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Planetary Biology Biocurator/Bioinformatician

European Molecular Biology Laboratory (EMBL)

Contract Duration-Is this renewable to 9 years?:

No, renewal up to 4 years as TREC funding is limited 

About the team/job

EMBL seeks a Biocurator/Bioinformatician in the context of the new transversal research theme Planetary Biology. We aim to understand, from the molecular to the population level, how microbes, plants, and animals respond to each other and to their environment in various habitats. The transversal research theme includes expeditions during which heterogeneous data and metadata are collected. The Planetary Biology flagship project TREC (Traversing European Coastlines) will be the focus of work for the staff member. Under TREC, we are going to sample the coastal land-water interfaces along the European coastlines to study the local and global human footprint on oceans, seas, and estuaries, with regard to urbanisation, agriculture, coastal exploitation, various forms of contamination as well as impacts of climate change.  

Your role

The Biocurator/Bioinformatician will provide crucial support for data annotation workflows, in the first instance by creating sampling log sheets and managing the unique identification of samples from the diverse types of sampling activities and protocols, ensuring that samples are tracked in a LIMS system, and furthermore by curating and archiving the provenance metadata, generating additional environmental context, and ensuring that environmental, imaging and omics data are easily linked and shared among partners. The Biocurator/Bioinformatician will work with the Data Coordination teams at both EMBL-EBI (UK) and Heidelberg (Germany) sites to provide support to our broad user base, which comprises researchers within EMBL, the extensive network of collaborators around TREC and the broader scientific community that will benefit from the reuse of Planetary Biology data. EMBL's established data resources and services will provide the foundations for the preservation and presentation of TREC data. The staff member will gain substantial knowledge and experience in the global life science data infrastructure and will gain hands-on experience, working on marine projects with major impact in a world-leading scientific institute. 

Your tasks include: 

  • Support for data workflows for the Planetary Biology flagship project, TREC, for example by programmatically generating PDFs based on structured layouts and content specifications, by developing a user-oriented web application that captures the content specifications, and by programmatically extracting printed and handwritten content from a PDF using text mining and artificial intelligence
  • Working alongside Biocurators, Bioinformaticians and Software Engineers across EMBL 
  • Engagement with synergistic marine projects, such as AtlantECO (2020-25), BIOcean5D (starting 2023) and BlueCloud2026 (starting 2023).
  • Contribution to metadata solutions aimed at (1) providing users with metadata collection tools and services, (2) ensuring that metadata are documented using controlled vocabularies and formats, and (3) providing a consistent and more extensive set of metadata describing the provenance and environmental context of samples.
  • Generation/addition of contextual markup, such as additional sample annotations from gazetteers, astronomical almanack, climatologies and satellite products
  • Ensuring that TREC data, existing and new data services from established data resources are highly visible and optimally presented
  • User support, that will include documentation, training and answering user queries, for TREC data.

Your work will be carried out in close communication with our international base of submitters and project partners. You will be required to take an active part in the development and delivery of data coordination services, attending and presenting at internal and international meetings. 

You have

  • Experience in biological fieldwork, preferably in the marine domain
  • Basic knowledge of relational database management systems and SQL query language
  • Experience in working with the Linux command line and utilities
  • Knowledge of structured information formats, such as XML or JSON
  • Working knowledge of Python or other scripting languages
  • Organisational skills and the ability to meet deadlines
  • A high level of attention to details
  • Ability to work both independently and as part of a team 

You might also have

  • Demonstrated experience working in multidisciplinary research collaborations in a community-facing role
  • Broad knowledge of molecular biology and next-generation sequencing technologies
  • Ability to develop Application Programming Interfaces
  • Experience of working across the structured data versus text divide, such as in the abstraction and structuring of information from human-written sample records and the writing of tools to automate reporting of structured information for human consumption
  • Excellent oral and written communication skills 

Why join us

EMBL is Europe’s flagship research laboratory for the life sciences – an intergovernmental organisation performing scientific research in disciplines including molecular biology, physics, chemistry and computer science. We are an international, innovative and interdisciplinary laboratory with approx. 2 000 employees from many nations, operating across six sites, in Heidelberg, Barcelona, Hinxton, Hamburg, Grenoble and Rome.

EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation with a very collegial and family friendly working environment. The remuneration package comprises a competitive salary, a comprehensive pension scheme, medical, educational and other social benefits. Excellent child care facilities are available on campus. 

What else you need to know

This position is full-time (39h per week), located at Heidelberg. The initial contract duration is 2 years, with another 2 years extension possibility. While this position cannot be entirely remote, flexible working (alternative work schedule, flexible hours) can be possible. Some out of hours work will be required in order to attend teleconferences with our collaborators. International travel may be required, including to EMBL-EBI.

EMBL is a signatory of the San Francisco Declaration on Research Assessment (DORA). We support fair and responsible research assessment, which includes its recruitment and performance assessment processes. We recognize a range of research outputs, discourage inappropriate use of proxies such as journal impact factors, and value research outputs based on their intrinsic merit.

Location: Heidelberg - Germany
Salary: Grade 4-5
Hours: Full Time
Contract Type: Fixed-Term/Contract
Placed On: 23rd November 2022
Closes: 16th December 2022
Job Ref: HD02316
 
   
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