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#93075 Research Applications Programmer

Extended Deadline: Tue 7/24/2018

UCSD Layoff from Career Appointment: Apply by 04/17/18 for consideration with preference for rehire. All layoff applicants should contact their Employment Advisor. Eligible Disability Counseling and Consulting services (DCC) or Special Selection clients should contact their Vocational Rehabilitation Counselor for assistance.

Posting will remain Open until filled. -- Initial Review Date: 4/27/2018


Under the direction of the CMI Director in conjunction with sponsoring PIs, the incumbent will serve as a principal programmer for the Center, applying skills as a seasoned, experienced software professional with a full understanding of industry practices, community standards and relevant policies and procedures to medium-sized projects or portions of large projects with moderate scope and complexity. Resolves a wide range of issues. Demonstrates competency in selecting tools, methods and techniques to obtain results.

Interacting with CMI researchers, the incumbent will plan, organize and direct the gathering of requirements and subsequent design, development and support of multiple CMI web applications. Design, develop and present prototypes that meet the requirements; turn these prototypes into production quality code; and perform extensive end-to-end testing to verify that system meets performance and reliability. Monitor and support deployed applications during field studies, detecting and correcting operational problems and resolving problems as required.

CMI labs develop a broad range of web-based and mobile applications that are critical to its research mission. For example:

• LabMan, a web-based platform to help and accelerate sample processing in the web lab by generating the processing sample plates and keeping track of all components and machines available in the laboratory. LabMan’s requirements were initially defined by the wet lab members of the Knight Lab and will be expanded by other members of the CMI.

Qiita is an open-source web-based platform that enables non-bioinformaticians to perform their own metagenomic analyses and meta-analyses easily using standardized pipelines such as such as Qiime2 and GNPS. Qiita’s requirements and improvements are guided on the expectation of its users and delivered by monthly releases. Qiita’s users ranges from experienced bioinformaticians doing complex meta-analysis to biologist, ecologist or clinicians processing their first study.

• Metadata Wizard, an open-source web-based platform to enable researchers to create rules and descriptions of their metadata to create Qiita-compliant sample information to streamline downstream analyses and metaanalyses for microbiome-related research projects.

• Global Natural Products Social Molecular Networking (GNPS, https://gnps.ucsd.edu/), a web-platform provides public data set deposition and/or retrieval through the Mass Spectrometry Interactive Virtual Environment (MassIVE) data repository. The GNPS analysis infrastructure further enables online dereplication, automated molecular networking analysis, and crowdsourced MS/MS spectrum curation. Each data set added to the GNPS repository is automatically reanalyzed in the next monthly cycle of continuous identification.

The web applications programmer will also have the opportunity to work with graduate students, postdoctoral fellows and staff scientists to create new tools to advance microbiome research and to promote a deeper integration of tools to address multi-omic analyses.


  • A Bachelor's Degree in related; area and/or equivalent experience/training.

  • Proven experience with programming in a linux environment using SQL databases as well as experience programming web pages for web-based applications using Apache/Tomcat.

  • Demonstrated experience in Java and Python.

  • Demonstrated experience with relational databases: PostgreSQL and MySQL.

  • Experience with variety of software applications such as Microsoft Office, Project ,Visio, Visua Studio and Eclipse.

  • Advanced skills associated with software design, modification, implementation and deployment, including object-oriented programming concepts.

  • Demonstrated experience designing web-based user interfaces.

  • Ability to understand functional needs and how systems can support those needs. Ability to develop conversion and system implementation plans.

  • Demonstrated broad problem solving skills.

  • Intermediate knowledge of secure software development.

  • Demonstrated ability to interface with management on a regular basis.

  • Proven ability to contribute technical narrative to grant proposals.

  • Solid experience with identification and use of code libraries and open-source forums.

  • Experience with planning for deployment and creation of feedback mechanisms.

  • Demonstrated software repository skills. Testing and test planning skills.

  • Strong experience with common programming tools. Ability to follow software specifications.

  • Ability to communicate technical information to technical and non-technical personnel at various levels in the organization.

  • Demonstrated effective communication and interpersonal skills.

  • Self-motivated and works independently and as part of a team. Able to learn effectively and meet deadlines.


  • A background check is required.

The University of California 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

UC San Diego is a smoke and tobacco free environment. Please visit smokefree.ucsd.edu for more information.

Payroll Title:
Hiring Salary Range
$59,700.00 - $92,000.00 / Year
Appointment Type:
Appointment Percent:
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Work Schedule:
Days, 8 hrs/day, M-F