This position will remain open until a successful candidate has been identified.
UCSD Layoff from Career Appointment or Special Selection: Apply by 06/28/16 for consideration with preference for rehire. All layoff applicants should contact their Employment Advisor. Eligible ACCES or Special Selection clients should contact their Vocational Rehabilitation Counselor for Special Selection.
The Department of Medicine is responsible for fulfilling the teaching, research, and clinical missions of the University of California, San Diego and employs 500+ full-time salaried faculty members and 150+ academic appointees. Staff personnel include 800+ staff in 9 bargaining units, students, and volunteers. There are over 250 clinical faculties practicing at multiple sites and hospitals. Professional fee billings for the department exceed $50 million with collections of over $19 million per year. The total annual budget is approximately $170 million, which includes contract and grant revenues, clinical practice and medical center funds, and other state and private endowment funds.
The Bioinformatics Programmer will work as a member of a team to design, implement, release, and maintain bioinformatics software. The team develops a number of software tools for biomedical research that have been used by more than 250,000 investigators worldwide. These tools include GenePattern, an environment for computational genomics research that provides users access to hundreds of bioinformatics analysis methods and visualization tools, without the need for programming.
Under general supervision, the Bioinformatics Programmer's development responsibilities will include adding complex analysis methods to Gene Pattern, including working with researchers on implementing and integrating new methodologies developed by the lab and with collaborating labs. Other GenePattern development will include updates and additions to the web client user interface. The incumbent will also develop and test Gene Pattern Notebooks, i.e., complete computational analysis narratives created with the Jupyter Notebook interface to the GenePattern environment.
As a member of the development team, the incumbent will participate in user support, including answering email help questions, writing documentation and training materials, and presenting at training workshops.
- Gather functional and non-functional requirements that define new features. Interact with collaborating researchers and computational biologists to determine and prioritize requirements and features.
- Investigate and evaluate alternative implementation options, including use of 3rd party libraries and components.
- Perform complex and thorough testing of the software. Identify appropriate use cases for testing. Develop deployment and test procedures, and execute for each update.
- Identify relevant datasets for testing the analysis methods, and make them available as sample datasets to users.
- Assess quality, consistency, and integrity of data.
- Perform hypothesis testing to answer specific question pertaining to the experimental goals.
- Use standardized software packages or generate own scripts whenever necessary.
- Identify inconsistencies or problems with statistical results.
- Identify irregularities and invalid results with research data.
- Interpret analyses.
USER SUPPORT AND OUTREACH
- Develop example computational analysis narratives using the Jupyter Notebook interface to GenePattern.
- Write and maintain software documentation.
- Help maintain the project website.
- Monitor the project help forums, respond to questions from users, and troubleshoot their problems with the software.
- Develop training materials.
- Present at training workshops.
A Bachelor's Degree in Bioinformatics, Computer Science, Mathematics, Statistics, Biology, Physical Sciences, or other relevant scientific discipline, and 4+ years of experience in software development.
Experience in the complete application cycle developmen