Job Description

The Pathology Department is seeking a Programmer Analyst who will work in collaboration with senior bioinformaticists, faculty, and other team members to maintain, build and develop clinical and/or research bioinformatics pipelines, databases, servers, and interfaces. The work will involve processing and analysis of large-scale biological and genomic data. The individual will use computer/data/biological science knowledge to learn new applications for data handling. Abilities will include writing and maintaining code, keeping clear data records, and communicating with both technically educated and non-technically educated colleagues. Accurate recording of code/build versions, both written and oral, and summarizing and presenting work products and data will be expected. The individual is expected to accept and integrate constructive guidance. A willingness, and ability, to learn and adapt is key. Excellent interpersonal and communications skills are needed. Independence and accountability are also highly desired.

Specific Duties & Responsibilities

• Maintain, build and develop clinical and/or research bioinformatics pipelines, databases, servers, and interfaces.
• Perform ongoing data processing and analysis.
• Regularly communicate with other team members and faculty members to discuss IT needs, progress and feedback.
• Prepare documentation for codes and versions.
• Prepare data summaries and progress reports.
• Prepare organized data for presentation and/or publication.
• Identify and resolve common problems and use analytical skills to implement assigned projects.

• Work requires track record of entry to mid-level usage of the Linux operating system. In addition, proficiency in at least one programming language, such as Python, Java, Javascript, R, Perl, Matlab, or shell. Knowledge of statistical programming is a plus. Knowledge of bioinformatics tools, such as SAMtool, BEDtools and GATK, is highly desired. Some knowledge of hardware, relational databases and distributed computing would be a plus.
• Excellent interpersonal skills in consulting with other team members and understanding the problems.
• Excellent writing and verbal skills in the preparation and presentation of reports.
• Excellent organizational skills, and attention to detail are required.

Work Environment

• While performing the duties of this job, the employee may remain in a stationary position (sitting or standing) up to 85% of the time. Occasionally required to traverse throughout the work area, or to retrieve equipment, supplies, or specimens from other locations on campus. The employee is required to operate computer keyboard and mouse 75% of the day and must have dexterity for handling small glass slides and other specimens. Constantly repositions self to perform duties at laboratory workstations, gathering specimens, and loading equipment.
• Prolonged vision requirements including viewing computer screen, paper reports/documents, charts and results. Visual acuity is required to distinguish fine gradation of color or structure and closely examine specimens (including via a microscope).
• Although this position works primarily in an office environment, there is activity in adjacent laboratory environments - Exposure to toxins and infectious agents exist, but potential for personal injury or harm is minimized if established safety and health precautions are followed. Must refer to and are expected to comply with procedure manuals, follow proper laboratory protocols and safety policy/procedures, and be familiar with material data safety sheets in assigned work areas. Able to read and understand all Health, Safety and Environment (HSE) guidelines applicable to assigned work area. Working in laboratory where there may be discomforts due to odors, noise, temperature fluctuations, and working around lab equipment. Research areas may include animal, human, human products, DNA, radiation protocols, and other bio-hazardous materials. Use of personal protective equipment may be advised or required.
• May transport equipment and supplies, usually less than 40 pounds, from one area to another (in the laboratory or on campus). May be required to lift and/or move up to 50 pounds, with proper training, or precautions/lifting aides (example: supply boxes or Formalin cubes). In some areas workspace is limited.
• Staff may be required to complete annual competency review, and must ensure compliance with Johns Hopkins Policy, Laboratory Policy & Procedure, Health, Safety & Environment regulations, and all applicable privacy & confidentiality laws/practices. Human subject research will require IRB training.

• Bachelor's Degree.
• One-year related experience.
• Additional related experience may substitute for required education, to the extent permitted by the JHU equivalency formula.

• Master's Degree in Computer Science, Electrical Engineering, Data Sciences, Programming / bioinformatics or related field.
• Experience in the digital pathology space and machine learning.
• Experience in digital pathology or digital imaging.

Classified Title: Programmer Analyst
Role/Level/Range: ATP/03/PC
Starting Salary Range: $53,300 - $93,500 Annually ($69,780 targeted; Commensurate with experience)
Employee group: Full Time
Schedule: M-F 8:30-5 is typical; some flexibility for earlier or later schedules
Exempt Status: Exempt
Location: School of Medicine Campus
Department name: SOM Pat Molecular Diagnostics Lab
Personnel area: School of Medicine

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