Our mission is to transform wastewater infrastructure into public health observatories. Biobot Analytics is a wastewater epidemiology company and uses technology developed at MIT to measure human health in sewage (based on what is excreted in urine and stool) to understand population health in cities. We first launched an opioid product to support government and public health officials in responding to the opioid epidemic, and have recently launched a Covid19 product to estimate the scope of the outbreak in communities. We are operating in almost 400 communities across 42 states, and generating Covid19 case estimates for over 10% of the U.S. population.

We are looking for a Software Engineer with previous bioinformatics experience to help our data engineering team design data pipelines as we launch new products, support the development and maintenance of Biobot’s existing Covid-19 data pipeline, and provide critical insight as you work with our software and product team to scale and deploy our infrastructure.

In this role you will:

• Collaborate with team members across software engineering, DevOps, data science and lab operations to design and implement robust, scalable, generalized pipelines for processing multiple types of scientific data (e.g. qPCR, LC-MS)
• Collaborate with our computational biology team to architect and build production NGS pipelines using common bioinformatic tools, including samtools, fastqc, and bwa.
• Integrate Biobot’s data into our customer-facing software platform and public data visualizations and establish ETL processes to ingest external datasets that add context to Biobot’s wastewater data.
• Design and architect data solutions to enable new capabilities on Biobot’s scientific platform and expand our product offerings

Who you are:

• 4+ years of experience in a software, data engineering, bioinformatics, or similar role, with data pipeline projects from design to implementation and maintenance required.
• Experience designing data pipelines for scientific data, including but not limited to molecular biology (qPCR, next-generation sequencing, etc) and/or chemistry data (targeted and non-targeted LC-MS/MS).

Technical expertise in:

• Python using object-oriented design
• Bioinformatic pipelining tools, including nextflow
• Shell/bash scripting
• ETL-based data pipelines, including both batch and stream processing
• AWS cloud compute platforms and services (e.g. S3, EC2, Lambda, Step Functions, etc)
• Data governance

Nice to have:

• Previous start-up experience
• Experience leading a technical team or mentoring junior engineers
• Technical proficiency in Docker (or similar)