Bioinformatician and System Administrator (9401U), Innovative Genomics Institute - 61219 About Berkeley

At the University of California, Berkeley, we are committed to creating a community that fosters equity of experience and opportunity, and ensures that students, faculty, and staff of all backgrounds feel safe, welcome and included. Our culture of openness, freedom and belonging make it a special place for students, faculty and staff.

The University of California, Berkeley, is one of the world's leading institutions of higher education, distinguished by its combination of internationally recognized academic and research excellence; the transformative opportunity it provides to a large and diverse student body; its public mission and commitment to equity and social justice; and its roots in the California experience, animated by such values as innovation, questioning the status quo, and respect for the environment and nature. Since its founding in 1868, Berkeley has fueled a perpetual renaissance, generating unparalleled intellectual, economic and social value in California, the United States and the world.

We are looking for equity-minded applicants who represent the full diversity of California and who demonstrate a sensitivity to and understanding of the diverse academic, socioeconomic, cultural, disability, gender identity, sexual orientation, and ethnic backgrounds present in our community. When you join the team at Berkeley, you can expect to be part of an inclusive, innovative and equity-focused community that approaches higher education as a matter of social justice that requires broad collaboration among faculty, staff, students and community partners. In deciding whether to apply for a position at Berkeley, you are strongly encouraged to consider whether your values align with our Guiding Values and Principles, our Principles of Community, and our Strategic Plan.

At UC Berkeley, we believe that learning is a fundamental part of working, and our goal is for everyone on the Berkeley campus to feel supported and equipped to realize their full potential. We actively support this by providing all of our staff employees with at least 80 hours (10 days) of paid time per year to engage in professional development activities. To find out more about how you can grow your career at UC Berkeley, visit grow.berkeley.edu.

Departmental Overview

The Innovative Genomics Institute is a joint effort between the Bay Area's leading scientific research institutions, UC Berkeley and UC San Francisco, with affiliates at UC Davis, Lawrence Berkeley National Laboratory, Lawrence Livermore National Laboratory, Gladstone Institutes, and other institutions. The IGI's diverse group of leading scientists have powerful interdisciplinary expertise. They conduct world-class research, driven by the real possibility of using genome engineering to treat human diseases, end hunger, and respond to climate change.

In addition to our scientific efforts, the IGI is committed to advancing public understanding of genome engineering, providing resources for the broader community, and guiding the ethical use of these technologies.

We are seeking a dedicated and skilled bioinformatician with system administrator experience to join the Innovative Genomics Institute (IGI). The successful candidate will play a pivotal role in ensuring the smooth operation of our high-performance computing (HPC) resources, deploying essential bioinformatic software, and providing bioinformatic support to scientists with a wide range of research goals. The successful candidate will be able to make a direct impact in enabling research that is essential for the application of genome engineering to health and climate problems.

Application Review Date

The First Review Date for this job is: November 16, 2023

Responsibilities

• Develops new algorithms and bioinformatic processing pipelines for genome reconstruction and analysis from massive metagenomic and metatranscriptomics data.
• Creates Bioinformatic algorithmic and processing pipelines so that they can scale to massive dataset sizes.
• Develops bioinformatic methods so they can be broadly applicable to data from different environmental sources and sequencing platforms. For example, developed tools must be able to process from both complex and simple communities, and data from both long and short read sequencing platforms.
• Creates bioinformatic pipelines deployed across heterogeneous computing system and be disseminated for use by users not part of the group.
• Ensures complete usage of group computing infrastructure by testing for inefficiencies.
• Oversees software being used in existing and new pipelines are properly configured to take advantage of highly distributed computing resources including bioinformatic software and pipelines are properly configured and deployed to take full advantage of computing infrastructure.
• Ensures the quality, standardization, and providence of new data. The group is constantly generating large amounts of novel sequencing data. The new data entering the lab must be processed in a way that is both standardized and usable by the whole group. This requires the development of practices and methods that ensure that all incoming data to the lab conforms to robust and standardized quality control. New data must also be processed in a way that is translatable to a large multi-user group with varying degrees of technical training. This can mean ensuring that new data is tagged in a way that is understandable by everyone in the lab to ensure that data processing pipelines are compatible with existing analysis infrastructure.
• Designs, deploys, and integrates large-scale cluster computing, storage, and network infrastructure. The group relies on the turnaround of large-scale sequencing data to biological relevant results in an extremely rapid way. This requires a large-scale computing system that integrates multiple compute servers into a single accessible compute cluster system. This requires an advanced understanding of Linux, x86, and cluster systems. This also includes an ability to manage and scale high-speed network infrastructure.
• Authors manuscripts for publication in research journals.
• Presents oral and poster presentations at research conferences. This requires the ability to write at a scientific level for publication in high-level journals. This also necessitates skills to create publication level quality graphics and figures from complex scientific data. Publications and presentations will also be done collaboratively, so this requires the ability to work with other members of the group and non-group collaborators.
• Manages data access and priorities for members of the group and international collaborators. The availability of the computational resources of the group is generally limited. As a result, one of the main goals is to ensure that computational infrastructure, specifically data storage, is properly balanced between archival and contemporary data sources. Additionally, data access must be carefully monitored as the bulk of data access and computational resources are meant for group members. Collaboration with outside members is also crucial. This means that data must be properly secured to ensure that member and collaborator data is not improperly used. This also extends to computational resource usage, as collaboration is essential to the group, but must not hinder internal group usage.
• Resolves problems with computing hardware and software.
• Fixes high end cluster computing infrastructure software and hardware failures.
• Rapidly identifies problems with compute infrastructure in a heterogeneous environment, ranging from small to large sized compute nodes. This include troubleshooting hardware system failures and network failures.
• Distinguishes true hardware failures from software and/or usage failures by the group. Requires direct hands on repair of computing infrastructure and a willingness to solve technical computing problems independently.
• Guides group members in the selection of appropriate bioinformatic analyses.
• Assists members of the group by selecting proper analysis methods for as wide variety of data types and analyses. These datatypes range from single gene surveys to complex metagenomic and metatranscriptomic large sequencing datasets. Analysis includes the selection of pipelines that will effectively take advantage of compute infrastructure while maintaining data and analysis integrity. Beyond bioinformatic guidance, advance statistical knowledge of the analysis of microbial communities. Guidance can also include the selection of correct wet-lab and field protocols that will affect downstream bioinformatic method selection and analyses.
• Train staff, graduate students, and postdoctoral researchers in directly performing bioinformatic programming development. This requires both direct one-on-one and group interactions with members of the group with varying degrees of bioinformatic expertise. This especially entails being able to directly communicate with group members that are primarily biologists and have little or no training in computational systems. This also includes being able to provide bioinformatic training to members of the group that have programming experience and so requires an ability to train all levels of computation and bioinformatic understanding.
• Interfaces with technology companies to enable the expansion of data analyses via scale up of computational resources. This involves communicating with high-level leadership to assess and facilitate potential collaborations and partnerships.

Required Qualifications

• Thorough knowledge of high-performance computational system administration (e.g. SLURM).
• Ability to deploy complex bioinformatic software using container technology.
• Knowledge of data and system security best practices.
• Ability to guide non-technical personnel on proper bioinformatic methods.
• Strong project management skills.
• Thorough knowledge of modern biology and research.
• Communication skills to work with both technical and non-technical personnel in multiple fields of expertise and at various levels in the organization.
• Ability to communicate technical information in a clear and concise manner.
• Ability to interface with management on a regular basis.
• Self-motivated, work independently or as part of a team, able to learn quickly, meet deadlines and demonstrate problem solving skills.

Education/Training:

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

Preferred Qualifications

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

Salary & Benefits

For information on the comprehensive benefits package offered by the University, please visit the University of California's Compensation & Benefits website.

Under California law, the University of California, Berkeley is required to provide a reasonable estimate of the compensation range for this role and should not offer a salary outside of the range posted in this job announcement. This range takes into account the wide range of factors that are considered in making compensation decisions including but not limited to experience, skills, knowledge, abilities, education, licensure and certifications, analysis of internal equity, and other business and organizational needs. It is not typical for an individual to be offered a salary at or near the top of the range for a position. Salary offers are determined based on final candidate qualifications and experience.

The budgeted salary or hourly range that the University reasonably expects to pay for this position is $95,300.00 - $130,000.00.

• This is a 50%, part-time (20 hours per week), career position that is eligible for UC benefits.
• This position is exempt and paid monthly.
• This is a remote-friendly position, eligible for up to 100% remote capability.

How to Apply

To apply, please submit your resume and cover letter.

Conviction History Background

This is a designated position requiring fingerprinting and a background check due to the nature of the job responsibilities. Berkeley does hire people with conviction histories and reviews information received in the context of the job responsibilities. The University reserves the right to make employment contingent upon successful completion of the background check.

Equal Employment Opportunity

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, sexual orientation, gender identity, national origin, disability, or protected veteran status. For more information about your rights as an applicant, please see the U.S. Equal Employment Opportunity Commission poster.

For the complete University of California nondiscrimination and affirmative action policy, please see the University of California Discrimination, Harassment, and Affirmative Action in the Workplace policy.



To apply, visit https://careerspub.universityofcalifornia.edu/psp/ucb/EMPLOYEE/HRMS/c/HRS_HRAM.HRS_APP_SCHJOB.GBL?Page=HRS_APP_JBPST&Action=U&FOCUS=Applicant&SiteId=21&JobOpeningId=61219&PostingSeq=1









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