Computational Systems Biology Researcher (R2-3) – Codesign activities (LS & CS)

Job Reference

211_24_LS_CB_R2

Position

Computational Systems Biology Researcher (R2-3) – Codesign activities (LS & CS)

Fecha de cierre

Sábado, 15 Junio, 2024
Reference: 211_24_LS_CB_R2
Job title: Computational Systems Biology Researcher (R2-3) – Codesign activities (LS & CS)

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

The Laboratory of Open Computer Architecture (LOCA) at Barcelona Supercomputing Center aims to break through traditional disciplinary silos and lead the research and development of European open software and hardware stacks based on the RISC-V Instruction Set Architecture for Exascale and beyond. This will be done with BSC’s scientific departments to produce highly optimized grand challenge scientific applications in climate modelling, personalized medicine and energy. LOCA spans topics ranging from Computer Architecture to System Software to Applications, in both traditional HPC and emerging High-Performance Data Analytics (HPDA) and is working towards EU autonomy in HPC technologies. BSC is looking for one domain expert for each of the centre’s application departments (Earth Science, Life and Engineering Sciences) to contribute to this aim.

In the Life Sciences area, we are looking for a Researcher to work in the computational systems biology approaches to simulate biological networks at different time-scales (Ponce-de-Leon et al., 2023). In particular, we are interested in the development of efficient multi-scale simulators that could leverage all the potential of parallel and distributed environments at the BSC and at other HPC centres in Europe. These agent-based tools will enable the simulation of real-sized organs with complex, heterogeneous microenvironmental architectures and will bridge from intracellular pathways to the organ-level.

The Researcher will work providing efficient HPC solutions to scale-up multi-scale simulation tools aimed at providing digital twins of patients. The specific tasks involve the development and implementation of parallel and distributed programming tools that leverage different heterogeneous HPC centres, as well as the co-design of these simulation tools to BSC’s RISC-V and other diverse architectures and accelerators.

The candidate will be working in close collaboration with all the different groups and departments to co-design these novels tools to new computer architectures (Kreuzer et al., 2021) in the context of the BSC’s Severo Ochoa award for the 2023-26 period, which aims to boost BSC capacities to codesign hardware and software, maximise internal and external synergies, expand international leadership, provide best-practice career development with strong gender actions, and enhance societal engagement and technology transfer (https://www.bsc.es/discover-bsc/research-excellence/severo-ochoa).

Key Duties

  • Design and implement efficient HPC solutions to simulate multi-scale biological processes using hundreds of thousands of CPUs in BSC clusters.
  • Optimize code for HPC platforms and maintain software performance.
  • Co-design multi-scale simulation tools to BSC’s RISC-V and other heterogeneous architectures.
  • Co-design multi-scale simulation tools to different accelerators such as GPUs, vectorisation and stencil.
  • Design, implement and deploy a set of unit tests to study the scalability and efficiency of the optimised and co-designed code.
  • Design and implement a CI/CD suite to test and deploy the code in several EuroHPC centres.
  • Provide technical expertise in the areas of parallel computing, distributed computing, and software performance.
  • Help to characterize the core applications for the department by using the resources available at BSC and contribute to the definition of Key Performance Indicators (KPI) for improving their performance.
  • Work to optimize domain applications for BSC-designed RISC-V HPC processors in collaboration with the multi-disciplinary team and contribute to enhancing the full HPC stack.

Requirements

  • Education
    • PhD in Computer Science or similar topic, with strong background on parallel and distributed computing.
  • Essential Knowledge and Professional Experience
    • Proved experience on computer science.
    • Strong background on scientific computing, scaling up of tools and performance analysis in HPC.
    • Very strong programming skills, in particular on C++ and Python language.
    • Administration level in Linux/Unix systems.
  • Additional Knowledge and Professional Experience
    • Interest in computational biology and the simulation of biological processes.
    • Experience in the preparation and presentation of scientific projects.
    • Experience in reporting progress.
    • Experience in mentoring/advising PhD students.
    • Good communication skills (verbal and written) in English.
  • Competences
    • Ability to effectively communicate technical concepts to non-experts.
    • Proactive and able to take the initiative when needed.
    • Creative thinking.
    • Operate independently but love being part of a collaborative team.

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 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 [at] bsc [dot] es.

    For more information follow this link

  • 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.
    For more information follow this link

    Application Form

    please choose one of this and if needed describe the option : - BSC Website - Euraxess - Spotify - HiPeac - LinkedIn - Networking/Referral: include who and how - Events (Forum, career fairs): include who and how - Through University: include the university name - Specialized website (Metjobs, BIB, other): include which one - Other social Networks: (Twitter, Facebook, Instagram, Youtube): include which one - Other (Glassdoor, ResearchGate, job search website and other cases): include which one
    Please, upload your CV document using the following name structure: Name_Surname_CV
    Los archivos deben ser menores que 3 MB.
    Tipos de archivo permitidos: txt rtf pdf doc docx.
    Please, upload your CV document using the following name structure: Name_Surname_CoverLetter
    Los archivos deben ser menores que 3 MB.
    Tipos de archivo permitidos: txt rtf pdf doc docx zip.
    Please, upload your CV document using the following name structure: Name_Surname_OtherDocument
    Los archivos deben ser menores que 10 MB.
    Tipos de archivo permitidos: txt rtf pdf doc docx rar tar zip.
    ** Consider that the information provided in relation to gender and nationality will be used solely for statistical purposes.