CBSE Staff Positions

We have these open positions:

Biological Database Testing & User Support Technician, UCSC Genome Browser
Software Developer, UCSC Genome Browser
Administrative Project Manager, CBSE
CBSE Cancer Genomics Director
Software Developer and Functional Genomics Database Curator

You can search and apply for additional jobs online at the UCSC Staff Employment web site and the UCSC Academic Employment Opportunities web site.

UCSC is an affirmative action/equal opportunity employer.

We recommend that you include the following in your application:

• A cover letter describing why you are interested in and qualified for this particular job
• A curriculum vita or resume
• Your salary history

Descriptions of open positions:

Biological Database Testing and User Support Technician, UCSC Genome Browser

Jack Baskin School of Engineering
RANK: Programmer/Analyst 1
Posted 10/19/09

The Center for Biomolecular Science & Engineering (CBSE, http://www.cbse.ucsc.edu/) at UC Santa Cruz seeks a customer-oriented individual with strong analytical skills and a commitment to quality to test biological software and data and to research and answer user questions. The successful candidate must be articulate, organized, detail-oriented, and adaptable. The position requires independence and self-motivation in a team environment.

OVERVIEW OF THE ORGANIZATION
The UCSC Center for Genomic Sciences, part of the CBSE, operates an important scientific website for use by researchers worldwide, genome.ucsc.edu. Thousands of scientists use the site every day to access the fruits of the human genome project. The site combines cutting-edge research in genomics with solid software engineering and maintains a simple but flexible user interface.

ESSENTIAL FUNCTIONS
Under close supervision of the Quality Assurance Manager, the selected candidate will systematically test software, data, and databases before public release and research answers to user questions regarding underlying biological assumptions and computational methods in the genome software and databases. This position works as part of a team of people performing similar work alongside a group of software developers. It interacts extensively with the manager, software developers, other team members, and genome researchers from throughout the world. The work is fast-paced and varied and requires both great attention to detail and a broad understanding of the entire genome browser.

JOB DUTIES
Study and learn the current web site thoroughly: Understand how biologists are using the genome browser now; recommend new features to help biologists.
Test new versions of the software: Run the software thoroughly with an eye to the needs of the biologists who will be using the site; use knowledge of human-interface interactions to assess usability of the site; follow up to ensure errors are resolved.
Examine new genomic data for quality: Read the text describing the data set and work with the authors to understand the data set; examine the data set via the web tools at all scales and in all display options to help ensure that the data are accurate and faithfully represented; apply an understanding of basic genomics to detect anomalies and catch annotation errors.
Support users: Assist in monitoring email communications received from scientists off-site to answer questions and troubleshoot problems; research answers to user questions regarding underlying biological assumptions and computational methods in the genome software and databases; follow through to ensure that user questions are answered satisfactorily; suggest improvements to the site that can make future questions less likely.
Report problems: Communicate effectively about technical problems with UCSC team members and with external scientists and researchers; using the existing reporting system, develop accurate, complete, terse descriptions of problems; develop an awareness of existing problems; assess the importance of problems; ensure that high priority problems are resolved.

QUALIFICATIONS
BA or BS in either a biological science or computer science plus coursework or experience in the other (or an equivalent combination of education and experience); general knowledge of UNIX; broad knowledge in biology and working knowledge of genomic sequence organization, genome maintenance, and gene expression and regulation in eukaryotes; ability to search the Internet to find answers to scientific questions; ability to analyze a large problem in a systematic manner, ascertain how its components interact, and to isolate problems by controlling conditions; ability to attend to detail and work to established quality standards; ability to communicate clearly and concisely verbally and in writing; ability to organize material, information, and projects to maximize productivity and efficiency; able to perform effectively in environments having frequent workload changes and competing demands; ability to communicate effectively and diplomatically with a wide range of people, including project colleagues and international researchers; ability to work as part of a team or collaborate with colleagues in a fast-paced setting; ability to work independently and follow through on assignments  

PREFERRED QUALIFICATIONS
Demonstrated experience with computer programming;  demonstrated experience and skill in a customer service environment; knowledge of bioinformatics methods and applications

• Get full information and apply for job #0902365

Software Developer, UCSC Genome Browser

Jack Baskin School of Engineering
RANK: Programmer/Analyst 3
Initially posted 3/13/09; now hiring for additional positions

The Center for Biomolecular Science & Engineering (CBSE) at UC Santa Cruz seeks an analytical problem-solver to develop software and databases for a major genome analysis resource for biologists. The successful candidate must be articulate, able to learn and integrate technical information quickly, and have a strong commitment to quality and best engineering practices. The position requires independence and self-motivation in a team environment.

OVERVIEW OF THE ORGANIZATION
The UCSC Center for Genomic Sciences, part of the CBSE, is a talented cross-disciplinary team that builds databases and develops software for the UCSC Genome Browser (http://genome.ucsc.edu), a tool that facilitates genome analysis and comparison within and across multiple species. The browser provides views of assembled genome sequences that are integrated with details of evolutionary conservation, synteny, genetic map markers, known and predicted genes, SNPs, transcript structure, alternative splicing, and a host of other critical data. The browser is used by thousands of scientists and biomedical researchers worldwide, providing the development team with many opportunities to interact with scientists and projects at the leading edge of genomics research. The group is currently developing a Cancer Genomics Browser to facilitate medical research of cancer and other diseases. The Center also serves as the Data Coordination Center for the National Human Genome Research Institute (NHGRI) Encyclopedia of DNA Elements (ENCODE) project, which is comprehensively exploring the functional elements in the human genome.

ESSENTIAL FUNCTIONS
Under general supervision, the Software Developer will be responsible for supporting and extending the UCSC Genome Browser (http://genome.ucsc.edu) database and software and interfacing with Genome Browser collaborators and users. This involves annotation database construction for a variety of genomes, program development and implementation, database utilization, and communication and collaboration.

JOB DUTIES
Annotation database construction for a variety of genomes (35%): Build the base genome database and tables for numerous annotation tracks of various genome assemblies using existing bioinformatics programs and shell scripts.
Program development and implementation (35%): Program CGI scripts and database loaders in C; test and debug programs; work with a large Linux cluster and program in a Linux environment; participate in engineering best practices, including software testing, documentation, paired engineering reviews, and design reviews.
Database utilization (15%): Interface with MySQL; adjust software to optimize database performance. 
Communication and collaboration (15%): Interact with scientific collaborators worldwide; understand and learn details of the scientific goals of the Genome Project at UCSC; create presentations and publications that educate Genome Browser users, collaborators, and developers about various technical aspects of the project.

MINIMUM QUALIFICATIONS (with or without accommodation)
BA or BS in computer science or equivalent experience; one year of college-level biology or equivalent experience; significant experience working with C and a scripting language in a UNIX or Linux environment; familiarity with relational database concepts and SQL; knowledge of bioinformatics methods and applications or a strong desire to learn them
Articulate, with strong verbal and written communications skills; analytical ability to study and assimilate technical structure, data, and requirements of genome analysis software; quickly grasps new concepts and integrates them into projects as appropriate, and rapidly determines the required action in a new situation; effectively identifies and solves challenging problems; demonstrates a commitment to software quality and engineering best practices; works effectively and diplomatically with a wide range of people, and works harmoniously in a fast-paced team environment; able to work in a self-motivated manner with a minimal amount of supervision

PREFERRED QUALIFICATIONS
Knowledge, background, or experience in molecular biology; extensive experience in programming languages in addition to C, in particular JavaScript or Perl

• Get full information and apply for job #0902109

Administrative Project Manager

Center for Biomolecular Science & Engineering
Jack Baskin School of Engineering
RANK: Senior Administrative Analyst
Posted 6/23/09, initial review date 7/7/09

The Center for Biomolecular Science & Engineering (CBSE) at the University of California Santa Cruz seeks an articulate, self-motivated problem solver with exceptional organizational skills to plan, implement, monitor, and report for grant projects associated with the Center for Biomolecular Science and Engineering and its principal investigators. The successful candidate will be highly effective and diplomatic, with excellent writing skills.

This active administrative office supports the scientific efforts of faculty of the CBSE, the California Institute for Quantitative Biosciences (QB3), the UCSC Institute for the Biology of Stem Cells (IBSC), and the UCSC Training Program in Systems Biology of Stem Cells (under the California Institute for Regenerative Medicine). It also supports the research and teaching efforts of the director, Professor David Haussler, which includes approximately 50 staff, postdocs, and students involved in the UCSC Genome Browser and other projects which are supported by funds from the federal and state governments and the Howard Hughes Medical Institute (HHMI).

Specifically, the incumbent works with staff to meet programmatic, financial, and reporting timelines and the scientific and logistic goals for the following projects: the UCSC Center for Genomic Science, the UCSC ENCODE Data Coordination Center, and the UCSC branch of the California Institute for Quantitative Biosciences. The manager works with scientific lead staff and directors to ensure that personnel, supplies, space, equipment, and reporting needs of the projects are met. This position has the potential to expand to additional projects, including research awards, program grants, training programs, facilities and equipment awards, events, and special projects as needed and as funding allows.

This office has a heavy work load, often with pressing deadlines requiring that work be done promptly and with a high degree of accuracy. Teamwork is essential.

• Get full information and apply for job #0902242

CBSE Cancer Genomics Director

RANK: Associate or Full Research Scientist
Posted 2/3/09, initial review date extended to 3/23/09

The UCSC Cancer Genomics Group in the Center for Biomolecular Science & Engineering (CBSE) invites applications from outstanding PhD- or MD-level scientists for the position of Cancer Genomics Director. We seek an independent, creative scientist with cancer research experience to guide the group in building our cancer genomics data analysis platform into an essential tool for cancer research and an engine for personalized, genome-based cancer treatment. The successful candidate will extend our existing cancer research collaborations, conceptualize new research directions, oversee their implementation by our outstanding postdoctoral students and scientific programming staff, write papers and present results at scientific meetings, and apply for additional grants. Our exceptional collegiality and interdisciplinary collaborations make UCSC an excellent environment for an innovative scientist who can benefit from and contribute to the rapid growth in the sciences and engineering at UCSC.

UCSC Cancer Genomics is the primary integrative bioinformatics group for the national I-SPY breast cancer trial (http://tr.nci.nih.gov/iSpy) and a key analysis group for The Cancer Genome Atlas project (http://cancergenome.nih.gov/), NCI's flagship cancer genomics project. The UCSC Cancer Genomics Browser (http://genome-cancer.ucsc.edu) is rapidly expanding with support from a number of additional collaborations. This browser is built on the popular UCSC Genome Browser, which receives an average of 600,000 page requests per day and is accessed by 80,000 different biomedical researchers monthly, making it one of the most important and widely used web-based resources for biomedical research.

This position will have access to a substantial budget, an existing group of six people, and the capability to hire additional team members to match the anticipated rapid growth of the project. The ideal candidate will have either a background in medical research with an appreciation of the power of the genomic approach or a genomics background with some experience in cancer research and an appreciation of the importance and the complexities of dealing with human subject data.

• Job # T09-37 Full information
• Apply

Software Developer and Functional Genomics Database Curator

RANK: Junior Specialist, Step 1-2
posted 1/14/08
Department of Biomolecular Engineering
Baskin School of Engineering

The Department of Biomolecular Engineering at the University of California-Santa Cruz has been awarded a grant from the National Science Foundation to fully develop a model organism database and genome browser for all Archaea and extremophile bacteria, similar in purpose to SGD, FlyBase, and other important organism-specific databases. A major objective of the database is seamless integration of functional genomic data from DNA microarrays, proteomics studies, and high-throughput cDNA sequencing. A functional genomics data repository also will be established specifically for the archaeal research community based on an existing system. Under the direction of Asst. Professor Todd Lowe, the Center for Archaeal and Extremophile Genome Research is now seeking to fill several new positions immediately, including the full-time position of Software Developer and Functional Genomics Database Curator. The Archaeal and Extremophile Genome Database (http://archaea.ucsc.edu) currently hosts 70+ archaeal and bacterial genomes, and will continue to expand in the number of genomes and sources of gene function information. As part of the Archaeal genome database team, duties will include improving and maintaining a microarray / proteomic data repository and CGI interface for submitting new data, helping design and implement new interfaces for functional genomic data queries and comparisons within the genome browser, automating gene keyword searches on scientific literature and helping automate content curation tasks, integrating new “tracks” of bioinformatic analyses into the genome browser, developing improved collaborative Wiki tools tied into the genome browser for community-based gene re-annotation efforts, and thoroughly testing new browser features and tracks, identifying and fixing bugs or systematic errors in the database. This is an ideal opportunity for a computer scientist/programmer with strong programming skills to gain highly valued skills in an interdisciplinary biological research setting, including advanced comparative genomics and computational biology analysis. Co-authorship on scientific publications also is possible, dependent on contributions to research projects in the lab.

• Job #T08-40 Full information