Bioinformatics Data Engineering Lead

13 hours ago


Remote Wrocław Warszawa Kraków, Czech Republic Holisticon Connect Full time

Holisticon Connect is a division within NEXER GROUP, a custom software development company. We started in Poland and are now a team of over 140 people with offices in Wrocław, Warsaw, and Cracow.

Job Description

We are looking for a Senior Bioinformatics Data Engineer to support the operation and engineering needs of cBioPortal. In this role, you will impact the delivery of bioinformatics data engineering and visualizations to the Oncology R&D organisation.

About the Role

Your work will be central to advancing data stack, as well as automation and observability capabilities. You will develop, execute, and maintain ETL pipelines for extracting, transforming, and loading data for use in cBio and other bioinformatics analysis and visualizations.

Key Responsibilities
  • Develop, execute, and maintain ETL pipelines for extracting, transforming, and loading data for use in cBio and other bioinformatics analysis and visualizations;
  • Ensure the reliability, scalability, and performance of ETL pipelines and data systems;
  • Troubleshoot and resolve issues related to data loading and integration into downstream systems;
  • Collaborate with bioinformaticians, data scientists, and other stakeholders to understand and meet the data needs and requirements of the organization;
  • Stay up-to-date with new technologies and best practices in bioinformatics.
Requirements

To succeed in this role, you should have:

  • Proficiency in SQL and Python programming languages;
  • Familiarity with data manipulation and analysis using pandas and NumPy;
  • Experience with big data storage solutions such as HDFS and NoSQL databases;
  • Knowledge of Unix and Linux operating systems;
  • Familiarity with ETL processes and data pipeline development;
  • Ability to interact with various data sources, both structured and unstructured;
  • Experience working across multiple scientific compute environments;
  • Familiarity with deployment and orchestration tools such as Airflow and AWS Glue.
Benefits

We offer a range of benefits to support your career and well-being:

  • Sport subscription;
  • Training budget;
  • Private healthcare;
  • Flat structure;
  • Small teams;
  • International projects;
  • Free coffee and beverages;
  • Modern office environment;
  • No dress code.


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