Bioinformatics Programmer

The Bioinformatics Programmer’s job involves developing and utilizing computational tools to analyze and interpret biological or other research data. Utilizes and develops algorithms, computational techniques, and statistical methodologies. Develops technical approaches on the design of new experiments. Implements end-user needs in database searching and integration. Maintains the computational infrastructure and tracks the flow of samples and information for large-scale studies. Provides web-based bioinformatics and access to public and proprietary databases. Develops data algorithms and performs computations, statistical analyses, interpretation and reporting of research. Mentors and provides technical guidance to others on data science approaches.
Involved in the development of server / OS / desktop / mobile applications and services including researching, designing, developing specifications for designing, writing, modifying, testing, debugging, troubleshooting and maintaining source code. Also having direct or related involvement in designing related databases, user interfaces, integration to other systems / applications, content or multimedia processes. Work includes analysis and design to post-production processes, quality assurance, maintenance and documentation.
The Bioinformatics Programmer uses professional bioinformatics concepts. This incumbent applies computational procedures to resolve a variety of analysis and research issues. Works on assignments of moderate to extended scope where analysis of data requires a review of a variety of factors. This incumbent develops additional analyses as needed to achieve research objectives.
The Bioinformatics Programmer will develop innovative approaches to apply AI/ML methods to clinical data sets and advise others on implementation of effective approaches. He/she will be required to utilize the elasticity of the AWS Cloud for Big Data Intensive (e.g. Hadoop/Spark) compute infrastructure and parallel system environment.
This incumbent assists in creating pipelines and configurations on a Linux-based distributed file system for Very Large health data, premise-hosted as well as public cloud based. Such data will be clinical, genotypic, phenotypic and population level data of several categories, structured, semi-structured and unstructured data. Non-structured data includes genetic, text, images, and “messy” alphanumeric data. Strong AWS and Linux system administration skills will be needed to build scalable general-purpose computational and inferential software tools to work with the data.
The Bioinformatics Programmer will work with current and prospective partners via UCSF Business Development functions like CRWE, to provide data-based analyses and consulting support to assist in developing and fulfilling partnerships. Typical partners are research labs, biotech or tech companies.
This incumbent will participate in working discussions with partners, as well as with UCSF business functions in support of the above goals. The Bioinformatics Programmer will also evaluate third party tools, especially for Next Generation Sequencing, Natural Language Processing (NLP), text mining and information retrieval, for adaptation into and use in our system, under guidance from the Bioinformatics manager. Further the candidate will work towards ensuring system compliance with the university’s policies with respect to privacy and security.
*NOTE: This is a full-time hybrid contract role for 2 years from DOH.

DEPARTMENT DESCRIPTION

The application of cutting-edge data science methods such as artificial intelligence and machine learning are coming at an unprecedented speed, but healthcare has long lagged in adopting new methodologies and maximizing the utilization of the underlying data. To stay ahead of the curve, the UCSF Helen Diller Family Comprehensive Cancer Center (HDFCCC) and the Bakar Computational Health Sciences Institute (BCHSI) have jointly launched the Center for Cancer Data Science (CCDS). This initiative brings together subject matter experts in both oncology and data science to conduct the most robust cancer research that is translational, clinically meaningful, and novel. To accomplish this goal, the CCDS is assembling a comprehensive cancer data asset repository that brings together and links multi-modal disparate data from across the cancer research and care continuum. This data infrastructure is critical for innovative data analysis and the application of sophisticated data science methods. The CCDS has also identified four priority areas that span every stage of cancer research and patient care. These areas will drive CCDS’s research portfolio and include: (1) Basic/Translational Research, (2) Clinical Research, (3) Optimization of Real-World Treatment, and (4) Population Sciences. Finally, CCDS encompasses an education and training component that will provide opportunities for young investigators and help foster the next generation of computational cancer leaders.
The UCSF Helen Diller Family Comprehensive Cancer Center (HDFCCC) is one of only two cancer centers in the Bay Area to receive the prestigious designation of “comprehensive” from the National Cancer Institute (NCI).The HDFCCC integrates the work of researchers and clinicians dedicated to four fundamental pursuits: laboratory research into the causes of cancer progression; clinical research to translate new knowledge into viable treatments; compassionate, state-of-the-art patient care; and population research that can lead to improvements in prevention, early detection, and quality-of-life for those living with cancer. The twin pillars of precision medicine and precision population health guide research and treatment at HDFCCC.
The Bakar Computational Health Sciences Institute (BCHSI) is a critical component of a global UCSF initiative in Precision Medicine, which seeks to aggregate and integrate vast, disparate datasets to advance understanding of biological processes, determine mechanisms of disease, and inform diagnosis and treatment of patients. Beginning with a base of excellent computational faculty dispersed among our four top-ranked professional schools (Dentistry, Medicine, Nursing and Pharmacy) and Graduate Division, superb research programs and outstanding Medical Center, BCHSI established a central convening center, hires additional faculty, and builds programs for research and education. BCHSI develops and enhances UCSF’s computational approaches and strategies in basic, translational, clinical and population-based biomedical research, working with partners in industry and academia where appropriate. It is a campus hub for computer scientists and for researchers who employ computation as a primary tool in their biomedical research.

REQUIRED QUALIFICATIONS

• Bachelor’s degree in biological science, computational / programming, or related area and / or equivalent experience / training.
• Minimum of 3 years of related experience.
• Experience of applying machine learning, statistical or similar data science techniques to real-world data.
• Experience of managing projects of moderate scope and complexity.
• Thorough knowledge of bioinformatics and data science methods, applications programming, web development and data structures.
• Thorough knowledge of bioinformatics programming design, modification and implementation.
• Understanding of relational databases, NoSQL and document stores, web interfaces, and operating systems.
• Proven skills and experience in independently resolving broad computing / data problems using introductory and / or intermediate principles.
• Experience writing queries, functions, scripts and procedures with SQL, PL/SQL, Shell and Python/R/Java.
• Demonstrated effective communication and interpersonal skills. Demonstrated ability to communicate technical information to technical and non-technical personnel at various levels in the organization and to external research and education audiences.
• Self-motivated, work independently or as part of a team, able to learn quickly, meet deadlines and demonstrate problem solving skills.
• Demonstrated experience and ability to collaborate effectively with all levels of staff; technical, students, faculty and administrators.

PREFERRED QUALIFICATIONS

• Certifications: AWS, Unix/Linux OS and shell scripting, Python, Java, Rstudio, Jupyter, Hadoop, Spark, Hive
• Experience analyzing data on the order of tens of billions of records. Strong database and big data structure design and querying.
• Experience with multiple database management systems; Demonstrated ability to work on multiple tasks.
• Advanced skills associated with software design, modification, implementation and deployment, including object-oriented programming concepts.
• Thorough experience with identification and use of code libraries and open-source forums.
• Demonstrated broad problem-solving skills.
• Intermediate knowledge of secure software development.
• Demonstrated ability to understand functional needs and how systems can support those needs. Demonstrated ability to develop conversion and system implementation plans.
• Demonstrated ability to interface with management on a regular basis.
• Ability to contribute technical narrative to grant proposals.
• Experience with planning for deployment and creation of feedback mechanisms.
• Demonstrated software repository skills. Demonstrated testing and test planning skills.
• Thorough experience with common programming tools. Demonstrated ability to follow software specifications.

Please refer the Job description for details