Bioinformatics Programmer 1 - 136064

Department of Pediatrics is one of the largest departments within the UCSD School of Medicine with comprehensive clinical programs, extensive basic science and clinical research, and diverse educational opportunities for students, residents and fellows. The internationally renowned faculty play a major role in medical and graduate student training, providing educational and programmatic offerings that span several disciplines and provide diversity to meet the interests of a broad spectrum of students and scholars. More than one hundred trainees at the graduate student and postdoctoral level, as well as more than 300 professional, research and administrative staff who along with the department administrators interact closely with the faculty. The diverse mix of ages, backgrounds, and talents creates a robust work environment with challenging career opportunities and a commitment to continued growth potential. We constantly seek to recruit highly motivated, technologically-advanced and interested individuals to become a part of our dynamic cutting-edge research, clinical, and educational environment.

Under the direct supervision of the PI, the incumbent will perform programming and/or assist in design and analysis of systems to decipher the role of genetic variation on human traits. Projects will focus on investigation of structurally complex regions of the genome associated with human diseases using a variety of techniques including graph-based genome representations. The incumbent will be responsible for maintaining computational pipelines for processing, analyzing, and visualizing large volumes of whole genome sequence data and analysis of large biobanks. Pipelines will consist of open source as well as custom software. The incumbent will also assist with the development and maintenance of web applications. Assists with packaging custom software as open source tools.

Under direct supervision, applies professional bioinformatics concepts and computational procedures to complete small projects or portions of projects. Works on assignments of limited scope and complexity. Follows standard programming procedures to analyze situations and data from which answers can be readily obtained.

• Four (4) years of related experience, education/training, or Bachelor's degree in biological science, computational / programming.

• Basic knowledge of bioinformatics methods and data structures.

• Basic knowledge of applications programming and web development. Familiarity with C/C++, Python, R with the ability to work comfortably in a Linux environment.

• Basic knowledge of databases.

• Basic project management skills.

• Basic knowledge of modern biology and applicable field of research.

• Interpersonal skills in order to work with both technical and non-technical personnel at various levels in the organization. Demonstrated interpersonal, written and verbal communication skills and ability to interact effectively and tactfully with individuals and groups, both within and outside the University.

• Ability to communicate technical information in a clear and concise manner.

• Self motivated, able to learn quickly, meet deadlines and demonstrate problem solving skills.

• Basic knowledge of application and data security concepts.

• Demonstrated ability to maintain high level of confidentiality in handling files and data and clear understanding of the Universities data privacy and acceptable use policies and procedures.

• Ability to assist with virtual machines and designing and creating web applications in HTML, CSS, and Javascript.

• Ability to assist with HPC, including job submission and resource management.

• Familiarity with Github or a related platform for code maintenance and collaboration.

• Understanding of whole genome sequencing using various technologies (e.g. short and long reads) and data structures including pangenome graphs.

• Demonstrated ability to work in cloud computing environments, such as Amazon Web Resources.

• Employment is subject to a criminal background check.