The Center for Biomolecular Science & Engineering offers unique opportunities for research, teaching, learning, and satisfying careers in bioinformatics and related fields—a rich working and learning environment at UC Santa Cruz.
We have these open positions:
High-Throughput Sequencing Analyst (Programmer/Analyst 3)
Executive Assistant, Howard Hughes Medical Institute, UCSC
Biological Data Engineer (Programmer/Analyst 3), UCSC Genome Browser
Biological Data Technician (Programmer/Analyst 2), UCSC Genome Browser
Molecular Biology/Virology Researcher
Protein Structure Bioinformatics Specialist
Biological Database Testing & User Support Technician, UCSC Genome Browser
Software Developer, UCSC Genome Browser
Administrative Project Manager, CBSE
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:
Jack Baskin School of Engineering
RANK: Programmer/Analyst 3
Posted 1/1/10, initial review date 2/4/10
The UCSC Genome Sequencing Center (GSC) seeks a PhD-level scientist with experience and detailed knowledge of high-throughput sequence analysis to help GSC users manage, analyze and publish their sequence-based research. The position requires demonstrated ability to work effectively with biologists to apply computational approaches to their experiments.
The GSC provides next-generation sequencing services to a wide community of researchers, including UCSC (multiple departments across several divisions), UC Berkeley, Monterey Bay Aquarium Research Institute (MBARI), UC San Francisco, and local biotech companies. Faculty members at UCSC now have the opportunity to use these approaches to address fundamental questions in molecular biology and genetics. Due to the newness of this technology, few research labs have the expertise necessary to analyze the enormous amount of sequence data (e.g., 17 billion bases of DNA from a single run) produced by these machines. This position is intended to bridge the gap between the technology and the analysis of the data it produces.
At present the GSC offers ABI SOLiD sequencing technology and Roche 454 Titanium Series sequencing technology; it is in the process of acquiring an Illumina Genome Analyzer. The GSC plans to remain at the forefront of technology through the judicious acquisition of high-caliber sequencing platforms as they are developed and by optimizing and further developing existing technologies.
SUMMARY OF DUTIES
Under general supervision and in consultation with an advisory committee, the HT sequencing analyst will provide data processing, mapping, and assembly support to users of the GSC. The analyst will also assist with experimental design and basic statistical comparisons between samples, implement and manage third-party software, and to a limited extent modify software for specific data analysis needs. The analyst will train researchers in basic data analysis and assist with data display on the UCSC Genome Browser. It is expected that the analyst will work closely with scientists on their research projects, understanding the scientific questions being addressed and making significant bioinformatic contributions.
SPECIFIC RESPONSIBILITIES
Sequence data processing and analysis: Process raw sequence reads. Map sequencing reads to a genome. Assemble reads and conduct primary analysis, including annotation and digital expression analysis. Assist with simple statistical comparisons of reads from different samples; for example, between wild type and mutant or between treatment sample and control.
Genome Sequencing Center support: Supervise student workers hired to help with data processing and analysis. Interact with the UCSC Genome Browser staff as necessary to facilitate the final display of data and analysis in a form suitable for publication and display on the UCSC Genome Browser. Assist Genome Sequencing Center staff in determining hardware needs associated with existing and new sequencing instruments; Implement a laboratory information management system (LIMS) based on existing systems to allow users to request services and access the results in an efficient manner.
Research support: Advise on experimental design as needed to maximize useful results and minimize cost. Work with scientists to help them understand and analyze their scientific data.
QUALIFICATIONS (with or without accommodation):
PhD in bioinformatics, computer science, bioengineering, or biology; experience in and detailed knowledge of high-throughput sequence analysis; experience in processing high-throughput sequence data and using established software; general knowledge of biological systems, their experimental uses and limitations, and the conceptual use of high-throughput sequencing data for biology; experience using the UCSC Genome Browser and related visualization tools; demonstrated ability to work effectively with biologists to apply computational approaches to their experiment. Ability to communicate effectively and diplomatically with a wide range of people; communicate clearly and concisely verbally and in writing; work as part of a team and collaborate with colleagues; work independently and follow through on assignments; organize material, information, and projects to maximize productivity and efficiency; and attend to detail and work to established quality standards
PREFERRED QUALIFICATIONS:
Experience training others in the management, processing, and analysis of high-throughput sequence data; experience in experimental design of high-throughput sequencing experiments and use of the UCSC Genome Browser and its related tools to analyze and display the data; experience working in a molecular biology lab
RANK: Administrative Assistant
posted 1/8/10, applications received after 2/3/20 may not be considered
Howard Hughes Medical Institute
Center for Biomolecular Science & Engineering
UC Santa Cruz Baskin School of Engineering
Howard Hughes Medical Institute (HHMI) seeks an articulate, seasoned senior-level administrative assistant to support HHMI Investigator David Haussler, Professor of Biomolecular Engineering at the University of California, Santa Cruz. The ideal candidate is highly organized, proficient in time management, detail-oriented, able to take initiative to function both independently and as a member of a team, and has sound judgment.
This position is part of an active administrative office that supports the scientific efforts of Professor Haussler and several research organizations that he directs or co-directs: the Center for Biomolecular Science & Engineering (CBSE), the California Institute for Quantitative Biosciences (QB3), and the UCSC Institute for the Biology of Stem Cells. Professor Haussler employs approximately 50 staff, postdocs, and students involved in the UCSC Genome Browser and other research projects supported by funds from federal and state governments, private institutions, and HHMI.
SUMMARY OF DUTIES: This position provides executive-level administrative support and serves as a key liaison between the investigator and the organizations he is involved with and that support him. Under direction of the Associate Director for Operations and Communications, the major responsibilities include maintaining the investigator’s calendar, making complex travel arrangements, managing the investigator’s financial business (reimbursements, purchasing, and direct pay), providing various forms of information to and in support of the investigator, his lab, and the HHMI Office of Administrative Services, and assisting with various document tasks such as manuscript support, letter writing, class support, and others. An awareness of university structure and norms, and an ability to work with confidentiality and diplomacy are required. This office has a heavy workload with constant deadlines.
Jack Baskin School of Engineering
RANK: Programmer/Analyst 3
Posted 1/11/10, initial review date 1/25/10
The Center for Biomolecular Science & Engineering (CBSE, http://www.cbse.ucsc.edu) at the University of California, Santa Cruz, seeks a talented bioinformatician, biologist, or software engineer with a strong biology background to work with an international consortium of scientists to collect and import their experimental results into the UCSC Genome Browser database and web site.
Candidates for the position of Biological Data Engineer must be proficient in UNIX/Linux command-line use, relational database concepts, and SQL, competent in UNIX shell scripting and Perl programming, and experienced in molecular biology concepts and current methods. Besides having the ability to quickly learn and interpret biological and technical information, the ideal candidate is an effective communicator, resourceful, and a diplomatic team player who is both quality-oriented and able to work independently and follow through on assignments with minimal direction.
The CBSE is a research group with a diverse set of projects at the cutting edge of biomedical research, focusing on high-throughput analysis of the human genome. The center develops and manages the widely used UCSC Genome Browser and associated tools and manages data coordination for the ENcyclopedia Of DNA Elements (ENCODE) consortium, funded by the National Human Genome Research Institute.
ESSENTIAL FUNCTIONS
Under general supervision of the engineering manager, the biological data technician imports biomedical data into the UCSC Genome Browser databases and web site and guides others in this function. This position works closely with external research laboratories to capture their experimental results and methods and with internal software developers and database testing staff to make the data accessible to the worldwide scientific community.
JOB DUTIES
Managing data: Determine appropriate database and file formats for biological data that will be imported; download data files from external databases or web sites, reformatting as needed using existing tools and developing new scripts if needed; collect experimental methods and parameters, incorporating into documentation and controlled vocabularies as required; manage data from automated submission pipelines; load databases and configure display settings for viewing in the UCSC Genome Browser; review data for quality and consistency, with an eye to biological significance; specify and implement validation tools; package data for release and work with quality assurance team to facilitate final review
Communication and collaboration: Serve as primary liaison with external laboratories to facilitate data import and appropriate representation of the data at UCSC; provide instruction and feedback regarding data formatting and quality issues to informatics staff at external laboratories; participate in relevant research group teleconferences and meetings; serve as knowledge resource within the UCSC Genome Bioinformatics group for experimental results in the data manager's purview; contribute to project discussions and informational documentation via collaborative tools such as Wiki and Google documents
Writing: Provide technical review and edit experiment documentation provided by research labs or from publications; expand and revise for clarity, consistency, and completeness; add background and overview for a broad audience of biomedical users; describe conventions and user guidance relevant to use within the UCSC web site; contribute to research papers and grant reporting; document processes used during data import; contribute to FAQs, tutorials, and user guides related to areas of expertise
Software design, documentation, and testing: Work with software developers to improve existing programs and create new programs, focusing on providing usability feedback and testing to ensure that the software works correctly
QUALIFICATIONS
Bachelor's degree in bioinformatics or a biological science or equivalent experience; demonstrated proficiency in UNIX/Linux command-line use; demonstrated competency in UNIX shell scripting and Perl programming (or a comparable programming language); proficiency with relational database concepts and SQL; knowledge, background, or experience in molecular biology concepts and current methods; ability to work effectively and diplomatically with a wide range of people in a fast-paced team environment; demonstrated ability to communicate effectively, both orally and in writing; ability to quickly learn and interpret biological and technical information; ability to organize work and manage time to effectively balance priorities and conflicting demands; ability to work independently and follow through on assignments with minimal direction; ability to ensure quality and timeliness in performance of work tasks; ability to complete assignments with a high level of attention to detail, following specified guidelines; ability to be resourceful when faced with obstacles and to show initiative in identifying resources and methods for resolving issues
PREFERRED QUALIFICATIONS
Masters degree in bioinformatics or a biological science or equivalent experience; knowledge, background, or experience in high-throughput sequencing technologies; familiarity with common bioinformatics tools and databases; experience in a large-scale scientific data management environment; experience with software engineering tools for version control, software build, automated testing; familiarity with current web technologies
Jack Baskin School of Engineering
RANK: Programmer/Analyst 2
Posted 12/9/09, initial review date 1/3/10
The Center for Biomolecular Science & Engineering (CBSE, http://www.cbse.ucsc.edu) at the University of California, Santa Cruz, seeks a talented bioinformatician, biologist, or software engineer with a strong biology background to work with an international consortium of scientists to collect and import their experimental results into the UCSC Genome Browser database and web site.
Candidates for the position of Biological Data Technician must be proficient in UNIX/Linux command-line use, competent in UNIX shell scripting and Perl programming, and familiar with relational database concepts and SQL. Besides having the ability to quickly learn and interpret biological and technical information, the ideal candidate is an effective communicator, resourceful, and a diplomatic team player who is both quality-oriented and able to work to deadline.
The CBSE is a research group with a diverse set of projects at the cutting edge of biomedical research, focusing on high-throughput analysis of the human genome. The center develops and manages the widely used UCSC Genome Browser and associated tools and manages data coordination for the ENcyclopedia Of DNA Elements (ENCODE) consortium, funded by the National Human Genome Research Institute.
ESSENTIAL FUNCTIONS Under the supervision of the engineering manager, the biological data technician imports biomedical data into the UCSC Genome Browser databases and web site. This position works closely with external research laboratories to capture their experimental results and methods and with internal software developers and database testing staff to make the data accessible to the worldwide scientific community.
JOB DUTIES
Managing data: Determine appropriate database and file formats for biological data that will be imported; download data files from external databases or web sites, reformatting as needed using existing tools and developing new scripts if needed; collect experimental methods and parameters, incorporating into documentation and controlled vocabularies as required; manage data from automated submission pipelines; load databases and configure display settings for viewing in the UCSC Genome Browser; review data for quality and consistency, with an eye to biological significance; specify and implement validation tools; package data for release and work with quality assurance team to facilitate final review
Communication and collaboration: Serve as primary liaison with external laboratories to facilitate data import and appropriate representation of the data at UCSC; provide instruction and feedback regarding data formatting and quality issues to informatics staff at external laboratories; participate in relevant research group teleconferences and meetings; serve as knowledge resource within the UCSC Genome Bioinformatics group for experimental results in the data manager's purview; contribute to project discussions and informational documentation via collaborative tools such as Wiki and Google documents
Writing: Provide technical review and edit experiment documentation provided by research labs or from publications; expand and revise for clarity, consistency, and completeness; add background and overview for a broad audience of biomedical users; describe conventions and user guidance relevant to use within the UCSC web site; contribute to research papers and grant reporting; document processes used during data import; contribute to FAQs, tutorials, and user guides related to areas of expertise
Software design, documentation, and testing: Work with software developers to improve existing programs and create new programs, focusing on providing usability feedback and testing to ensure that the software works correctly
QUALIFICATIONS
Bachelor's degree in bioinformatics or a biological science or equivalent experience; demonstrated proficiency in UNIX/Linux command-line use; demonstrated competency in UNIX shell scripting and Perl programming (or a comparable programming language); familiarity with relational database concepts and SQL Ability to work effectively and diplomatically with a wide range of people in a fast-paced team environment; demonstrated ability to communicate effectively, both orally and in writing; ability to quickly learn and interpret biological and technical information; ability to organize work and manage time to effectively balance priorities and conflicting demands; ability to ensure quality and timeliness in performance of work tasks; ability to complete assignments with a high level of attention to detail, following specified guidelines; ability to be resourceful when faced with obstacles and to show initiative in identifying resources and methods for resolving issues
PREFERRED QUALIFICATIONS
Knowledge, background, or experience in molecular biology concepts and current methods, especially newer high-throughput technologies; familiarity with common bioinformatics tools and databases; experience in a large-scale scientific data management environment; experience with software engineering tools for version control, software build, automated testing; familiarity with current web technologies
RANK: Assistant Specialist, Step 1 to Full Specialist, Step 2
posted 12/17/09
Department of Biomolecular Engineering
Baskin School of Engineering
Applications are invited for a Research Specialist position focused on HIV vaccine research within the Department of Biomolecular Engineering. Under the direction of the principal investigator, the selected candidate will join a well-funded research program focused on the development and testing of antigens that could be included in candidate AIDS vaccines. The individual's primary responsibilities will involve cloning, mutagenesis, and expression of HIV envelope genes for immunological characterization and analysis. The cloned genes will be expressed in transfected mammalian cells and pseudotype viruses. Mutant proteins will be used for antibody binding studies, epitope mapping studies, monoclonal and polyclonal antibody production, and the development of multivalent HIV vaccine cocktails. A high level of expertise is required in the construction and analysis of plasmids for bacterial and mammalian cell expression, primer design and the use of PCR for in vitro mutagenesis, and the analysis of nucleic acid sequences by restriction mapping, gel electrophoresis, and DNA sequence analysis. Also required is experience in detection of protein expression by gel electrophoresis, immunoblotting, or enzyme linked immunosorbent assay (ELISA). Preference will be given to applicants with additional training in protein chemistry, the growth and transfection of mammalian cells, and monoclonal antibody production. The successful candidate will be highly motivated, self directed, have a strong work ethic, keep regular hours, and work well with others. The candidate will be expected to design their own experiments, keep complete and accurate records in laboratory notebooks, provide written reports of their work, and be able to trouble-shoot technical problems. Good writing skills and experience writing scientific reports using standard software including Microsoft Word, Excel, and PowerPoint is required. Experience with scientific software and databases such as MAFFT, Jalview, ApE, GenBank, and EndNote is desirable. The position does not require the growth or cultivation of HIV; however, the candidate will be expected to work safely with human blood products and common laboratory chemicals.
RANK: Assistant Specialist, Step 1-3
posted 12/15/09
Department of Biomolecular Engineering
Baskin School of Engineering
The Department of Biomolecular Engineering at the University of California-Santa Cruz invites applications for one part-time Bioinformatics Assistant Specialist position at a minimum of 50% time in the research group of Assistant Professor Dietlind Gerloff. The successful candidate will maintain and streamline an existing Bioinformatics Web Server and participate in research on computational protein-protein interaction prediction. Primary tasks include database updating and management of domain-specific programs, data, and computational equipment. Secondary tasks will involve training of users and written outreach efforts.
Minimum qualifications: bachelor degree (or foreign equivalent) in bioinformatics or related field; experience in application of protein bioinformatics tools; computational programming skills (language: Perl) and database experience (SQL); ability to learn new techniques and work independently; strong interpersonal and communication skills (oral and written); good organizational, time management, and problem-solving skills; knowledge of basic general-purpose computer software (e.g. Microsoft Word, Excel).
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
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
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.
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.