Nr ref.: LP/SPD/ZD/09
In gRED (Genentech Research & Early Development) there are various groups that run experiments on laboratory instruments, analyze the output and support scientific decisions through the analysis. These analyses often involve multiple-step workflows that must be assembled on demand from a variety of stand-alone, command-line tools. There is a need for a solution that allows scientists with little computational knowledge to collect data, configure analyses using a web UI, and execute multi-step workflows. This system also must provide a common programmatic framework for the management of data and its descriptive metadata, and also provide key visualizations of the data using interactive web interfaces.
One of the research groups is Proteomics, who utilizes technology including lab instruments such as mass spectrometers to analyze the protein components of cells and tissues in a high-throughput way. While the system being developed is generalized to support many laboratory workflows, proteomics presents a compelling first use case as the raw data that is generated must be processed through a set of different tools before the data can be interpreted. These separate tools must work together in a coordinated fashion at scale.
The Ana2 system is a unified platform to automatically archive, index and share raw instrument data for groups across Genentech. Ana2 automatically copies raw data files off of instruments to a central location, automatically tags the copied data and stores it in a standardized format, and automatically indexes the data for viewing and retrieval through a web-based user interface. Ana2 can also be configured to automatically send the processed data downstream to network storage or to other custom data platforms.
The Bluecopper system which purpose is to facilitate the analysis and visualization of laboratory data with analysis pipelines and meta data management, focusing first on proteomic analyses.
- Remove lines from script areaAt least 5+ years of experience in Python (numpy, scipy, scikit-learn, tensorflow, matplotlib)
- At least 6+ years of experience in SQL
- At least 4-year experience in software development
- Helping to resolve any technical challenges for the team (Troubleshoot and bug fix reported issues with the system)
- Lead improvement initiatives
- End to end technical responsibility (shared with development team) for the Ana2/Bluecopper systems, including:Design the system’s architecture according to established industry best practices and in line with infrastructure capabilities and enterprise standards at Roche
- Analyse requirements and provide delivery estimates
- Design solutions for requested functionality
- Resolve differences in design or implementation direction within the development team
- Design and implement integration solutions with up- and downstream systems
- Ensure quality of the product
- Implement features
- Deploy new releases of the system to production upon agreement of Product Owner
- Keep the code libraries and based technology up to date
- Create and maintain documentation for the application
- Collaborate with Product Owner, Testers and business users in PST time zone and technical resources in connected systems and platforms
- Assure consistency of technical components and code base across environments
- Python (must have), including the following frameworks/libraries (nice to have)
- MySQL (must have)
- Jenkins (must have)
- Bitbucket (must have)
- Docker (must have)
- Process orchestration in high-performance computing environments (nice to have)
- CI pipelines (must have)
- Building distributed systems (must have)
- Automated testing - unit, int, e2e, performance, regression (must have)
- CD pipelines (nice to have)
- Chaos testing (nice to have)
Other requirements (team must cover all of the following)
- Strong ownership and accountability mindset
- Fluent in English
- Excellent communication skills
- Experience in working with distributed development teams
- Experience in working in a global environment
- Expertise in agile delivery in Scrum
- Quick learner
- Self organized, reliable and precise
- Available for remote meeting after 5pm 2-3 times per week
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