), a pan-European initiative aiming to generate high-quality reference genomes for a variety of non-model eukaryotic species. The BGE project (
) is funded by the Horizon Europe Programme under the Research and Innovations Action Call on Biodiversity and Ecosystem Services "European participation in global biodiversity genomics endeavours aimed at identifying all biodiversity on Earth.
Role 1: Project Data Manager supporting large-scake genome sequencing and assembly project
We seek a highly motivated individual for a Post-doctoral position to coordinate biogenome project data and metadata management for the European Reference Genome Atlas (ERGA) stream of the BIODIVERSITY GENOMICS EUROPE (BGE) project. Working with others across Europe, the project offers opportunities to discuss, design, and implement innovative research data management solutions, with parallel needs for visualisations and interoperability with major European data infrastructures.
The position has an annual salary of €33,000 (€27,000 for Italian residents) and is available for up to three years, subject to annual review, starting from March 1, 2023 at the Department of Biology, University of Florence (Italy). The successful candidate will have the liberty of working on site and/or remotely upon mutual agreement.
Scientific contextSpecific measures for preserving European ecosystems as a part of the European Commission Biodiversity Strategy are devoted to a comprehensive description of wildlife genomics. In particular, the characterization of high-quality, chromosome-level reference genomes of key European species can help understand past and present demographic trends and predict if, how and to which extent species important to ecosystem services will cope with habitat changes, how their distribution can respond to the ongoing shifts in habitat quality, and what their level of resilience will be in terms of e.g. susceptibility to pathogens and adaptation to a changing environment. Understanding features of the genome related to the ability of organisms to respond to such challenges will help better understand how to preserve ecological community and ecosystem functions.
One of the main goals of the BGE Project is to establish the European node of the Earth BioGenome Project (EBP) and coordinate and upscale a distributed infrastructure for generating reference-quality genome sequences of European biodiversity. The BGE Project will also enable population genomic studies on organisms relevant to ecosystem function, agriculture, fishery as well as endangered species and endemisms.
Candidate profile and dutiesThe position is meant to support efficient and accurate data and metadata collection under the BGE project respecting Findable, Accessible, Interoperable, and Reusable (FAIR) standards. The ideal candidate will have experience with databases, data wrangling, good knowledge of some scripting language (e.g. Python and/or Bash) and good interpersonal and communication skills. Prior experience with the COPO data brokering platform (
https://f1000research.com/articles/9-495), genomic workflows and the ENA database are desirable but not compulsory.
The postdoctoral appointee will help coordinate the activities of the ERGA stream of the BGE project regarding sample acquisition and metadata collection, and implement, maintain, and update data management systems and software infrastructure that will be used to collect the metadata associated with all the samples processed under the BGE Project. The person will also support the data wrangling process across the multiple BGE institutions and the public archives (particularly the European Nucleotide Archive, ENA), work closely with members from the ERGA scientific committees and participate in discussion groups around metadata collection connected to ERGA through the EBP.
ApplicationInterested candidates should have a PhD in Biology, Bioinformatics, Computer Science or related areas. They may want to submit a preliminary enquiry including
- a cover letter presenting the research interests and relevant experience of the applicant (max. 1 page),
- a Curriculum Vitae including the list of publications, and
- the names and e-mail addresses of two referees to: <chairs@erga-biodiversity.eu>.
The deadline for applications is January 31, 2023. By this date, applicants will need to fill in the online application form here:
https://stlabtest.dinfo.unifi.it/beta/akademia-candidature/announcements-search(The application form can be accessed by first clicking the upper right "A" icon to switch language into English and then Search structure: BIO-Biologia, Title: Supporting large-scale genome sequencing and assembly projects)
Additional Information on the call and an additional list of official documents to be submitted to the Italian Ministry of University and Research by the application deadline can be found here:
ENGLISH,
ITALIANShort-listed candidates will be interviewed on February 13, 2023 in video conference mode.
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Role2: Knowledge Transfer & Scientific Training Officer to support capacity building in biodiversity genomics
We seek a highly motivated scientist to develop and implement strategies in training and knowledge transfer for the European Reference Genome Atlas (ERGA) stream of the BIODIVERSITY GENOMICS EUROPE (BGE) project.
This position will run initially for 12 months and is meant to design and establish the short, mid and long-term strategies for the training of scientists and nonscientists in connection with ERGA. The person appointed to the position will work closely with members of the Training and Knowledge Transfer (TKT) and Citizen Science (CS) ERGA committees.
The position has an initial annual salary of €27,560 (€25,941 for Italian residents) and is available for up to three years, subject to annual review, starting from March 1, 2023 at the Department of Biology, University of Florence (Italy). The successful candidate will have the liberty of working on site and/or remotely upon mutual agreement.
Scientific context
Genomics, the study of the entire genetic material of individuals and communities, represents an information rich and quantitatively accurate way to measure and monitor the status of biodiversity and the success of its restoration efforts. In particular, the characterization of high-quality, chromosome-level reference genomes can provide important background data for population genomic studies aimed at understanding demographic trends, susceptibility to pathogens and level of resilience and adaptation of key European species to a changing environment.
Understanding features of the genome related to the ability of organisms to respond to such challenges will help better understand how to preserve ecological community and ecosystem functions. Rapid advances in technology are driving reference genomes to become a fundamental tool in scientific research. New sequencing methods are fostering an increasing number of genome assembly projects and chromosome-level scaffolds are now obtained for all sorts of eukaryote species. One of the main goals of the ERGA stream of the BGE Project is to implement, coordinate and upscale training and knowledge transfer initiatives in genome high-quality sequencing, bioinformatics and application of reference genomes to population genomic studies of European biodiversity. Training activities will boost capacity building in genomics and computational biology and foster networks of scientists that can benefit from reciprocal long-term support and exchange of expertise.
Candidate profile and duties
The ideal candidate will have a PhD in Biology or related areas, good knowledge of English (written and spoken), a genuine interest in scientific training in the areas of Genomics and Biodiversity, interest and ability to work with a diverse community of scientists, experience in writing grant proposals and good interpersonal and communication skills. The successful candidate will work closely with members of the ERGA community to support, organize and further develop training and knowledge transfer activities, workshops and tutorials in genome sequencing, bioinformatics and population genomic data analysis, allowing trainees to have an opportunity of learning basic concepts or developing advanced skills in areas they are already familiar with.
Organization of training activities will also entail capacity building for ERGA members of European countries where research in biodiversity genomics is yet to be fully developed, so as to facilitate establishment of reference genome sequencing initiatives and creation of new expertise in regions outside of the current strongholds of the discipline.
Additional tasks:- Coordinate the activities of the TKT ERGA committee;
- Design strategies for knowledge transfer and scientific training of the ERGA community to enhance synergies for the production and analysis of reference genomes of European biodiversity;
- Design strategies for the scientific training of citizens and/or non-experts to support the activities of ERGA across Europe.
- Identify and help in the application relevant grants to support strategies for knowledge transfer and scientific training of the ERGA community;
- Build catalogues of all ERGA-relevant TKT/CS activities organised within or outside ERGA to keep the community informed of activities they might want to join;
- Identify and showcase (through e.g. invited talks at ERGA plenary meetings) worldwide projects and actions of scientific, structural or strategic interest for ERGA;
- Support the identification of topic-related expertise as well as existing gaps within the ERGA community;
- Administrative and logistic support (registrations, bookings, communications, etc.) for ERGA members organising TKT/CS workshops and meetings connected for instance to other national/thematic conferences relevant to ERGA activities.
Application:
Interested candidates may want to submit a preliminary enquiry including
- a cover letter presenting the research interests and relevant
- experience of the applicant (max. 1 page),
- a Curriculum Vitae including the list of publications,
- the names and e-mail addresses of two referees to: <chairs@erga-biodiversity.eu>.
The deadline for applications is January 31, 2023. By this date, applicants will need to fill in the online application form here:
https://stlabtest.dinfo.unifi.it/beta/akademia-candidature/announcements-search(The application form can be accessed by first clicking the upper right "A" icon to switch language into English and then Search structure: BIO-Biologia, Title: Training and knowledge transfer in genomics for biodiversity)
Additional Information on the call and an additional list of official documents to be submitted to the Italian Ministry of University and Research (art. 4 and 5) by the application deadline can be found here:
ENGLISH,
ITALIANShort-listed candidates will be interviewed on February 13, 2023 in video conference mode.
For additional information and enquiries please contact:
Claudio Ciofi (
claudio.ciofi@unifi.it) Department of Biology, University of Florence, Via Madonna del Piano 6 – 50019 Sesto Fiorentino (FI) - ITALY
