Senior Bioinformatics Data Engineer

2 months ago

Remote Wrocław Warszawa Kraków, Czech Republic Holisticon Connect Full time

You might be the perfect match if you are/have:

  • 5 years of relevant experience;
  • Familiar with bioinformatics visualizations in different omics domains including genomics, transcriptomics, proteomics, DNA methylation, etc;
  • Extensive experience with Python and Python data/scientific libraries like pandas, numpy/scipy, polars, etc;
  • Proven experience with bioinformatics visualization systems like cBioPortal, including data loading and troubleshooting;
  • Strong understanding of ETL processes and data pipeline development;
  • Ability to interact with various data sources, both structured and unstructured (e.g. HDFS, SQL, noSQL);
  • Experience working across multiple scientific compute environments to create data workflows and pipelines (e.g. HPC, cloud, Unix/Linux systems).


Moreover, we appreciate skills in these areas:

  • Experience with deploying data pipelines using orchestration services like Airflow, Prefect, AWS Glue, Dagster, etc.;
  • Experience using AWS services such as S3/EBS, EC2, CloudWatch, SNS, and Lambda;
  • Understanding of software development, testing and quality processes with experience with testing frameworks and documentation;
  • Expertise with biological/health data, especially genomics and other omics technologies;
  • Ability to understand, map, integrate, and document complex data relationship and business rules.

Holisticon Connect is a division within NEXER GROUP - a custom software development company. We started in Poland in 2017 and are now a team of over 140 people with offices in Wrocław, Warsaw, and Cracow. We have the opportunity to work with world-renowned brands from Scandinavia, the UK, and Western Europe. Our goal is to grow stronger, in competence rather than in numbers. If you like what we do, check out our offer, maybe we will have the pleasure of meeting you 😊  

We are looking for 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. Your work will be central to advancing data stack, as well as automation and observability capabilities.

If you apply for this position and match our expectations, then: 

1) You will be invited to an HR Screening with our IT Recruiter. 

2) You will have a recruitment task. 

3) You will meet with a client. 

Submit your application online in one easy step Apply now

,[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: SQL, Python, pandas, NumPy, HDFS, NoSQL, Unix, Linux, ETL, Data pipelines, Airflow, AWS, Glue, AWS S3, AWS EC2, CloudWatch, SNS, AWS Lambda, Testing Tools: Agile, Scrum. Additionally: Sport subscription, Training budget, Private healthcare, Flat structure, Small teams, International projects, Free coffee, Free beverages, Modern office, No dress code.

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