Reference: 173_23_LS_INB_RE3
Job title: Senior Research Engineer on Research Infrastructures for Precision Medicine projects (RE3)
About BSC
The Barcelona Supercomputing Center - Centro Nacional de Supercomputación (BSC-CNS) is the leading supercomputing center in Spain. It houses MareNostrum, one of the most powerful supercomputers in Europe, was a founding and hosting member of the former European HPC infrastructure PRACE (Partnership for Advanced Computing in Europe), and is now hosting entity for EuroHPC JU, the Joint Undertaking that leads large-scale investments and HPC provision in Europe. The mission of BSC is to research, develop and manage information technologies in order to facilitate scientific progress. BSC combines HPC service provision and R&D into both computer and computational science (life, earth and engineering sciences) under one roof, and currently has over 900 staff from 55 countries.
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We are particularly interested for this role in the strengths and lived experiences of women and underrepresented groups to help us avoid perpetuating biases and oversights in science and IT research. In instances of equal merit, the incorporation of the under-represented sex will be favoured.
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.
- 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
Applications procedure and process
All applications must be made through BSC website application form and contain:
- A full CV in English including contact details
- A Cover Letter with a statement of interest in English, including two contacts for further references - Applications without this document will not be considered
In accordance with the OTM-R principles, a gender-balanced recruitment panel is formed for every vacancy at the beginning of the process. After reviewing the content of the applications, the panel will start the interviews, with at least one technical and one administrative interview. A profile questionnaire as well as a technical exercise may be required during the process.
The panel will make a final decision and all candidates who had contacts with them will receive a feedback with details on the acceptance or rejection of their profile.
At BSC we are seeking continuous improvement in our recruitment processes, for any suggestions or feedback/complaints about our Recruitment Processes, please contact recruitment@bsc.es.
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Deadline
The vacancy will remain open until a suitable candidate has been hired. Applications will be regularly reviewed and potential candidates will be contacted.
OTM-R principles for selection processes
BSC-CNS is committed to the principles of the Code of Conduct for the Recruitment of Researchers of the European Commission and the Open, Transparent and Merit-based Recruitment principles (OTM-R). This is applied for any potential candidate in all our processes, for example by creating gender-balanced recruitment panels and recognizing career breaks etc.
BSC-CNS is an equal opportunity employer committed to diversity and inclusion. We are pleased to consider all qualified applicants for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, age, disability or any other basis protected by applicable state or local law.
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This position is reserved for candidates who meet the requirements and have the legal status of disabled persons with a degree of disability equal to or greater than 33%. In case there are no applicants with disabilities that meet the requirements, the rest of the candidates without declared disability will be evaluated
Original source: https://www.bsc.es/join-us/job-opportunities/17323lsinbre3