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

23 Mar 2024
Job Information

Organisation/Company

Barcelona Supercomputing Center (BSC)

Research Field

Computer science » Other

Researcher Profile

Recognised Researcher (R2)
Leading Researcher (R4)
First Stage Researcher (R1)
Established Researcher (R3)

Country

Spain

Application Deadline

30 Apr 2024 - 00:00 (UTC)

Type of Contract

To be defined

Job Status

Negotiable

Is the job funded through the EU Research Framework Programme?

Not funded by an EU programme

Is the Job related to staff position within a Research Infrastructure?

No

Offer Description

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 new approaches to the simulation of different molecular networks and of different type of cells, with emphasis on genome-scale metabolic models, Boolean regulatory networks and agent-based models, as well as the integrations of omic information to validate model predictions. These multi-scale models simulations should be able to be adapted to parallel environments to be deployed to HPC platforms at the BSC and at other HPC centres in Europe.

The Researcher will work in the construction and simulation of context-specific cell-decisions multi-scale models for predictive analysis. The specific tasks involve the development and application of bioinformatics and computational methods to integrate (epi)genomic, proteomic and transcriptomic data into predictive models, with an emphasis on context-specific intracellular models that combine metabolic and signalling pathways and that could be integrated in multi-scale models for personalised medicine.

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

• Co-design multi-scale simulation tools to BSC’s RISC-V and other heterogeneous architectures.
• Design, implement and deploy a set of unit tests to study the scalability and efficiency of the co-designed code and architecture.
• Implement efficient tools to simulate biological processes at different time scales through the integration of different modeling approaches (e.g. kinetic modeling, agent-based modeling, constraint-based modeling).
• Integrate multi-omics data in the model and identify actionable patient-specific targets of therapeutic interest.
• 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, Bioinformatics or similar topic, with strong background on computational biology.
• Essential Knowledge and Professional Experience
  Proved experience on bioinformatics and computational biology.
  Strong background on computer simulation of biological processes (constraint-based, Boolean, kinetic or agent-based modelling).
  Strong programming skills, in particular on C++ and Python language.
  Administration level in Linux/Unix systems.
  Experience in HPC.
• Additional Knowledge and Professional Experience
  Experience in the preparation and presentation of scientific projects.
  Experience in reporting progress.
  Experience in mentoring/advising PhD studentes.
  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.

Requirements
Additional Information

Website for additional job details

https://www.hipeac.net/jobs/14607/computational-biology-systems-researcher-r2-3…

Work Location(s)

Number of offers available

1

Company/Institute

Barcelona Supercomputing Center (BSC)

Country

Spain

Geofield

Where to apply

Website

https://www.bsc.es/join-us/job-opportunities/18324lscbr2-3

Contact

City

Barcelona

Website

https://www.youtube.com/user/BSCCNS
https://www.bsc.es/
https://twitter.com/BSC_CNS
https://www.linkedin.com/company/barcelona-supercomputing-center/

STATUS: EXPIRED