the cause of Africa Horizon Europe Development and Cooperation. Since its foundation in 2012, the AERAP platform has widened its scope beyond radio astronomy sciences to serve as an engagement platform for broader Africa-EU science collaboration, one of its main results being ontgoing EU-AFRICA cooperation and the establishment of the SKA (Square Kilometre Array) Research Infrastructure https://www.skatelescope.org/.

LifeWatch ERIC was represented by its Chief Technology Officer, Juan Miguel González-Aranda, who made two presentations to help reinforce the infrastructure’s collaboration with African communities of practice on Biodiversity & Ecosystem Research. The presentations emphasised not only the nature and potential of LifeWatch ERIC, but also the active roles of the co-chairs of the EU-AFRICA AERAP Working Group on Green Deal, Transition & Energy Access: González-Aranda on behalf of the European Union side, by representing the ENVRI cluster on Research Infrastructures as also Member of the ERIC FORUM Executive Board; and Georgina Ryan, Department of  Science and Innovation, Pretoria, representing the Government of the Republic of South Africa on behalf of the African Union.

SItE Roundtable event

SItE Roundtable

When the annual Congress of the Italian Society of Ecology (Società Italiana di Ecologia – SItE), planned for 14-18 September in Lecce had to be postponed until next year because of Covid-19, the organising committee, in conjunction with LifeWatch Italy and the Ecology Laboratory at the University of Salento, decided to offer its members a day of online Roundtables entitled “SItE – Towards Lecce 2021” to celebrate Ecology Day on 14 September. Around 300 registrations were made to follow the 20 presentations offered across a comprehensive range of topics:

• Ecosystem health and chemical mixture risk assessment and management

• Ecosystems and their services for human well-being 

• Healthy Ecosystems, Healthy People

• Landscape ecology: sustainable landscape management, and

• Arctic and Alpine ecosystems in the face of climate change.

Dr Christos Arvanitidis was called up from LifeWatch ERIC to contribute to the Healthy Ecosystems, Healthy People session, which was organised by the European Ecological Federation and chaired by its President, Cristina Maguas. Dr Arvanitidis’ talk was on the topic of ‘Biodiversity and Emerging Infectious Diseases: the role of the RIs in combating threats to public health’, starting with the connection between environmental factors during the Plague of Athens (430 BC) and moving forward on to how modern European Research Infrastructures (RIs) contribute to analysing the connections between human and ecosystem health. An RI like LifeWatch ERIC offers a one-stop disruptive technology-based architecture combined with docker technology, that guarantees authentication, transparency and reproducibility, which form the cornerstones of the modern process of scientific knowledge production. In addition, Dr Arvanitidis argued, it enables “the linking of facts and fact-based theory across disciplines to create a common groundwork of explanation”. Click here to download the presentation. The 2021 Italian Society of Ecology congress will take place in Lecce, from 13 to 17 September.

Four post-doc positions at URT CNR IRET Lecce

Four post-doc positions have just been announced at URT-CNR IRET in Lecce for research activities in the framework of LifeWatch Italy.

The application deadline for all these calls is 10 September 2020.

Please check these attached documents for more information:

Development of data quality control and data analysis services in the context of e-Science 

Semantic technologies to support the distributed data centres of LifeWatch in biodiversity and ecosystem research

Development of a Virtual Research Environment for the implementation of scientific applications in a distributed cloud infrastructure

Harmonisation and analysis of morpho-functional trait data and the organisation of phytoplankton guilds.

The tripod frame: mooring acoustic receivers on the seabed

Acoustic telemetry

A new design to overcome the challenges of installing acoustic telemetry receivers on the seabed

Installing scientific instruments in a marine environment comes with many challenges. Equipment has to withstand the physical forces of tides, currents and storms. Researchers have to take into account the effects of biofouling, corrosion and human activities. Even access to the study site can pose its difficulties, as diving is limited by depth and weather conditions. Practical deployment mechanisms are therefore needed to sustain consistent data flows.

Acoustic telemetry enables the observation of animal movements in aquatic environments. Individual animals are fitted with a transmitter, relaying a signal that can be picked up by acoustic receivers. To facilitate a convenient installation of these instruments, the LifeWatch VLIZ team developed and tested a new design, mounting a receiver with an acoustic release on a tripod frame. This frame enables the recovery of all equipment and better yet, improves the quality of the data.

In a blog post published recently on Methods.blog, Jolien Goossens from Ghent University (and formerly LifeWatch VLIZ) tells us about the challenges of installing acoustic receivers on the seabed and this new tripod frame to overcome them. Click here for the full blog post and here for the scientific article published in the journal “Methods in Ecology and Evolution“. 

HIRING | 3 open vacancies

LifeWatch ERIC is looking to hire a:

  1. Scientific developer for essential biodiversity variables workflows 

LOCATION: LifeWatch ERIC Virtual Laboratory and Innovation Centre, Amsterdam, The Netherlands.

POSITION: Full-time, 24 months, with possible extension

DEADLINE for applications: 31 August 2020

Information is available on the website, in the Work with us section.

  1. Developer for Cloud-based Virtual Research Environments

LOCATION: LifeWatch ERIC Virtual Laboratory and Innovation Centre, Amsterdam, The Netherlands.

POSITION: Full-time, 24 months, with possible extension

DEADLINE for applications: 31 August 2020

Information is available on the website, in the Work with us section.

  1. Scientific developer for ecological applications of LiDAR Remote Sensing

LOCATION: LifeWatch ERIC Virtual Laboratory and Innovation Centre, Amsterdam, The Netherlands.

POSITION: Full-time, 24 months, with possible extension

DEADLINE for applications: 31 August 2020

Information is available on the website, in the Work with us section.

Towards the ENVRI Community Winter School

Data FAIRness Webinar Programme, July–September 2020

For two years in a row already, the ENVRI Community International Summer School on Data FAIRness has been assembling in Lecce, in the middle of the summer season, those researchers, experts and technical staff from different environmental and research infrastructures who want to deepen their knowledge on this topic. Unfortunately, the ongoing COVID-19 restrictions have ordained the postponement of the current edition until the beginning of next year, when the ‘ENVRI Community Winter School on Data FAIRness‘ will take place, still in Lecce. The delay has created the opportunity to enrich our training offerings on the subject, with a series of online webinars dedicated to data management, leading the way ‘Towards the ENVRI community Winter School’.

A Data FAIRness Webinar Programme featuring three webinars have been jointly organised by ENVRI-FAIR and LifeWatch ERIC from July to September 2020, with a focus on helping end users, particularly ENVRI-FAIR project partners and data centre staff, make the best use of their data. Registration for the webinars is free and anyone working in environmental and Earth science research is welcome to take part.

Under the heading of ‘Towards the ENVRI Community Winter School’, the online training series debuts on Monday 13 July 2020. The first broadcast is presented by Zhiming Zhao, from the University of Amsterdam, and will go to air from 9:30 to 12:00 CEST, providing ‘An introduction to Cloud Computing’. 

The second webinar on ‘Workflows Orchestration and Execution’ will follow on Tuesday 14 July, from 10:00-12:00, presented by Nicola Fiore and Lucia Vaira, both from LifeWatch ERIC. 

The third webcast is scheduled for 22 September and will feature Claudio D’Onofrio and Karolina Pantazatou, both from ICOS ERIC, with ‘An Introduction to Jupyter’.

Dates for the ENVRI Community Winter School on Data FAIRness, still to be hosted by the University of Salento in Lecce, will be available soon.

LifeWatch Polls #LWpoll

#LWpoll

Planned as part of the escalation of online communications, #LWpoll is a new initiative launched at the beginning of April 2020 by the infrastructure on Twitter to further connect with its scientific community.

The inspiration from the start was to understand the needs of scientists and to engage them in the development of the research infrastructure. Moreover, the initiative was thought of in an unprecedented time of our history, the COVID-19 pandemic, during which many scientists experienced limitations to their normal activity, and have had to adapt and find alternative solutions for their work. 

Now reaching its fifth edition, the LifeWatch Polls has been relaunching debates on hot topics and trying to understand the implications of the lockdown for ecologists and biologists in their field work, and if and how open access data repositories are used. Every poll is accompanied by a ‘Did You Know’ #DYK page with plenty of useful resources on the topics dealt with.

The #LWpoll on 6 May delved into the scale of biodiversity research, trying to catch a glimpse of which the most investigated domains are. In the spirit of two-way communication, quite apart from the many replies and Retweets, we’d welcome an email to suggest more topics. 

Previous polls:

LifeWatch Species Information Backbone

LifeWatch Species Information Backbone

The LifeWatch Species Information Backbone (LW-SIBb) facilitates the standardisation of species data and the (virtual) integration of many distributed biodiversity data repositories and operating facilities. Built on expert-validated and literature-based information, the LW-SIBb is structured in different open data systems for taxonomy, biogeography, genetics and species traits. It is the driving force behind the species information services of the Belgian LifeWatch.be e-Lab. Several taxonomic data systems, species registers, nomenclatures and taxonomy-related projects contribute to the LifeWatch Species Information Backbone. They all help to make the Species Information Backbone more complete, either by an active collaboration to fill gaps, opening their data system for data exchange or by making their data accessible through web services. Recently, two major milestones were reached within the Backbone. 

Firstly, the data rescue and secured continuation of the Global Compositae Database into the Aphia platform has become a fact. Although Compositae (or Asteraceae) are not even remotely linked to the marine environment, the Aphia database – the platform behind the World Register of Marine Species (WoRMS) – is suitable for managing non-marine taxa as well. Rather than letting this enormous resource of Compositae information run the risk of disappearing, the WoRMS Data Management Team undertook to transfer it to the Aphia platform, starting work in 2017. That transfer has now been completed.

Secondly, the Interim Register of Marine and Nonmarine Genera (IRMNG) is a compilation of genus names that covers both living and extinct biota in a single system to support taxonomic and other queries dealing with e.g. homonyms, authorities, parent-child relationships, spelling variations and distinctions between marine and non-marine or fossil and recent taxa. IRMNG provides  the most complete and consistent coverage of all kingdoms of life presently available in such a form and serves to illustrate the scope of a project for a more detailed survey of “all the genera of the world” as well as providing a comparison with existing lists and preliminary content that can be of value for the compilation of new lists. 

Like the Compositae Database, IRMNG, which was originally started and managed by the CSIRO in Australia, has also experienced a major data rescue and become an integrated part of the LifeWatch Species Information Backbone, accessible through its very own portal, and through the LifeWatch e-services.

Opportunity for early stage researchers

The European Training Network RIBES “River flow regulation, fish BEhaviour and Status”, funded by the European Commission under the EU Horizon 2020 programme Marie Skłodowska-Curie Actions Innovative Training Network (Grant no. 860800), announces 15 positions for Early Stage Researchers (ESRs) giving the opportunity of being awarded a Doctoral Degree, with innovative complementary training activities and attractive travel, laboratory and research opportunities.

RIBES ESRs will be trained by international leaders in the interdisciplinary field of Ecohydraulics to find innovative solutions for freshwater fish protection and river continuity restoration in anthropogenically altered rivers within a European consortium of universities, research institutions and companies in Italy, Sweden, Germany, UK, Estonia and Belgium in an excellent scientific environment with state-of-the-art technologies.

The 15 ESRs will have access to a number of laboratory and field facilities, modelling techniques,  experimental practices and instrumental technologies, to expand current understanding of fish bio-mechanical, behavioural and physiological processes, and to promote development of novel tools and management solutions in the area of freshwater fish protection, ameliorating passage of migratory fish species in regulated rivers.

Deadline: 31 May 2020
Euraxess call: https://euraxess.ec.europa.eu/jobs/510615
For further info contact Prof. Claudio Comoglio at:
coordinator[@]msca-ribes.eu