The Center for Inherited Disease Research (CIDR) (https://cidr.jhmi.edu/) was established in 1996 and serves as a national resource for investigators finding genes and variants that contribute to health and disease. CIDR provides high-throughput sequencing and genotyping services to Hopkins investigators as well as to hundreds of other academic investigators who gain access through NIH contract and grant mechanisms. CIDR is also part of the Johns Hopkins Genomics (JHG: http://jhgenomics.jhmi.edu/) that provides clinical services. CIDR generates genomic data on average, for over 100,000 DNA samples and 50 different studies per year.
We are seeking a Senior Programmer Analyst who is a member of the Genetic Analysis team with a focus on pipeline and tool development. The genetic analysis team 1) performs quality control on production data generated from both genotyping and sequencing labs, 2) evaluate new technologies by writing customer scripts/tools and bring them to production if adopted, 3) test or write in-house new analytical approaches and tools to be used on new dataset and improve workflows, and/or work with IT department to translate them into software.
The Senior Programmer Analyst will be involved in tools/software development, application maintenance, and communication with IT group. The position works closely with genetic analysts and statistical geneticists, providing technical expertise in, but not limited to, software development, hardware configuration, database structure and cloud computing. The Senior Programmer Analyst participates in software/tool development and maintenance, provide informatics and computational support for both research and clinical lab by working closely with both CIDR and JHG staff.
Specific Duties & Responsibilities:
Develop, maintain and document data processing and analysis pipelines and tools using programming languages.
Develop and implement methods and systems to ensure the consistency and quality of genotyping and sequencing data including data generation, processing, interpretation and release.
Assist in the evaluation of new technology such as Next Generation sequencing methods including analysis of generated data, evaluation and testing of software and interfaces.
Assist in the integration of new technology into the production lab when these are adopted including: data cleaning, annotation, release, posting and analysis.
Independently review the literature and evaluate analytical methods and software and translate them into tools for general use.
Participate in design, write, test, implement and document software programs and/or create detailed functional specifications for the software development team, working with that group to test and implement the software for both research and clinical use.
Prepare abstracts, presentations, reports and papers for national/international meetings and scientific journals.
Minimum Qualifications (Mandatory):
3 years related experience.
Additional education may substitute for required experience, and additional related experience may substitute for required experience, to the extent permitted by the JHU equivalency formula.*
* JHU Equivalency Formula: 30 undergraduate degree credits (semester hours) or 18 graduate degree credits may substitute for one year of experience. Additional related experience may substitute for the required education on the same basis. For jobs where equivalency is permitted, up to two years of non-related college course work may be applied towards the total minimum education/experience required for the respective job.
** Applicants who do not meet the posted requirements but are completing their final academic semester/quarter will be considered eligible for employment and may be asked to provide additional information confirming their academic completion date.
Master's Degree in Informatics, Computational Biology, Computer Science, or Data Science.
Experience in software development using programming languages such as Java, Python, R, C, Visual Basic, SQL and WDL is preferred.
Experience with data visualization and management, cloud computing is preferred.
Experience with high performance computing environments (e.g., Sun Grid Engine).
Experience with sequencing variant calling or analysis of sequencing data using packages such as Picard, GATK, BWA, SAMtools etc. Familiarity with relevant databases such as dbSNP, HapMap, 1000Genomes, topMed.
Special Knowledge, Skills & Abilities:
Demonstrated ability to work independently and in a team environment.
Excellent written and oral communication skills.
Commitment to a diverse and inclusive environment.
Demonstrated ability to work in a fast-paced environment with shifting priorities.
Sitting in a normal seated position for extended periods of time.
Reaching by extending hand(s) or arm(s) in any direction.
Finger dexterity to manipulate objects with fingers rather than with whole hand or arm, for example, using a keyboard.
Communication skills using the spoken word.
Ability to see and hear within normal parameters.
Ability to move about workspace.
Lift, carry, move supplies, computers, etc.
Classified Title: Sr. Programmer Analyst Role/Level/Range: ATP/04/PD Starting Salary Range: $59,870 - $82,245 annually (commensurate with experience) Employee group: Full Time Schedule: Monday-Friday 8:30 AM- 5 PM Exempt Status: Exempt Location: Telecommute Department name: SOM Genetics Ctr for Inhrtd Dis Res CIDR Personnel area: School of Medicine
The successful candidate(s) for this position will be subject to a pre-employment background check.
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The pre-employment physical for positions in clinical areas, laboratories, working with research subjects, or involving community contact requires documentation of immune status against Rubella (German measles), Rubeola (Measles), Mumps, Varicella (chickenpox), Hepatitis B and documentation of having received the Tdap (Tetanus, diphtheria, pertussis) vaccination. This may include documentation of having two (2) MMR vaccines; two (2) Varicella vaccines; or antibody status to these diseases from laboratory testing. Blood tests for immunities to these diseases are ordinarily included in the pre-employment physical exam except for those employees who provide results of blood tests or immunization documentation from their own health care providers. Any vaccinations required for these diseases will be given at no cost in our Occupational Health office.
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