Pro Tem Software Developer / Research Scientist

Department Summary

The Institute of Ecology and Evolution (IE²) facilitates research and graduate education in ecology and evolutionary biology. The institute fosters a collegial and stimulating intellectual environment for world-class research in molecular evolution, evolutionary genetics, evolution of development, and microbial, population, community, and ecosystems ecology.

Position Summary

We seek qualified applicants for a Software Developer / Research Scientist to join the lab group of Dr. Stilianos Louca in the Institute of Ecology and Evolution at the University of Oregon. Our lab is broadly interested in quantitative aspects of microbial ecology and evolution and their interaction with Earth-system processes. Our work includes large-scale bioinformatics analyses of microbial DNA sequences, mathematical modeling of microbial communities and biogeochemical cycles, advancing macroevolution theory, and development of new scientific software. While our lab also performs experiments and field surveys, this advertised position focuses on computational tasks.

We are looking for an experienced software developer who will lead or assist with the development of scientific software and data analysis workflows for our projects. One example task is the development of automated workflows for downloading, managing, visualizing and locally querying data from public sources such as NCBI, NASA or NOAA via their APIs, such that these data can be incorporated into our analysis workflows using a unified interface. Another example task is the installation, configuration and testing of a global ocean general circulation model code (such as MITgcm) on our local machines, such that it can be integrated into our analyses of global microbial dispersal.

The candidate will need to interact closely with their supervisor (Dr. Louca) and be able to translate rough and sometimes abstract given goals into concrete computer code, preferably in Python, C++ or bash, as appropriate. In some isolated cases the candidate may need to use other programming languages such as R or Fortran, for example to perform minor modifications of 3rd party code. The candidate will generally strive to write robust code that can deal with the erroneous or gappy input data and exceptions often encountered in science and maximizes longevity by limiting dependencies to well-established libraries. In addition, the candidate will be expected to thoroughly document their computer code using embedded comments and README files, to prepare technical reports and user manuals, and to write up related methods sections for scientific papers. While the ability to develop novel scientific hypotheses and to spearhead scientific articles is of benefit, this is not an important aspect of this position.

The candidate is expected to meet objectives and deadlines and produce work of high quality. Provided that performance is satisfactory, the candidate will have great flexibility in scheduling their daily work hours. Work-from-home and remote work arrangements will be possible. The Institute of Ecology and Evolution and the Department of Biology provide a vibrant environment for collaboration, networking and continuing education, through seminars, journal clubs and social events.

Minimum Requirements

• Bachelor's degree in computer science, physics, bioinformatics, applied mathematics or related field.
• Three years of experience in scientific computer programming, including proficiency in Python and experience in a compiled language such as C++ or Fortran.