Research Support Engineer – Data Science and AI in Bioinformatics and Systems Medicine (RE2)

Job Reference

46_20_LS_ICB_RE123

Position

Research Support Engineer – Data Science and AI in Bioinformatics and Systems Medicine (RE2)

Closing Date

Tuesday, 15 September, 2020
Reference: 46_20_LS_ICB_RE123
Job title: Research Support Engineer – Data Science and AI in Bioinformatics and Systems Medicine (RE2)

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, and is a hosting member of the PRACE European distributed supercomputing infrastructure. 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 650 staff from 49 countries.

Look at the BSC experience:
BSC-CNS YouTube Channel
Let's stay connected with BSC Folks!

Context And Mission

Professor Nataša Pržulj is looking for a Research Support Engineer to work in her Integrative Computational Network Biology (ICONBI) group (overview of the group is at https://www.bsc.es/discover-bsc/organisation/scientific-structure/integrative-computational-network-biology-iconbi).The post-holder will participate in the process of finding, designing and implementing new algorithms, Data Science and AI solutions to challenges related to the research projects the group is working on.

The ICONBI research group performs research in the design of novel network science and machine learning algorithms carefully tuned to extract new biomedical information from systems-level omics data to aid Personalized Medicine. The group actively collaborates with researchers from other fields, with the goal of applying machine learning to challenging problems in systems biology and precision medicine. The group is involved in multiple research projects, including the prestigious ERC Consolidator grant of Prof. Pržulj. Although ICONBI is open to all aspects of algorithmic development and AI, currently the main lines of research are omics data fusion by non-negative matrix tri-factorization (NMTF) and graph (or network science) algorithms.

The Researcher will work in a highly sophisticated HPC environment, will have access to state-of-the-art systems and computational infrastructures, and will establish collaborations with experts in different areas both at the local and international levels.

Key Duties

  • Work, in collaboration with the members of the group, on the design and implementation of new Machine Learning and other algorithms and solutions needed to achieve the goals of the group’s research projects
  • Interact with relevant stakeholders of the group’s research projects to understand their problems and the available data in order to formulate useful algorithmic solutions
  • Provide processing, quality and annotation of NGS and other omics data sets, as needed
  • Implement and maintain the source code, the software platform and any required databases for storing and manipulating the omics data with the group’s new methods
  • Data visualization and report generation
  • Develop web interfaces for the computational solutions of the group, that provide data analytics, interpretation and dissemination
  • Contribute to the design and development of HPC and cloud-based workflows and software solutions required by the group
  • Maintain the group’s web pages and provide online dissemination of the group’s results
  • Provide support in the design and preparation of new projects
  • Follow software development best practices
  • Maintain a current knowledge of related technologies
  • Collaborate with the members of the group in the project management activities

Requirements

  • Education
    • BSc in Computer Science, Applied Mathematics, or a related discipline
    • MSc in Bioinformatics, Computer Science, Artificial Intelligence, Machine Learning, or a related discipline
  • Essential Knowledge and Professional Experience
    • Good knowledge of C/C++ and Python
    • Knowledge of Test-Driven Design and/or Development
    • Knowledge of Continuous Integration/Delivery/Deployment, including tools such as (or similar to) Terraform, GitLab CI, Docker and/or Ansible
    • Knowledge of mathematics, optimization and statistics applied to Machine Learning
    • Knowledge of molecular data and bioinformatics tools and algorithms
  • Additional Knowledge and Professional Experience
    • Knowledge of: Javascript/node.js, C#, Matlab and/or Java
    • Experience in machine learning and data mining, including knowledge of Keras, PyTorch, Tensorflow, Pandas, Scikit-learn and/or Numpy.
    • Knowledge of agile methodologies for project management, eg. Kanban
    • Experience in optimisation and parallelisation, ideally in HPC clusters
    • Theoretical broad knowledge of AI techniques, such as Deep Neural Networks, Natural Language Processing (NTLK), Reinforcement Learning
    • Experience in configuring and querying Database Systems, such as SQL (e.g. MySQL) and NoSQL (e.g. MongoDB, Elasticsearch), and in Unix
    • Experience in working with source code repositories (e.g. Github, BitBucket, etc.)
    • Experience in -omics bioinformatics techniques, including NGS data processing pipelines (mapping, variant calling, filtering, etc), integration of clinical and experimental data from different sources, reproducibility and portability of analysis workflows
    • Experience using public databases (Reactome, OMIM, GO, PharmGKB, PDB, TCGA, ClinVar, dbSNP etc)
    • Experience in research and in dissemination activities, including paper writing
  • Competences
    • Fluency in spoken and written English
    • Capacity to explore new research lines
    • Good communication and presentation skills
    • Ability to work within a team and within a pair (pair programming)

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 working hours, extensive training plan, tickets restaurant, private health insurance, fully support to the relocation procedures
  • Duration: Temporary - 1 year 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: 01/04/2020]

Applications Procedure

All applications must include:

  • A Cover Letter with a statement of interest in English, including two contacts for further references - Applications without this document will not be considered
  • A full CV in English including contact details
  • All university transcripts (BSc and MSc)

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

Please, upload your CV document using the following name structure: Name_Surname_CV
Files must be less than 3 MB.
Allowed file types: txt rtf pdf doc docx.
Please, upload your CV document using the following name structure: Name_Surname_CoverLetter
Files must be less than 3 MB.
Allowed file types: txt rtf pdf doc docx zip.
Please, upload your CV document using the following name structure: Name_Surname_OtherDocument
Files must be less than 10 MB.
Allowed file types: 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.