Job Description:
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. SOFTWARE DEVELOPMENT: -Design, implement, and extend large components of complex software as required by the project, and deliver production-quality software to be used by a large user community. The types of software will include computational analysis methods and client web applications. These will require a broad range of skills, including programming in a variety of languages (Java, Python, R, JavaScript), experience with a complete web development technology stack, and understanding of statistical and biological concepts. -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. STATISTICAL ANALYSES: -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. MINIMUM QUALIFICATIONS: -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 development including the development and delivery of production-quality software. -Proficiency in web technologies (JavaScript, jQuery, HTML5, CSS, etc.), as well as experience in web services. -Proficiency in both compiled and scripted programming languages. -Thorough working Knowledge, skill and ability of basic statistical methodologies and analysis including experience with statistical analyses tools. -Experience working in a Unix environment. -Strong experience with development tools, including source control systems, and bug tracking systems. -Excellent written and verbal communication skills, and demonstrated presentation skills. -Demonstrated ability to troubleshoot and problem solve in computational work. Self-starter with excellent problem-solving skills. -Ability to deal with a rapidly-changing and high-demand environment. -Strong decision making skills and ability to use independent judgment and discretion to quickly set priorities and establish new procedures when needed. -Demonstrated ability to research, analyze, recommend, communicate, and implement solutions. Must be able to function successfully with minimal direction. -Experience in bioinformatics software development. -Experience in using statistical languages, such as R or MATLAB. -Knowledge of bioinformatics file formats PREFERRED QUALIFICATIONS: -Experience with Java and Python. -Experience in using statistical languages, such as R or MATLAB. -Knowledge of bioinformatics file formats. SPECIAL CONDITIONS: -Must be able to work outside normal hours to meet project deadlines, as well as system maintenance and emergencies. -Must be able to answer work related questions while not physically at the work location. -Must be able to work in situations where all intellectual property created will be released under a permissive open-source license.
Additional Info:
Filing Deadline: Tue 2/21/2017 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. UC San Diego Health is the only academic health system in the San Diego region, providing leading-edge care in patient care, biomedical research, education, and community service. Our facilities include two university hospitals, a National Cancer Institute-designated Comprehensive Cancer Center, Shiley Eye Institute, Sulpizio Cardiovascular Center, and several outpatient clinics. UC San Diego Medical Center in Hillcrest is a designated Level I Trauma Center and has the only Burn Center in the county. U.S. News and World Report’s annual "America’s Best Hospitals" report has repeatedly ranked UC San Diego Health as the #1 health system in San Diego. We invite you to join our dynamic team! Applications/Resumes are accepted for current job openings only. For full consideration on any job, applications must be received prior to the initial closing date. If a job has an extended deadline, applications/resumes will be considered during the extension period; however, a job may be filled before the extended date is reached. UC San Diego Health is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, disability, age, protected veteran status, gender identity or sexual orientation. For the complete University of California nondiscrimination and affirmative action policy see: http://www-hr.ucsd.edu/saa/nondiscr.html[Click Here to Access the Original Job Post]
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. SOFTWARE DEVELOPMENT: -Design, implement, and extend large components of complex software as required by the project, and deliver production-quality software to be used by a large user community. The types of software will include computational analysis methods and client web applications. These will require a broad range of skills, including programming in a variety of languages (Java, Python, R, JavaScript), experience with a complete web development technology stack, and understanding of statistical and biological concepts. -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. STATISTICAL ANALYSES: -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. MINIMUM QUALIFICATIONS: -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 development including the development and delivery of production-quality software. -Proficiency in web technologies (JavaScript, jQuery, HTML5, CSS, etc.), as well as experience in web services. -Proficiency in both compiled and scripted programming languages. -Thorough working Knowledge, skill and ability of basic statistical methodologies and analysis including experience with statistical analyses tools. -Experience working in a Unix environment. -Strong experience with development tools, including source control systems, and bug tracking systems. -Excellent written and verbal communication skills, and demonstrated presentation skills. -Demonstrated ability to troubleshoot and problem solve in computational work. Self-starter with excellent problem-solving skills. -Ability to deal with a rapidly-changing and high-demand environment. -Strong decision making skills and ability to use independent judgment and discretion to quickly set priorities and establish new procedures when needed. -Demonstrated ability to research, analyze, recommend, communicate, and implement solutions. Must be able to function successfully with minimal direction. -Experience in bioinformatics software development. -Experience in using statistical languages, such as R or MATLAB. -Knowledge of bioinformatics file formats PREFERRED QUALIFICATIONS: -Experience with Java and Python. -Experience in using statistical languages, such as R or MATLAB. -Knowledge of bioinformatics file formats. SPECIAL CONDITIONS: -Must be able to work outside normal hours to meet project deadlines, as well as system maintenance and emergencies. -Must be able to answer work related questions while not physically at the work location. -Must be able to work in situations where all intellectual property created will be released under a permissive open-source license.
Requeriments :
Skills :
- Biology
- JavaScript
- Lunix/Unix
- Programing in Python
- Programing Skills
- Programming in Java
- Programming in Matlab
- Programming in R
- Software Design
- Statistics
Areas :
Additional Info:
Filing Deadline: Tue 2/21/2017 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. UC San Diego Health is the only academic health system in the San Diego region, providing leading-edge care in patient care, biomedical research, education, and community service. Our facilities include two university hospitals, a National Cancer Institute-designated Comprehensive Cancer Center, Shiley Eye Institute, Sulpizio Cardiovascular Center, and several outpatient clinics. UC San Diego Medical Center in Hillcrest is a designated Level I Trauma Center and has the only Burn Center in the county. U.S. News and World Report’s annual "America’s Best Hospitals" report has repeatedly ranked UC San Diego Health as the #1 health system in San Diego. We invite you to join our dynamic team! Applications/Resumes are accepted for current job openings only. For full consideration on any job, applications must be received prior to the initial closing date. If a job has an extended deadline, applications/resumes will be considered during the extension period; however, a job may be filled before the extended date is reached. UC San Diego Health is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, disability, age, protected veteran status, gender identity or sexual orientation. For the complete University of California nondiscrimination and affirmative action policy see: http://www-hr.ucsd.edu/saa/nondiscr.html[Click Here to Access the Original Job Post]