Research Programmer - Carl R. Woese Institute For Genomic Biology

Research Programmer - Carl R. Woese Institute for Genomic Biology

Carl R. Woese Institute for Genomic Biology

The Carl R. Woese Institute for Genomic Biology (IGB) is an interdisciplinary unit whose mission is to advance life science research at the University of Illinois Urbana-Champaign, meaningfully engage with the public to understand the impact of genomic research, and to stimulate bio-economic development in the state of Illinois. IGB members conduct path-breaking genomic research to address societal issues in the areas of food security, energy, health, technology, and environmental conservation. Our outreach and public engagement programs have been nationally recognized in its efforts to bring scientific understanding to the public, with partners such as the American Association for the Advancement of Science, the National Academy of Sciences, and the National Institutes of Health.

Job Summary

Responsible for integrating web tools with the KBase platform. Developing new data processing workflows and database programming.

Duties & Responsibilities

• The programmer's responsibility will be integrating the Enzyme Function Initiative (EFI - https://efi.igb.illinois.edu/) web tools into the KBase data science platform hosted at the U.S. Department of Energy. The EFI web tools are composed of a UI frontend and a Perl-based back-end. The programmer will interact with the project's senior research programmer to develop solutions in appropriate scripting languages for integrating the back-end with KBase. Additional components will involve writing code that produces results and reports that are available offline and downloadable. Innovative thinking will be required to merge the EFI tools into the KBase workflow. The KBase API is well-documented, but also imposes significant limitations on applications and how those applications can be executed. Interest in taking ownership of this project is key to success. Collaboration with external developers will be required (travel is not anticipated at this time).

• The programmer will also be responsible for providing support for additional databases in the EFI tools. Opening the EFI tools to the KBase API will provide access to an enhanced set of sequences and these need to be supported by the tools. Other database programming, such as downloading and synchronizing data, developing new databases, and improving existing workflows and optimizing databases will be involved.

• In addition to the above, the programmer may assist in the following: Exploration of new approaches to current bioinformatics processes, such as the use of sequence embedded vectors and machine learning, Improvement of web-based user interfaces and developing new applications using JavaScript, Improving software deployment workflow

Additional Physical Demands

Competent in interacting with developers and non-developers, and translating requirements into code.

Minimum Qualifications

Bachelor's degree in computer science or related field. Two years of programming experience and software development coding in Perl, Python, or PHP.

Specialty Factors

Proven experience or study of image recognition or other AI programming.

Preferred Qualifications

Four years of programming experience. HPC experience; bioinformatics background

Knowledge, Skills and Abilities

• Required:

• Proficient with Linux command line

• Proficient with Perl, Python, or PHP

• Proficient in use of sed and associated text processing utilities (cat, cut, sort, uniq)

• Proficient in use of SQL databases

• Proficient in using GIT software version control

• Familiarity with using REST and other HTTP-based APIs

• Preferred

• Proficient with Perl

• Experience in HPC Environments

• Use of Globus and other synchronization technologies

• Familiarity with technologies such as PHP, JavaScript, Singularity and/or Docker

• Knowledgeable in the use of bioinformatics tools such as BLAST

• Experience working in an agile development environment

Appointment Information

This is a 100% full-time Academic Professional position, appointed on a 12-month basis. The expected start date is as soon as possible after August 1, 2024. The salary range begins at $70,000. Salary is competitive and commensurate with qualifications and experience, while also considering internal equity.

Application Procedures & Deadline Information

Applications must be received by 6:00 pm (Central Time) on July 15, 2024. Apply for this position using the Apply Now button at the top or bottom of this posting. Applications not submitted through https://jobs.illinois.edu will not be considered. For further information about this specific position, please contact Jana Lenz at janalenz@illinois.edu. For questions regarding the application process, please contact 217-333-2137.

The University of Illinois System is an equal opportunity employer, including but not limited to disability and/or veteran status, and complies with all applicable state and federal employment mandates. Please visit Required Employment Notices and Posters to view our non-discrimination statement and find additional information about required background checks, sexual harassment/misconduct disclosures, and employment eligibility review through E-Verify.

Applicants with disabilities are encouraged to apply and may request a reasonable accommodation under the Americans with Disabilities Act (2008) to complete the application and/or interview process. Requests may be submitted through the reasonable accommodations portal, or by contacting the Accessibility & Accommodations Division of the Office for Access and Equity at 217-333-0885, or by emailing accessibility@illinois.edu.

Requisition ID: 1025467

Job Category: Research

Apply at: https://jobs.illinois.edu