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Senior Java Developer for Bioinformatics
Posted: June 13, 2014
Expires: July 31, 2014
Science jobs from QIAGEN:
As a senior back end developer, you will develop software and infrastructure used to deliver the entire Ingenuity cloud-based product line to a global community of researchers, scientists, clinicians and medical geneticists. You will work closely with our scientific product leads, bioinformaticians, and front end developers on developing big data management frameworks, tooling, applications and reporting / visualizations that support large-scale, sophisticated data analysis and interpretation of genomic and genetic data. The solutions you develop will be used by molecular biologists, clinical geneticists and researchers, and biomedical informaticians, and will fundamentally enable the application of Ingenuity technologies for the improvement of human health.
A good fit would be a rock star Java developer with an aptitude for tackling complex data processing, analysis and workflow challenges in the life sciences. You will need a strong analytical mindset and a talent for executing quickly while still following best practices and who thrives on new technology and has an avid interest in bioinformatics and genomics. We use a hybrid web stack, with mostly Java on the back end but some Python and Perl as well. You will be expected to help make decisions on server-side library and framework usage, including both generic software frameworks as well as ones focused on life sciences and bioinformatics, as well as scaling our distributed computing cloud configuration supporting large scale data management and processing for our customers around the world.
A bioinformatics degree is not required for this position, but experience building high-quality, scalable, broadly adopted software for biomedical researchers, scientists and clinicians is a must.
Position Requirements: Technical Requirements
5+ years of recent Java development experience - this is a primary requirement. 5+ years' working experience involving Bioinformatics software bioinformatics tools and biological databases 3+ years' experience building NGS pipelines for processing human sequencing data from at least Illumina and Ion Torrent platforms 3+ years working in a team-based agile development environment Familiarity with Linux required, experience with Python and Bash scripting preferred Understanding of Next Generation Sequencing technique and expertise with NGS bioinformatics tools such as GATK, Bowtie, etc Advanced skills utilizing and in depth knowledge of bioinformatics algorithms, tools and resources, e.g. sequence retrieval, alignment and clustering techniques, expression profiling and protein related analysis, major databases and standards in the field Strong programming skills by having experience of designing complex software solutions (i.e. not limited to writing scripts) in Java Must be familiar with cloud and high performance computing (HPC) environment as well as familiarity with web services and cloud computing Hands-on experience with high dimensional biological data with focus on `omics data generated by NGS technologies Fluency in agile development practices Ability to work quickly and independently with minimal guidance while consistently exercising good judgment * Excellent interpersonal skills to interact with both technical and business staff research and technical staff
Bachelor's or Master's Degree in Bioinformatics, Computational Science, Biological Life Science PhD in Bioinformatics or Computational Science preferred 8+ years bioinformatics development experience in a research or translational setting Experience working with both DNA-Seq and RNA-Seq data Experience with commercial and open source NGS pipeline infrastructure tooling and cloud infrastructure like Amazon Web Services, Heroku, etc Strong experience with Python language and libraries; 3+ years applying Python scripting to bioinformatics preferred You have strong communication skills and willingness to ask a question. We do not typically assign 100% specced-out tasks that always must be implemented an exact way; you'll be given a business problem to solve for the user, and expected to understand and explore the space of design alternatives to come up with a good solution, using rapid prototyping to test your design hypotheses. Questions will occur and it is important that you be comfortable asking them and chasing down answers. You know how to optimizing complex distributed software systems in a cloud deployed environment. You are a strong believer in version control tooling and know your way around git and Github. You're resourceful and can pull down a Java or Python project and get running on development the same day. * You like working with teams on large apps where modularity, performance, flexibility, maintainability, and API integration are fundamental concepts that inform your code and architecture decisions.
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