Job Description:
The USTAR Center for Genetic Discovery (http://ucgd.genetics.utah.edu) at the University of Utah seeks an Associate Software Developer to help maintain, optimize, and develop our bioinformatics pipeline to investigate the genetic basis for human disease in large-scale genome sequencing projects. The successful candidate will join a growing team of scientists and software developers working to integrate computational genomics into health care. Our team analyzes genome sequences from multiple large-scale genome sequencing projects across a broad range of inherited disorders, including lung and heart disease, familial cancers, inflammatory and immune conditions, metabolic disease, and neurological conditions. We also partner with life science and technology companies to develop novel software tools, diagnostics, and precision therapies based on our research. We are looking for a highly motivated individual with strong Linux command-line skills, a combination of BASH, Perl and/or Python scripting, familiarity with HPC environments, familiarity with standard genomics command-line tools and data sources. In addition an ability and willingness to work in a collaborative team environment to manage the daily operations and development needs for our genome analysis projects is critical. Responsibilities The successful candidate will: • Transfer and validate large genomic datasets from external collaborators to the University CHPC resources. • Set up, track, debug genomic data workflows on large NGS datasets. • Work on development of computation workflows for NGS data analysis. • Interact with collaborators at the University of Utah and externally to set up data access, and to resolve data access and quality issues. • Routine monitoring of the quality of data produced by the various computational workflows. • Work with members of the CHPC staff and other University IT staff to monitor and maintain the UCGD computational resources. • Create and maintain documentation in variety of formats such as markdown, wiki, and screen casting. Minimum Qualifications: Requires a bachelor’s degree in a related area or equivalency and 1-3 years of experience in the field or in a related area. Applicants must demonstrate the potential ability to perform the essential functions of the job as outlined in the position description. Preferences: • Strong Linux command-line skills and power tools to move, validate, and manipulate big genomic datasets. • Ability to write clean, efficient code in one or more of BASH, Perl and/or Python to automate data analyses and the ability to maintain that code for use by other in revision controls systems. • Experience with HPC compute clusters (TACC, XSEDE, SDSCC, CHPC etc.) and their job management systems (SLURM, PBS, SGE etc.) is preferred. • Experience with workflow management frameworks such as Snakemake, Nextflow, Queue, WDL etc) a plus. • Ability to use team and project management tools such as Trello, JIRA, GitHub, MantisBT to work collaboratively in a agile team environment.
Additional Info:
The University of Utah is an Affirmative Action/Equal Opportunity employer and is committed to diversity in its workforce. In compliance with applicable federal and state laws, University of Utah policy of equal employment opportunity prohibits discrimination on the basis of race or ethnicity, religion, color, national origin, sex, age, sexual orientation, gender identity/expression, veteran’s status, status as a qualified person with a disability, or genetic information. Individuals from historically underrepresented groups, such as minorities, women, qualified persons with disabilities, and protected veterans are strongly encouraged to apply. Veterans’ preference is extended to qualified applicants, upon request and consistent with University policy and Utah state law. To inquire about this posting, email: employment@utah.edu or call 801-581-2300. Reasonable accommodations in the application process will be provided to qualified individuals with disabilities. To request an accommodation or for further information about University AA/EO policies, please contact the Office of Equal Opportunity and Affirmative Action, 201 S. Presidents Cr., Rm 135, (801) 581-8365 (V/TDD), email: oeo@umail.utah.edu. The University is a participating employer with Utah Retirement Systems (“URS”). To be eligible for retirement contributions, you must be hired into a benefit-eligible position. Certain new hires are automatically assigned to the URS retirement plan and other employees with prior URS service, may elect to enroll in the URS within 30 days of hire. Regardless of whether they are hired into a benefit-eligible position or not, individuals who previously retired and are receiving monthly retirement benefits from URS must notify the Benefits Department upon hire. Please contact Utah Retirement Systems at (801)366-7770 or (800)695-4877 or the University’s Benefits Department at (801)581-7447 for information. This position may require the successful completion of a criminal background check and/or drug screen.[Click Here to Access the Original Job Post]
The USTAR Center for Genetic Discovery (http://ucgd.genetics.utah.edu) at the University of Utah seeks an Associate Software Developer to help maintain, optimize, and develop our bioinformatics pipeline to investigate the genetic basis for human disease in large-scale genome sequencing projects. The successful candidate will join a growing team of scientists and software developers working to integrate computational genomics into health care. Our team analyzes genome sequences from multiple large-scale genome sequencing projects across a broad range of inherited disorders, including lung and heart disease, familial cancers, inflammatory and immune conditions, metabolic disease, and neurological conditions. We also partner with life science and technology companies to develop novel software tools, diagnostics, and precision therapies based on our research. We are looking for a highly motivated individual with strong Linux command-line skills, a combination of BASH, Perl and/or Python scripting, familiarity with HPC environments, familiarity with standard genomics command-line tools and data sources. In addition an ability and willingness to work in a collaborative team environment to manage the daily operations and development needs for our genome analysis projects is critical. Responsibilities The successful candidate will: • Transfer and validate large genomic datasets from external collaborators to the University CHPC resources. • Set up, track, debug genomic data workflows on large NGS datasets. • Work on development of computation workflows for NGS data analysis. • Interact with collaborators at the University of Utah and externally to set up data access, and to resolve data access and quality issues. • Routine monitoring of the quality of data produced by the various computational workflows. • Work with members of the CHPC staff and other University IT staff to monitor and maintain the UCGD computational resources. • Create and maintain documentation in variety of formats such as markdown, wiki, and screen casting. Minimum Qualifications: Requires a bachelor’s degree in a related area or equivalency and 1-3 years of experience in the field or in a related area. Applicants must demonstrate the potential ability to perform the essential functions of the job as outlined in the position description. Preferences: • Strong Linux command-line skills and power tools to move, validate, and manipulate big genomic datasets. • Ability to write clean, efficient code in one or more of BASH, Perl and/or Python to automate data analyses and the ability to maintain that code for use by other in revision controls systems. • Experience with HPC compute clusters (TACC, XSEDE, SDSCC, CHPC etc.) and their job management systems (SLURM, PBS, SGE etc.) is preferred. • Experience with workflow management frameworks such as Snakemake, Nextflow, Queue, WDL etc) a plus. • Ability to use team and project management tools such as Trello, JIRA, GitHub, MantisBT to work collaboratively in a agile team environment.
Requeriments :
Skills :
Additional Info:
The University of Utah is an Affirmative Action/Equal Opportunity employer and is committed to diversity in its workforce. In compliance with applicable federal and state laws, University of Utah policy of equal employment opportunity prohibits discrimination on the basis of race or ethnicity, religion, color, national origin, sex, age, sexual orientation, gender identity/expression, veteran’s status, status as a qualified person with a disability, or genetic information. Individuals from historically underrepresented groups, such as minorities, women, qualified persons with disabilities, and protected veterans are strongly encouraged to apply. Veterans’ preference is extended to qualified applicants, upon request and consistent with University policy and Utah state law. To inquire about this posting, email: employment@utah.edu or call 801-581-2300. Reasonable accommodations in the application process will be provided to qualified individuals with disabilities. To request an accommodation or for further information about University AA/EO policies, please contact the Office of Equal Opportunity and Affirmative Action, 201 S. Presidents Cr., Rm 135, (801) 581-8365 (V/TDD), email: oeo@umail.utah.edu. The University is a participating employer with Utah Retirement Systems (“URS”). To be eligible for retirement contributions, you must be hired into a benefit-eligible position. Certain new hires are automatically assigned to the URS retirement plan and other employees with prior URS service, may elect to enroll in the URS within 30 days of hire. Regardless of whether they are hired into a benefit-eligible position or not, individuals who previously retired and are receiving monthly retirement benefits from URS must notify the Benefits Department upon hire. Please contact Utah Retirement Systems at (801)366-7770 or (800)695-4877 or the University’s Benefits Department at (801)581-7447 for information. This position may require the successful completion of a criminal background check and/or drug screen.[Click Here to Access the Original Job Post]