Research Applications Programmer - 139365

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 (https://qiita.ucsd.edu), 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.

~Cover letter required for a complete application.

• Bachelor's degree in related area and/or equivalent experience/training.

• Intermediate knowledge of secure software development.

• Advanced skills associated with software design, modification, implementation and deployment, including object-oriented programming concepts. Proven experience designing web-based user interfaces. Experience in Java and Python. Must have 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 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.

• Demonstrated ability to contribute technical narrative to grant proposals.

• Thorough 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. Demonstrated testing and test planning skills.

• Thorough experience with common programming tools. Demonstrated ability to follow software specifications.

• Demonstrated effective communication and interpersonal skills.

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

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

• Demonstrated broad problem-solving skills.

• Demonstrated experience with relational databases: PostgreSQL and MySQL.

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

• Must pass a background check.

• Cover letter required for a complete application.

If employed by the University of California, you will be required to comply with our Policy on Vaccination Programs, which may be amended or revised from time to time. Federal, state, or local public health directives may impose additional requirements.

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Misconduct Disclosure Requirement: As a condition of employment, the final candidate who accepts an offer of employment will be required to disclose if they have been subject to any final administrative or judicial decisions within the last seven years determining that they committed any misconduct; or have filed an appeal of a finding of substantiated misconduct with a previous employer.

a. "Misconduct" means any violation of the policies governing employee conduct at the applicant's previous place of employment, including, but not limited to, violations of policies prohibiting sexual harassment, sexual assault, or other forms of harassment, or discrimination, as defined by the employer. For reference, below are UC's policies addressing some forms of misconduct:

• UC Sexual Violence and Sexual Harassment Policy
• UC Anti-Discrimination Policy
• Abusive Conduct in the Workplace