Research Engineer – EUCANCan project

Date limit
13-01-2019
Institution
Barcelona Supercomputing Center (BSC-CNS)

About BSC and the Life Sciences Department

The Barcelona Supercomputing Center - Centro Nacional de Supercomputación (BSC-CNS) is currently the leading supercomputing center in Spain, housing the MareNostrum, one of the most powerful supercomputers in Europe. The mission of the BSC is to foster scientific progress by developing and managing information technologies in different relevant research areas. The BSC provides an international research environment, access to sophisticated high-performance computing, and extensive training opportunities for researchers at all stages of their career development.

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The Life Sciences department at the BSC is focused on the development and application of bioinformatics solutions to the analysis of big data. We aim at contributing to the understanding of biological and biomedical processes, as well as to build the methodological and technological frame for its translation into clinical environments of Personalized Medicine. The department is currently participating and leading world-wide initiatives for the analysis and management of omics data in research and clinical scenarios (e.g. ELIXIR, ICGC, GA4GH). Within this research frame, the Computational Genomics group, led by the ICREA Research Professor David Torrents, is intensively involved in developing and applying genome analysis tools to understand the molecular and genomic determinants of complex diseases and cancer. This research activity, which is carried out within a dynamic and multidisciplinary environment, has contributed to position our group and the department, as one of the leading bioinformatics nodes internationally. During the past ten years, the group has contributed and led several cutting edge studies in the field of cancer genomics that were reported, among others, in the following publications: Moncunill et al, Nature Biotech. 2014; Puente et al, Nature 2015; Henssen et al, Nat. Genetics 2017; Waage et al, Nature Genetics, 2018; Beekman et al, Nat. Med. 2018; Bonas-Guash et al, Nat. Comms 2018.

 

Context And Mission

 
The Computational Genomics group is looking for a highly motivated Research Engineer willing to contribute to the field of cancer genomics. The group is currently pushing and coordinating different international initiatives to develop and implement bioinformatics and computational infrastructures for genomic oncology, which will support personalized diagnosis, prevention and treatment protocols within a Personalized Medicine environment. All this activity is carried out within a international and collaborative working environment that involves leading groups and consortia in the field of oncology, bioinformatics and computing.

In particular, the group is coordinating the EUropean-CANadian Cancer (EUCANCan) project, which aims at supporting and enhancing modern oncology, by implementing a cultural, technological and legal integrative framework across Europe and Canada, for the efficient analysis, management and sharing of cancer genomic data. This cooperative framework is not only expected to immediately contribute to improve biomedical research in cancer, but to also serve as a model for globalizing and enriching Personalized Medicine initiatives around the world, allowing the exchange of data, clinical experience and information across different healthcare systems. The project involves leading participant centers in Canada and Europe, such as the Ontario Institute for Cancer Research (OICR), the International Cancer Genome Consortium (ICGC), the Institute Curie in Paris, the Carité Hospital in Berlin, as well as three of the major hospitals and research centers of our country (IDIBAPS-Hospital Clinic, VHIO-Hospital Vall d’Hebron, and IDIBELL-Hospital de Bellvitge), which also generates an ideal network and environment to foster computing and bioinformatic professional careers.

In order to build the computing and methodological infrastructure within this project we seek motivated researchers with strong computational background able to contribute to overcome the challenges of developing and integrating different methods and pipelines for the analysis of genomic NGS sequences, into high performance and cloud supercomputing environments. Specifically, this involves dealing with, among others, container-based virtualization (eg. docker and singularity), big data, protocols and/or technologies to deploy tools and pipelines both locally and remotely, working with container and pipeline repositories (eg. Dockstore and ESOC BioContainers) and workload orchestration with tools like Docker Swarm, Kubernetes or OpenShift.

Priority will be given to highly motivated, persistent and proactive candidates with a computer-related background and with the ambition to develop their career in the field of computational genomics and biomedicine.
 
 

Key Duties

  • Development and automation of genomic data analysis workflows in both HPC and cloud environments
  • Porting of containerized pipelines into HPC and cloud infrastructures
  • Research and benchmarking of bioinformatics tools and pipelines for the analysis of omic data in biomedicine
  • Contribute to the development of technical standards and protocols to improve genomic and clinical data sharing
  • Implement software pipelines for the identification and interpretation of somatic and germline variants in disease genomes
  • Attendance to project meetings around the world
  • Contribution to project deliverables

 

Requirements

  • Education
    • Diploma/Bachelor degree in Computer Science or related disciplines. Candidates with a Biology background and demonstrated strong technical expertise will also be considered.
  • Essential Knowledge and Professional Experience
    • Minimum 4 years of experience in UNIX/Linux environments, shell scripting and system tools
    • Minimum 2 years of experience with container technologies (e.g. Docker, Singularity)
    • Preferred with 3 years of academic or professional experience in bioinformatics resources, databases and tools.
    • Experience with two or more of the following scripting languages: Perl, Python, Bash, R
  • Additional Knowledge and Professional Experience
    • Knowledge in cancer genomics
    • Experience in version control systems (git)
    • Experience in high performance computing
    • Experience in virtualization/cloud infrastructures (OpenNebula)
    • Experience in participation in projects with international consortia
  • Competences
    • Fluency in spoken and written English
    • Ability to work in a professional environment within a multidisciplinary and international team
    • Ability to work independently and in a team
    • Ability to take initiative, prioritize and work under set deadlines and pressure
    • Quick and enthusiastic learner
    • Good technical skills in at least two of the following: bioinformatics, cancer genomics, NGS analysis, scripting languages, virtualization and container technologies, using a parallel computing environment, using cloud infrastructures

 

Conditions

  • The position will be located at BSC within the Life Sciences Department
  • We offer a full-time contract, a good working environment, a highly stimulating environment with state-of-the-art infrastructure, flexible hours, extensive training plan, tickets restaurant, private health insurance, fully support to the relocation procedures
  • Duration: Temporary - 2 years renewable
  • 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

All applications must include:

  • A motivation letter with a statement of interest, including two contacts for further references - Applications without this document will not be considered
  • A full CV including contact details

 

Deadline

The vacancy will remain open until suitable candidate has been hired. Applications will be regularly reviewed and potential candidates will be contacted.

 

Diversity and Equal Opportunity Employment

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.
 
 
Application form and original source: https://www.bsc.es/join-us/job-opportunities/298lscgre23