Senior Research Engineer on Research Infrastructures for Precision Medicine projects (RE3) Primary tabs Edit

Context And Mission

ELIXIR (European Life Science Infrastructure for Biological Information) is a pan-European organization founded in 2014 which aims to integrate and harmonize European bioinformatics infrastructures. ELIXIR coordinates the participation of more than 22 countries; engages with other strategic European initiatives and projects, e.g. ESFRI, Research Data Alliance, EUDat and EGI; promotes specific training activities and workshops on ELIXIR resources, partners with industry, and play a key role in shaping the bioinformatics landscape. Spain has been a member of ELIXIR since 2015, with the Spanish National Bioinformatics Institute (INB) as the Spanish national node. Within ELIXIR, the INB is responsible for the bioinformatics infrastructure offered by Spain and, therefore, should guarantee its alignment with the strategic areas put forward by ELIXIR.

Since 2018, the INB has two overarching objectives: deepen the alignment of its activities with ELIXIR, and increase the translational impact of INB actions towards the Spanish National Health System (SNS). For the latter objective, the INB has created and supports TransBioNet (Translational Bioinformatics Network), which aims to structure, bring together and work with bioinformatics groups in healthcare settings with a particular focus on the Health Research Institutes (IIS) recognized by the ISCIII. Since 2021, the INB has continued its activities in the context of IMPaCT-Data, the Data Science programme of IMPaCT. IMPaCT is the Spanish National Infrastructure for Personalized Medicine associated with Science and Technology by the National Health Research Institute Carlos III (ISCIII).

In 2022, the European Commission launched several flagship projects focused on using and re-using biomedical data to enable and accelerate research activities. In this context, the BSC participates in the European Genomic Infrastructure (GDI) and the EUropean federation for CAncer IMages (EUCAIM). The GDI project will enable access to genomic and related phenotypic and clinical data across Europe. It is doing that by establishing a federated, sustainable and secure infrastructure to access the available data. GDI builds on the outputs of the Beyond 1 Million Genomes (B1MG) project and is realising the ambition of the 1+Million Genomes (1+MG) initiative and represents the implementation phase of the overall ambition of enabling the use of genomics data for precision medicine. Regarding EUCAIM, it is the cornerstone of the European Commission-initiated European Cancer Imaging Initiative, a flagship of Europe’s Beating Cancer Plan (EBCP), which aims to foster innovation and deployment of digital technologies in cancer treatment and care to achieve more precise and faster clinical decision-making, diagnostics, treatment and predictive medicine for cancer patients. The ultimate goal is to deploy a pan-European digital federated infrastructure of FAIR cancer-related, de-identified, real-world images. The infrastructure is designed to preserve the data sovereignty of providers and provide a platform, including an Atlas of Cancer Images, for the for developing and benchmarking AI tools towards precision medicine. EUCAIM will address the fragmentation of existing cancer image repositories by building on repositories from the AI4HI initiative, European research infrastructures and national/regional repositories including clinical images, pathology, molecular and laboratory data.


Key Duties

- Share the responsibilities on the developments of flagship projects like the European Genomic Data Infrastructure (GDI), the EUropean federation for CAncer IMages (EUCAIM) and the reference implementation for IMPaCT-Data.
- Develop, document and maintain software for the integration and biological data following the guidelines of ELIXIR.
- Responsibly participate in relevant technical activities within ELIXIR platforms, communities and focus groups.
- Responsibly participate in relevant technical activities within ELIXIR platforms, communities and focus groups.
- Contribute to supervising junior members at the INB/ELIXIR-ES units.


Requirements

Education
- BSc or MSc. in bioinformatics, computational biology or computer sciences with significant bioinformatics experience.

Essential Knowledge and Professional Experience
- At least 3 years of professional experience with a similar role.
- Experience with software life cycle involving repositories, continuous integration and public releases. using software ecosystem repositories, like maven repositories, PyPI, npmjs, composer or CPAN.
- Experience in cloud deployments.
- Experience in data management APIs and most common bioinformatics data sources and formats.
- Experience in query building and optimization in at least one SQL and one NoSQL ecosystem: MySQL/MariaDB, PostgreSQL, SQLite or similar; MongoDB, ElasticSearch, Cassandra or similar.
- Experience with advanced software packaging procedures.
- At least 3 years of continuing professional experience in at least one programming language ecosystem such as C++, Perl, Python, PHP and/or Java.
- Vast experience working with Unix/Linux systems.
- Experience in data management.
- Experience in developing project technical specifications.

Additional Knowledge and Professional Experience
- Experience in the use, generation and development of reproducible recipes for software containers, base on some established technology like docker, singularity/apptainer or podman.
- Experience designing and using software infrastructure deployment techniques which involve docker compose, Kubernetes, Ansible or similar.
- Experience in scientific workflow engines, like Galaxy, Nextflow or similar.
- Experience in database design and database management are a plus.
- Fluency in English written and spoken.
- At least basic knowledge of Spanish.

Competences
- Ability to understand scientific literature and software documentation.
- Ability to communicate scientific results.
- Ability to work independently.
- Ability to represent the team in international project meetings.
- Used to work under pressure under strict deadlines.


Conditions

- The position will be located at BSC within the Life Sciences Department
- We offer a full-time contract (37.5h/week), a good working environment, a highly stimulating environment with state-of-the-art infrastructure, flexible working hours, extensive training plan, restaurant tickets, private health insurance, support to the relocation procedures
- Duration: Open-ended contract due to technical and scientific activities linked to the project and budget duration
- Holidays: 23 paid vacation days plus 24th and 31st of December per our collective agreement
- Salary: we offer a competitive salary commensurate with the qualifications and experience of the candidate and according to the cost of living in Barcelona
- Starting date: asap