Posted to MedZilla on 4/30/2017


United States, Bioinformatics Engineer US_IT_CF_11789-MZ


A small biotechnology company headquartered in California is seeking a Bioinformatics Engineer to join their team. 

Job Role:

This Bioinformatics Engineer job will be primarily responsible for implementing, optimizing and maintaining Next Generation Sequencing Analysis & Annotation Pipelines in an Amazon Web Services environment, and further drive innovation through the use of machine learning and data mining techniques. 

Job Responsibilities:

  • Design bioinformatics solutions that fit within the enterprise's larger technology strategy or initiative, including recommending frameworks, tools and identifying relevant source data.
  • Extend functionality and optimize processing time of the Core Services (CCS) and Core Annotation Pipeline (CAP)
  • Create automated workflows to update and version CCS / CAP data sources and tools
  • Establish protocol for running and managing multiple, parallel versions of CCS / CAP
  • Create automated systems tests and integrate other bioinformatics tools and databases to CCS / CAP
  • Deliver high quality software in an agile environment by actively leading the bioinformatics efforts through sprint planning, daily scrum meetings, development and product deployment.
  • Participate in the innovation, design and development of statistical and analytical solutions.
  • Participate in projects to ensure the highest quality of the CCS / CAP product releases, data analysis and mining processes and data integrity in support of the Genomics Interpretation Analysis and Annotation solutions.
  • Work collaboratively with the Software Engineering and Bio Science Teams to implement commercial clinical grade solutions
  • Work with application, systems and enterprise architects to choose a reference architecture or integration style to meet the needs of each project - for example, bulk data delivery, data federation, message-oriented movement and real-time data.
  • Assist the DevOps and Data Admin team with operational support
  • Ensure that the implemented solutions follow best practices and governance principles that adhere to compliance regulations, while working with business stakeholders to ensure the clinical and corporate solutions meet data delivery and quality SLAs / KPIs
  • Ensure that critical information assets modeled as part of any project are represented in the enterprise information architecture (EIA) and follow the design guidelines and requirements of EIA.

Education, Skills and Experience:

  • A bachelor's or master's degree in computer science, bioinformatics, information systems or other related field; or equivalent work experience.
  • Professional data management training and/or certifications related to Web Services Development, Database Design / Administration for a variety of Data Solutions including but not limited to RDBMS, NoSQL, Hadoop and related data management technologies, or other similar credentials, is desired.
  • Formal training in a relevant enterprise architecture methodology (for example, the Zachman Framework or TOGAF), is desired.
  • Three years or more experience in the following disciplines:
  • Hands-on experience with scaling up a systems to tera/petabyte data handling.
  • Expert knowledge in modern data storage techniques both in the cloud (AWS S3, Google Cloud Storage, etc) and on premise (RAID systems, NFS).
  • Experience with Apache Spark, HDFS and other distributed file systems.
  • Knowledge of MySQL, PostgreSQL and NoSQL databases such as HBase, CouchBase, Vertica, MongoDB, Cassandra.
  • Advanced knowledge of a programming language such as Java/Python and a shell scripting language.
  • Experience using version control tools like git or SVN.
  • Strong experience in the following areas:
  • Understanding of architectural principles and data integration styles.
  • Experience building bioinformatics pipelines.
  • Experience working with Docker and Agile development methodologies and tools (Jira, Confluence, Asana)
  • Experience with the entire process of software development life cycle: design, implementation, testing, and maintenance.
  • Ability to perform root-cause analysis and work with other administrators or integration developers to drive resolution.
  • Familiarity with software deployment tools like Puppet or Chef and data integration development using tools such as Informatica is a plus.

To Apply:

Please click on the Apply button. Please include a short note outlining why you are interested in the role and why you think you are suitable.
In case you have difficulty in applying or if you have any questions, please call Christopher Frank on +1 267 405 6996 or upload your CV on our website
A full job description is available on request.
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