Job:Bioinformatics engineering CO-OP / Contractor supporting gene therapy

Question

[samesense]

Spark Therapeutics is fully integrated, commercial company committed to discovering, developing and delivering gene therapies. We challenge the inevitability of genetic diseases, including blindness, hemophilia, lysosomal storage disorders and neurodegenerative diseases.

Founded in March 2013 as a result of the technology and know-how accumulated over two decades at Children’s Hospital of Philadelphia (CHOP), our investigational therapies have the potential to provide long-lasting effects, dramatically and positively changing the lives of patients with conditions where no, or only palliative, therapies exist. Greater understanding of the human genome and genetic abnormalities have allowed our scientists to tailor investigational therapies to patients suffering from very specific genetic diseases. This approach holds great promise in developing effective treatments to a host of inherited diseases. Our initial focus is on treating orphan diseases.

The Bioinformatics Group within the Data Science Organization at Spark Therapeutics is seeking an engaged and passionate CO-OP/Contractor with a focus on bioinformatics engineering to participate in and support capability builds involving omics and other high-dimensional data across the Technology & Research Organizations. We are seeking a graduate level computational scientist with an interest in developing software to support bioinformatics engineering work. This a 9 month part-time (20 hours a week) position with competitive pay. On site work in Philadelphia is preferred, but remote is possible.

Responsibilities

Refactor and combine NGS workflows for automated solution

• We have three NGS similar workflows written in Snakemake
• Combine these where possible using Nextflow

Refactor and combine Rstudio NGS reports

• We have two NGS interactive HTML reports
• Combine these where possible using Rstudio, Shiny, and python dash
• Add additional NGS features parsed from Illumina pdfs/xml

Sequencing database and API

• Develop a data model and python API for storing and query NGS data
• Develop a web portal to query NGS data

Education and Experience Requirements

• Enrolled in computational graduate program
• Nextflow or equivalent workflow language
• R
• Python
• GitHub
• Docker
• AWS CLI
• Linux CLI

If interested, contact [e-mail]