Research Assistant Professor Software Engineering

The University of Texas at El Paso (UTEP) is a Carnegie R1 equal opportunity and community engaged university at the heart of the U.S.-Mexico border region that is increasing access to excellent higher education. We advance discovery of public value and positively impact the health culture education and economy of the community we serve. UTEP enrolls more than 25000 students 85% of whom are Hispanic and half of whom are the first in their families to attend college. UTEP offers 171 bachelors masters and doctoral degree programs at the only open-access top-tier research university in America.

Located at the westernmost tip of Texas El Paso is set against the backdrop of the Franklin Mountains and the Chihuahuan Desert in one of the largest binational communities in the world. A family-oriented community that is one of the safest large cities in the U.S. the cost of living in El Paso is very reasonable with an average home value of $224000 in 2025 and Texas has no income tax. The regions rich culture includes a vibrant street art and mural scene art galleries a new childrens museum and science center the states longest-running symphony orchestra and a full schedule of seasonal events and festivals. Sports fans will enjoy Division I college athletics Triple-A baseball affiliate the El Paso Chihuahuas and professional soccer team El Paso Locomotive FC and outdoor enthusiasts will be drawn to year-round hiking mountain biking and rock climbing in nearby state and national parks.

About the Department of Biological Sciences

The Department of Biological Sciences offers two Ph.D. tracks (Bioscience and Ecology and Evolutionary Biology) and has over 100 graduate students and over 2000 undergraduate majors including over 150 neuroscience majors. Biological sciences faculty maintain strong collaborative and programmatic ties with several other departments including Psychology Pharmacy Physics Chemistry and Computer Science -the last of which also houses UTEPs Master of Science in Software Engineering program.

The department hosts a vibrant neuroscience research community with an active program in mesoscale chemoarchitectural mapping of the rat brain spanning experimental neuroanatomy atlas-based data integration and computational tools that preserve the spatial provenance of molecular and physiological datasets.

The cluster hire described in this announcement extends these strengths toward an integrated research program on the neural circuitry of craving reward and addiction. This work is anchored by an NIH-funded Imaging & Behavioral Neuroscience Core Facility which provides three-dimensional microscopic imaging of the brain at the microcircuit level and is supported by multiple active federal awards in neuroscientific research. The department also sits within a broader collaborative research environment with access to core facilities in imaging computing and data science.

The Department of Biological Sciences at The University of Texas at El Paso (UTEP) is hiring a non-tenure-track Research Assistant Professor in Software Engineering. The position is one of four in a coordinated cluster hire -joining colleagues in behavioral neuroscience brain circuit imaging and atlas mapping and machine learning and AI -that will expand a cross-college team studying the brain circuits underlying craving reward and addiction. The hire will lead software development for an integrated rat-to-atlas brain mapping pipeline and its atlas infrastructure: the open-access atlas Brain Maps 4.0 and the recently released Chemopleth 1.0 spatial database. The role pairs naturally with UTEPs Master of Science in Software Engineering program offering opportunities to mentor graduate student teams draw practicum projects from the clusters atlas work and engage with the programs professional curriculum. The position also carries a distinctive responsibility in the current moment: as AI-assisted development matures the engineer at the center of this project will supply the human judgment and anatomical-domain expertise that a production-grade brain atlas platform needs using modern AI tools where they accelerate the work and pushing back with rigor on outputs that compromise spatial accuracy anatomical interpretability or release readiness.

Position Responsibilities

• Lead the adoption of software engineering best practices for the clusters research software development including Agile project management (e.g. Scrum or Kanban) code review automated testing continuous integration and release management.
• Architect and develop software components of the rat-to-atlas mapping pipeline including data ingestion processing and visualization tools.
• Develop the Brain Maps 4.0 and Chemopleth 1.0 software toward robust public releases building on existing prototypes with latitude to refactor or rebuild as engineering judgment requires and ensuring interoperability with international neuroinformatics infrastructure such as EBRAINS and with Python-based community tooling such as the BrainGlobe Atlas API.
• Collaborate with cluster-hire colleagues in behavioral neuroscience circuit imaging and mapping and ML/AI to translate research requirements into reliable software and to support multi-modal data integration and atlas development.
• Contribute to peer-reviewed publications and federal grant applications describing the clusters software data and infrastructure outputs including the open-access digital atlas of brain reward circuits.
• Mentor graduate and undergraduate trainees to contribute their efforts to the research pipeline.

• Ph.D. in computer science software engineering biomedical informatics computational science or a related field; or a Masters degree with substantial professional research software engineering experience.
• Experience with software engineering best practices including Agile project management (e.g. Scrum or Kanban) version control automated testing code review and documentation.
• Demonstrated experience designing and shipping non-trivial scientific or research software evidenced by repositories releases or production deployments.
• Proficiency in Python and at least one additional language relevant to scientific computing or web infrastructure.
• Experience mentoring or training undergraduate or graduate students in software engineering practice including supervision of student software projects.
• Demonstrated interest in or experience with neuroscience biomedical imaging or related scientific domains.
• Demonstrated ability to work in interdisciplinary teams that translate scientific and experimental requirements into reliable software.

Preferred Qualifications

• Experience working in academic or research-intensive environments including open-source scientific projects
• Familiarity with neuroscience or biomedical data formats and standards
• Track record of independent grant submissions or co-authored funded proposals related to research software infrastructure or scientific computing.
• Experience with web-based scientific applications data visualization or large-image rendering
• Experience with containerization (e.g. Docker) and cloud or HPC deployment of scientific software.
• Engagement with FAIR data principles and shared neuroscience infrastructure (e.g. EBRAINS NIH BRAIN Initiative resources)

Appointment: Non-tenure-track Research Assistant Professor. Initial appointment is for 12 months renewable contingent on performance and funding availability. The position can be renewed for a maximum of 3 years; renewal beyond 3 years will depend on the candidates ability to secure extramural funding.

Salary: Commensurate with experience and qualifications. The salary will depend on the candidates qualifications and experience and includes excellent fringe benefits. Hiring decisions are based on budget approval.

In keeping with its access excellence and impact mission The University of Texas at El Paso is committed to an open diverse and inclusive learning and working environment that honors the talents respects the differences and nurtures the growth and development of all. We seek to attract faculty and staff who share our commitment.

The University of Texas at El Paso is an Equal Opportunity Employer. The University does not discriminate on the basis of race color national origin sex religion age disability genetic information veteran status or sexual orientation and gender in employment or the provision of services in accordance with state and federal law. Discrimination on the basis of sex includes an employees or prospective employees right to be free from sexual harassment under Title IX of the Higher Education Amendments of 1972. Inquiries-including the filing of a Formal Complaint or reporting an incident-about the application of Title IX may be referred to the Title IX Coordinator who can be reached by phone at by email at or by mail at 500 W. University Ave. El Paso TX Kelly Hall Room 312.

For accommodation information for employees and applicants with disabilities please contact UTEPs Equal Opportunity Office at .

To the extent that this position involves research work or access to critical infrastructure as referenced in Executive Order GA-48 being hired for and continuing to be employed in this position requires the ability to maintain the security or integrity of the infrastructure.

A complete application includes:

• Cover letter describing research interests relevant experience and fit with the position
• Curriculum vitae
• Statement of research (maximum of 2 pages)
• Names and contact information for three professional references
• Up to three representative publications preprints or software/data artifacts

Review of applications will begin immediately and continue until the position is filled. Questions about the position may be directed to the search committee chair Dr. Arshad M. Khan ().