Bioinformatics Engineer

Cypher Genomics
Job Location: 
San Diego, California
Job Description: 

At Cypher Genomics, the Bioinformatics Engineer is primarily responsible for optimizing and maintaining the Cypher Annotation Pipeline in an HPC environment. The candidate will have experience working with batch job scheduling systems such as SGE, TORQUE, and PBS, build automated and version-controlled pipelines, and be familiar with genetics and general systems biology concepts. The candidate will also assist in creating automated deployment workflows and implement the application in other parallel, large-scale distributed frameworks such as Hadoop. The Bioinformatics Engineer must also be comfortable with writing systems tests including unit tests, functional tests, and integration tests.


• Extend functionality and optimize processing time of the Cypher Annotation Pipeline (CAP)
• Create automated workflows to update and version CAP data sources and tools
• Establish protocol for running and managing multiple, parallel versions of CAP
• Create automated systems tests and integrate other bioinformatics tools and databases to CAP
• Deliver high quality software in an agile environment.
• Willing to be part of and work in a fast paced startup culture.

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• 0 to 5+ years experience delivering sophisticated multi-tier solutions.
• Superb software architecture skills and object oriented programming.
• Knowledgeable in Bioinformatics and general systems biology concepts.
• Expert in Python and familiar with Java.
• Familiar with SGE/TORQUE/PBS batch job scheduling systems.
• Experience interacting with relational and/or NoSQL databases.
• Experience working with Hadoop MapReduce and HDFS.
• Self-starter, excellent critical thinking, problem solving and analytical skills.
• B.S. in Computer Science/Engineering/Physics/Mathematics/Bioinformatics, or related field.
• Passion for perfection!

Contact Information: 
About Our Organization: 

Cypher Genomics is the most accurate, rapid and comprehensive cloud based genomic interpretation solution for genome analysis. As leaders in genomic medicine, quantitative genetics and systems biology, the Cypher team created a cloud based platform that puts reliable, clinically and biologically relevant answers at your fingertips with great speed and precision. We are an early stage company looking for the best developers in the world to come be part of our growing team. If you have a passion for delivering world-class cloud based solutions in an agile environment then we’d like to meet you.

Have a look at our site: to learn more.