We are in the process of hiring software engineers and bioinformaticians, so please feel free to send your recent resume to stqa8350@gmail.com
I. Systems Architect
- Institution: Massachusetts General Hospital, Boston, MA
- Department: Pathology
- Position: Systems Architect
- Salary: Commensurate with level of experience
- Hours: 40+ Hrs/week
- Status: Full-time
The MGH Pathology Department and Cancer Center have led the field of clinical genetic profiling for personalized cancer diagnosis. Wed developed the MGH SNaPshot assay, one of the first multi-gene cancer genotyping tests to be used in routine clinical practice (http://abcnews.go.com/video/playerIndex?id=7740568). The assay allows for molecular stratification of cancer patients, and in some cases placement of patients into trials of novel agents that target specific mutated gene products. We are now in the process of introducing next generation sequencing technologies to push patient care to the next level.
We are building a state-of-the-art system to analyze and interpret next generation sequencing data from clinical cancer samples and integrate the system with current and future hospital workflows both for production and research use. This system is central to MGH efforts in personalized diagnosis and treatment and provides a once-in-a-lifetime opportunity to impact clinical care of thousands of patients.
Responsibilities:
- Interact with the various user groups to help define system specifications and use cases.
- Oversight of technical design and implementation of system architecture, including data flow, NGS data storage, sample and analysis results databases, reporting and visualization.
- Design and implement APIs allowing connectivity between the NGS assay system and other hospital systems
- Establish pipeline version control procedures
- Oversee day-to-day operation of the research and production systems
- Perform project planning and report progress to the management team
Required Qualification and Skills:
- 5+ years: Development of multi-component production software systems
- 3+ years: Relational database design and management
- Linux system administration
Preferred Qualification and Skills:
- Experience with NoSQL databases
- HPC resource management experience (e.g. LSF, SGE)
- Experience with web development frameworks
II. Computational Biologist / Bioinformatics Engineer
- Institution: Massachusetts General Hospital, Boston, MA
- Department: Pathology
- Position: Computational Biology
- Salary: Commensurate with level of experience
- Hours: 40+ Hrs/week
- Status: Full-time
The MGH Pathology Department and Cancer Center have led the field of clinical genetic profiling for personalized cancer diagnosis. Wed developed the MGH SNaPshot assay, one of the first multi-gene cancer genotyping tests to be used in routine clinical practice (http://abcnews.go.com/video/playerIndex?id=7740568). The assay allows for molecular stratification of cancer patients, and in some cases placement of patients into trials of novel agents that target specific mutated gene products. We are now in the process of introducing next generation sequencing technologies to push patient care to the next level.
We are building a state-of-the-art system to analyze and interpret next generation sequencing data from clinical cancer samples. We are looking to expand our bioinformatics team with a computational biologist who will help develop and maintain our clinical and research analysis pipelines. This system is central to MGH efforts in personalized diagnosis and treatment and provide a once-in-a-lifetime opportunity to impact clinical care of thousands of patients.
Responsibilities:
- Implement and adapt NGS analysis tools (e.g. aligners, variant callers, annotation packages) for use in the MGH clinical and research cancer sequencing pipelines
- Evaluate emerging tools for potential inclusion in analysis pipelines.
- Develop testing and validation procedures for analysis pipelines
- Data analysis to assist wet lab in protocol optimization
Qualification and Skills:
- Strong programming skills (preferably R, Python, Perl and/or Java) in a Linux environment
- Familiarity with major bioinformatics tools and databases
- Experience with NGS data analysis
- Experience in cancer genomics, molecular biology or a related field is a plus.
- Experience in HPC environments is a plus
