13077: Scientific Software Consultant: Bioinformatics Programmer

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Scientific Software Consultant: Bioinformatics Programmer - Archive
College of Arts and Sciences

Posting: 13077
Location: Eugene
Closes: 2013-06-23

Job Context:

The College of Arts and Sciences at the University of Oregon has established a scientific software consulting team to support the UO research community in the use of high-performance cluster and cloud computing systems.  We have already hired experts in parallel programming and open source programming as the initial scientific programming support group and wish to hire additional members of that group. In particular, we are seeking a bioinformatics programmer to support scientific research being carried out in a newly funded Center of Excellence in Systems Biology.  Researchers in the new center, named META, are studying the assembly, dynamics, and evolution of host-associated microbial communities.  The new programmer will also work with other research projects in the Institute of Ecology and Evolution, Institute of Molecular Biology, and Neuroscience Institute.

The University of Oregon has recently commissioned a $2 million parallel compute cluster designed to tackle large-scale scientific data sets and simulations.  Known as ACISS (Applied Computational Instrument for Scientific Synthesis), the system provides a private cloud computing environment consisting of over 2700 compute cores, 156 GPUs, 19 TB system memory, and 420 TB storage.  Additional computational resources are located in labs and core facilities associated with the META Center.

The new team member will provide the following services:

• Consultation with individual researchers on methods for analyzing large data sets generated by Illumina sequencers in the UO’s Genomics Core Facility or sequence data from other sources
• Help researchers develop data management strategies for all stages of the data “life cycle”: transferring data from sequencing centers to ACISS or other computational resources, passing it through a variety of analysis pipelines, publishing results, and arranging for long term archival storage
• Design and implement new techniques for analyzing bioinformatics data.
• Use programming expertise, graphics, and technology tools to present data in ways that are accurate, innovative, accessible, and appealing
• Provide education and training to faculty, postdocs, and graduate students on basic tools and techniques in bioinformatics
• Participate in the planning process for acquisition of new computational and storage infrastructure

Core competencies and skill sets that are required for this position as a bioinformatics programmer include the following:

• At least 5 years of experience with C++ or Java
• Substantial experience with Perl, Python, or similar scripting language; knowledge of OpenBio libraries (e.g. BioPerl or Biopython) is a plus
• Substantial experience with R, MAtLAb, Mathematica, or similar software
• Familiarity and experience with major bioinformatics applications and packages such as BLAST, Velvet, Trinity, Bowtie, QIIME, mothur, PhyML, MrBayes, etc
• Experience with file formats used to store sequence or experimental data
• Substantial knowledge and experience in applied mathematics and statistics
• Experience teaching classes, workshops, tutorials, or other educational settings
• Ability to effectively communicate with domain scientists
• Experience working in an environment of a collaborative programming team.

Successful applicants will have an advanced degree and excellent oral and written communications skills.  The applicant must demonstrate the ability to administer affirmative action policies effectively and supervise in a culturally diverse workplace.

Minimum Qualifications:

• M.S. degree in math, computer science, biology, or a related field
• Five years' working experience as a programmer or research assistant
• Familiarity with major bioinformatics packages
• Experience with file formats used to store sequence or experimental data
• Ability to work both independently and in a collaborative problem solving environment, meeting goal-oriented deadlines
• Excellent oral and written communications skills particularly the ability to effectively communicate with domain scientists

Desired Qualifications:

• Ph.D. degree
• Previous experience with next generation sequencing laboratory protocols
• Prior experience assisting with bioinformatics needs in a scientific laboratory
• Teaching experience
• Demonstrated ability to administer affirmative action policies effectively and supervise in a culturally diverse workplace

Background Check Statement:  Criminal background check required for the position

Employment Beginning:  June 1, 2013

Appointment Percentage: 12-month; full-time

Salary:  Competitive salary based on qualifications and experience

Benefits:

In addition to the above mentioned salary, this position has an excellent benefits package including health, dental, insurance, retirement plan, employee tuition rates (transferable to immediate family members under specific circumstances) and excellent vacation and sick leave provisions.

Application Procedures:

This position is open until filled.  To ensure full consideration, all materials should arrive by April 24, 2013

Complete applications must include the following:

• Answers to the following questions.  Please be as detailed as possible and provide what your role was in all projects and how you influenced any decision that was made during the course of the specific project:

        1. Detail your experience working on programming projects as a member of a team. What characteristics do you possess that make you a valuable team member and why? How do you handle conflict in a team?

        2. What is your communication style? Give an example of a project you worked on where the client’s expectations were markedly different from what you could feasibly deliver. What techniques did you use to bring the client’s expectations in line with what actually could be done?

        3. Describe your experience with bioinformatics programming, data analysis, and statistics. List the software packages you have used and describe your proficiency with each. Which of these core competencies would you consider your strengths and why? If you have little or no experience in one or some of the competencies, please note that.

       4. Describe your teaching experience.  What role did you take in designing the courses or workshops?

       5. Summarize the projects and specific types of problems you have worked on in the last two years. Include a discussion of the field and area of science as well as the different techniques that you used.  Be explicit in describing your role in the project, the problems you worked on, what kinds of programming languages and techniques you used to solve these problems, and how you interacted with the team.

  • A letter of application addressing your qualifications and interest in the position
  • A current resume
  • The names, addresses, phone numbers and email addresses of three references that can speak to your qualifications for this position

The application materials should be packaged as a single PDF file, using the position number and applicant’s last name as the document name, and uploaded to: https://casitweb.uoregon.edu/jobs/          

Incomplete or improperly submitted applications may be excluded from consideration.

Review of applications will begin April 25, 2013

The University of Oregon is an equal opportunity, affirmative action employer committed to cultural diversity and compliance with the Americans with Disabilities Act.