Bioinformatics Software Engineer

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ctechny.com
Published
March 25, 2020
Location
Gaithersburg, Maryland
Category
Job Type

Description

Our client is looking for a software engineer to support the bioinformatics team in their T-cell therapy group where they are developing personalized T-cell treatments to combat cancer. Bioinformatics plays a key role in this therapeutic platform for identifying cancer targets and tumor active T-cells. The software engineer will have a passion for developing and integrating distributed computational solutions in biotechnology, cloud-based automation, and implementing best programming practices.

Responsibilities:

  • Convert serial computational pipelines into robust distributed pipelines using CWL in Seven Bridges platform and in AWS, as well as using NextFlow in AWS
  • Develop cloud-based data infrastructure capabilities in AWS. For example, design workstreams leveraging S3, EC2, AWS Batch, Lambda, and DynamoDB
  • Convert development code into productionized bioinformatics pipelines with a focus on optimization, distributed processing, modularity, and parameterization
  • Create unit testing frameworks for essential pipelines and code development
  • Create tools for automatically moving data to AWS and Seven Bridges, deploying specific pipelines, organizing data tagged with metadata to make data FAIR

Requirements:
Must Have

  • 2-3+ years experience developing production level code and a strong foundation in Python including package development and unit testing
  • Experienced in creating and deploying Docker images and working on AWS

A Plus

  • General knowledge of methods used in biotechnology, next generation sequencing, and developing bioinformatics pipelines
  • 1+ years experience developing pipelines using a workflow language such as CWL, nextflow, WDL, or snakemake
  • Experience with Ansible to automate deployment and configuration

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